151
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Zhang K, Qin Y, Sun W, Shi H, Zhao S, He L, Li C, Zhao J, Pan J, Wang G, Han Z, Zhao C, Yang X. Phylogenomic Analysis of Cytochrome P450 Gene Superfamily and Their Association with Flavonoids Biosynthesis in Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1944. [PMID: 37895293 PMCID: PMC10606413 DOI: 10.3390/genes14101944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Cytochrome P450s (CYPs) constitute extensive enzyme superfamilies in the plants, playing pivotal roles in a multitude of biosynthetic and detoxification pathways essential for growth and development, such as the flavonoid biosynthesis pathway. However, CYPs have not yet been systematically studied in the cultivated peanuts (Arachis hypogaea L.), a globally significant cash crop. This study addresses this knowledge deficit through a comprehensive genome-wide analysis, leading to the identification of 589 AhCYP genes in peanuts. Through phylogenetic analysis, all AhCYPs were systematically classified into 9 clans, 43 gene families. The variability in the number of gene family members suggests specialization in biological functions. Intriguingly, both tandem duplication and fragment duplication events have emerged as pivotal drivers in the evolutionary expansion of the AhCYP superfamily. Ka/Ks analysis underscored the substantial influence of strong purifying selection on the evolution of AhCYPs. Furthermore, we selected 21 genes encoding 8 enzymes associated with the flavonoid pathway. The results of quantitative real-time PCR (qRT-PCR) experiments unveiled stage-specific expression patterns during the development of peanut testa, with discernible variations between pink and red testa. Importantly, we identified a direct correlation between gene expression levels and the accumulation of metabolites. These findings offer valuable insights into elucidating the comprehensive functions of AhCYPs and the underlying mechanisms governing the divergent accumulation of flavonoids in testa of different colors.
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Affiliation(s)
- Kun Zhang
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan 250100, China; (K.Z.); (Y.Q.); (J.Z.)
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (S.Z.); (C.L.); (J.P.); (G.W.); (C.Z.)
| | - Yongmei Qin
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan 250100, China; (K.Z.); (Y.Q.); (J.Z.)
| | - Wei Sun
- Linyi Academy of Agricultural Sciences, Linyi 276003, China;
| | - Hourui Shi
- Shandong Seed Management Station, Jinan 250100, China;
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (S.Z.); (C.L.); (J.P.); (G.W.); (C.Z.)
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.H.); (Z.H.)
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (S.Z.); (C.L.); (J.P.); (G.W.); (C.Z.)
| | - Jin Zhao
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan 250100, China; (K.Z.); (Y.Q.); (J.Z.)
| | - Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (S.Z.); (C.L.); (J.P.); (G.W.); (C.Z.)
| | - Guanghao Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (S.Z.); (C.L.); (J.P.); (G.W.); (C.Z.)
| | - Zhuqiang Han
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.H.); (Z.H.)
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (S.Z.); (C.L.); (J.P.); (G.W.); (C.Z.)
| | - Xiangli Yang
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan 250100, China; (K.Z.); (Y.Q.); (J.Z.)
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152
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Chaturvedi A, Li X, Dhandapani V, Marshall H, Kissane S, Cuenca-Cambronero M, Asole G, Calvet F, Ruiz-Romero M, Marangio P, Guigó R, Rago D, Mirbahai L, Eastwood N, Colbourne J, Zhou J, Mallon E, Orsini L. The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome. Nucleic Acids Res 2023; 51:9785-9803. [PMID: 37638757 PMCID: PMC10570034 DOI: 10.1093/nar/gkad685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.
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Affiliation(s)
- Anurag Chaturvedi
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Hollie Marshall
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Cuenca-Cambronero
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Aquatic Ecology Group, University of Vic - Central University of Catalonia, 08500 Vic, Spain
| | - Giovanni Asole
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Paolo Marangio
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Daria Rago
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Niamh Eastwood
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn Mallon
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- The Alan Turing Institute, British Library, London NW1 2DB, UK
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153
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Wang Y, Li W, Qu J, Li F, Du W, Weng J. Genome-Wide Characterization of the Maize ( Zea mays L.) WRKY Transcription Factor Family and Their Responses to Ustilago maydis. Int J Mol Sci 2023; 24:14916. [PMID: 37834371 PMCID: PMC10573107 DOI: 10.3390/ijms241914916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens.
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Affiliation(s)
- Yang Wang
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China;
| | - Wangshu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China;
| | - Jianzhou Qu
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
| | - Fenghai Li
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
| | - Wanli Du
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China;
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154
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Habib KA, Islam MJ, Sakib MN, Brishti PS, Neogi AK. DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh. Ecol Evol 2023; 13:e10641. [PMID: 37877103 PMCID: PMC10590961 DOI: 10.1002/ece3.10641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.
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Affiliation(s)
- Kazi Ahsan Habib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Jayedul Islam
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Nazmus Sakib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Parsha Shanjana Brishti
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Amit Kumer Neogi
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
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155
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Shin NR, Pauchet Y. First evidence of a horizontally-acquired GH-7 cellobiohydrolase from a longhorned beetle genome. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-14. [PMID: 37533217 DOI: 10.1002/arch.22039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
Xylophagous larvae of longhorned beetles (Coleoptera; Cerambycidae) efficiently break down polysaccharides of the plant cell wall, which make the bulk of their food, using a range of carbohydrate-active enzymes (CAZymes). In this study, we investigated the function and evolutionary history of the first identified example of insect-encoded members of glycoside hydrolase family 7 (GH7) derived from the Lamiinae Exocentrus adspersus. The genome of this beetle contained two genes encoding GH7 proteins located in tandem and flanked by transposable elements. Phylogenetic analysis revealed that the GH7 sequences of E. adspersus were closely related to those of Ascomycete fungi, suggesting that they were acquired through horizontal gene transfer (HGT) from fungi. However, they were more distantly related to those encoded by genomes of Crustacea and of protist symbionts of termites and cockroaches, supporting that the same enzyme family was recruited several times independently in Metazoa during the course of their evolution. The recombinant E. adspersus GH7 was found to primarily break down cellulose polysaccharides into cellobiose, indicating that it is a cellobiohydrolase, and could also use smaller cellulose oligomers as substrates. Additionally, the cellobiohydrolase activity was boosted by the presence of calcium chloride. Our findings suggest that the combination of GH7 cellobiohydrolases with other previously characterized endo-β-1,4-glucanases and β-glucosidases allows longhorned beetles like E. adspersus to efficiently break down cellulose into monomeric glucose.
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Affiliation(s)
- Na Ra Shin
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
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156
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Tu J, Abid M, Luo J, Zhang Y, Yang E, Cai X, Gao P, Huang H, Wang Z. Genome-wide identification of the heat shock transcription factor gene family in two kiwifruit species. FRONTIERS IN PLANT SCIENCE 2023; 14:1075013. [PMID: 37799558 PMCID: PMC10548268 DOI: 10.3389/fpls.2023.1075013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/28/2023] [Indexed: 10/07/2023]
Abstract
High temperatures have a significant impact on plant growth and metabolism. In recent years, the fruit industry has faced a serious threat due to high-temperature stress on fruit plants caused by global warming. In the present study, we explored the molecular regulatory mechanisms that contribute to high-temperature tolerance in kiwifruit. A total of 36 Hsf genes were identified in the A. chinensis (Ac) genome, while 41 Hsf genes were found in the A. eriantha (Ae) genome. Phylogenetic analysis revealed the clustering of kiwifruit Hsfs into three distinct groups (groups A, B, and C). Synteny analysis indicated that the expansion of the Hsf gene family in the Ac and Ae genomes was primarily driven by whole genome duplication (WGD). Analysis of the gene expression profiles revealed a close relationship between the expression levels of Hsf genes and various plant tissues and stress treatments throughout fruit ripening. Subcellular localization analysis demonstrated that GFP-AcHsfA2a/AcHsfA7b and AcHsfA2a/AcHsfA7b -GFP were localized in the nucleus, while GFP-AcHsfA2a was also observed in the cytoplasm of Arabidopsis protoplasts. The results of real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assay revealed that the majority of Hsf genes, especially AcHsfA2a, were expressed under high-temperature conditions. In conclusion, our findings establish a theoretical foundation for analyzing the potential role of Hsfs in high-temperature stress tolerance in kiwifruit. This study also offers valuable information to aid plant breeders in the development of heat-stress-resistant plant materials.
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Affiliation(s)
- Jing Tu
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Muhammad Abid
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Juan Luo
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Yi Zhang
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Endian Yang
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Xinxia Cai
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Puxin Gao
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hongwen Huang
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Zupeng Wang
- College of Life Science, Nanchang University, Nanchang, China
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157
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Liu Q, Wen J, Wang S, Chen J, Sun Y, Liu Q, Li X, Dong S. Genome-wide identification, expression analysis, and potential roles under low-temperature stress of bHLH gene family in Prunus sibirica. FRONTIERS IN PLANT SCIENCE 2023; 14:1267107. [PMID: 37799546 PMCID: PMC10548393 DOI: 10.3389/fpls.2023.1267107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
The basic helix-loop-helix (bHLH) family is one of the most well-known transcription factor families in plants, and it regulates growth, development, and abiotic stress responses. However, systematic analyses of the bHLH gene family in Prunus sibirica have not been reported to date. In this study, 104 PsbHLHs were identified and classified into 23 subfamilies that were unevenly distributed on eight chromosomes. Nineteen pairs of segmental replication genes and ten pairs of tandem replication genes were identified, and all duplicated gene pairs were under purifying selection. PsbHLHs of the same subfamily usually share similar motif compositions and exon-intron structures. PsbHLHs contain multiple stress-responsive elements. PsbHLHs exhibit functional diversity by interacting and coordinating with other members. Twenty PsbHLHs showed varying degrees of expression. Eleven genes up-regulated and nine genes down-regulated in -4°C. The majority of PsbHLHs were highly expressed in the roots and pistils. Transient transfection experiments demonstrated that transgenic plants with overexpressed PsbHLH42 have better cold tolerance. In conclusion, the results of this study have significant implications for future research on the involvement of bHLH genes in the development and stress responses of Prunus sibirica.
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Affiliation(s)
- Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Qingbai Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Xi Li
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
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158
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Huang Y, Zhao X, Zheng Q, He X, Zhang MM, Ke S, Li Y, Zhang C, Ahmad S, Lan S, Liu ZJ. Genome-Wide Identification of TCP Gene Family in Dendrobium and Their Expression Patterns in Dendrobium chrysotoxum. Int J Mol Sci 2023; 24:14320. [PMID: 37762622 PMCID: PMC10531990 DOI: 10.3390/ijms241814320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The TCP gene family are plant-specific transcription factors that play important roles in plant growth and development. Dendrobium chrysotoxum, D. nobile, and D. huoshanense are orchids with a high ornamental value, but few studies have investigated the specific functions of TCPs in Dendrobium flower development. In this study, we used these three Dendrobium species to analyze TCPs, examining their physicochemical properties, phylogenetic relationships, gene structures, and expression profiles. A total of 50 TCPs were identified across three Dendrobium species; they were divided into two clades-Class-I (PCF subfamily) and Class-II (CIN and CYC/TB1 subfamilies)-based on their phylogenetic relationships. Our sequence logo analysis showed that almost all Dendrobium TCPs contain a conserved TCP domain, as well as the existence of fewer exons, and the cis-regulatory elements of the TCPs were mostly related to light response. In addition, our transcriptomic data and qRT-PCR results showed that DchTCP2 and DchTCP13 had a significant impact on lateral organs. Moreover, changes in the expression level of DchTCP4 suggested its important role in the phenotypic variation of floral organs. Therefore, this study provides a significant reference for the further exploration of TCP gene functions in the regulation of different floral organs in Dendrobium orchids.
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Affiliation(s)
- Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Xin He
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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159
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Cao H, Tian Q, Ju M, Duan Y, Li G, Ma Q, Zhang H, Zhang X, Miao H. Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1261238. [PMID: 37810391 PMCID: PMC10558006 DOI: 10.3389/fpls.2023.1261238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]
Abstract
Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.
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Affiliation(s)
- Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xianmei Zhang
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Luohe Academy of Agricultural Sciences, Luohe, Henan, China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
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160
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Xiao R, Sun Y, Yang S, Yang Y, Wang D, Wang Z, Zhou W. Systematic Identification and Functional Analysis of the Hypericum perforatum L. bZIP Gene Family Indicating That Overexpressed HpbZIP69 Enhances Drought Resistance. Int J Mol Sci 2023; 24:14238. [PMID: 37762543 PMCID: PMC10531856 DOI: 10.3390/ijms241814238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Basic leucine zipper (bZIP) transcription factors play significant roles in plants' growth and development processes, as well as in response to biological and abiotic stresses. Hypericum perforatum is one of the world's top three best-selling herbal medicines, mainly used to treat depression. However, there has been no systematic identification or functional analysis of the bZIP gene family in H. perforatum. In this study, 79 HpbZIP genes were identified. Based on phylogenetic analysis, the HpbZIP gene family was divided into ten groups, designated A-I and S. The physicochemical properties, gene structures, protein conserved motifs, and Gene Ontology enrichments of all HpbZIPs were systematically analyzed. The expression patterns of all genes in different tissues of H. perforatum (i.e., root, stem, leaf, and flower) were analyzed by qRT-PCR, revealing the different expression patterns of HpbZIP under abiotic stresses. The HpbZIP69 protein is localized in the nucleus. According to the results of the yeast one-hybrid (Y1H) assays, HpbZIP69 can bind to the HpASMT2 (N-acetylserotonin O-methyltransferase) gene promoter (G-box cis-element) to activate its activity. Overexpressing HpbZIP69 in Arabidopsis wild-type lines enhanced their tolerance to drought. The MDA and H2O2 contents were significantly decreased, and the activity of superoxide dismutase (SOD) was considerably increased under the drought stress. These results may aid in additional functional studies of HpbZIP transcription factors, and in cultivating drought-resistant medicinal plants.
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Affiliation(s)
| | | | | | | | | | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (R.X.); (Y.S.); (S.Y.); (Y.Y.); (D.W.)
| | - Wen Zhou
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (R.X.); (Y.S.); (S.Y.); (Y.Y.); (D.W.)
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161
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Tang X, Sun F, Zhang N, Rana BB, Kharel R, Luo P, Si H. RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1268448. [PMID: 37780518 PMCID: PMC10539648 DOI: 10.3389/fpls.2023.1268448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties "DM1-3", "Atlantic" and "Cooperation-88" downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the "Atlantic", and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress.
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Affiliation(s)
- Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Birendra Bahadur Rana
- Nepal Agricultural Research Council, National Potato Research Program, Lalitpur, Nepal
| | - Raju Kharel
- Department of Genetics and Plant Breeding, Agricultural and Forestry University, Chitwan, Nepal
| | - Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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162
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Dai Y, Wang Y, Zeng L, Jia R, He L, Huang X, Zhao H, Liu D, Zhao H, Hu S, Gao L, Guo A, Xia W, Ji C. Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya. Int J Mol Sci 2023; 24:14039. [PMID: 37762345 PMCID: PMC10531014 DOI: 10.3390/ijms241814039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.
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Affiliation(s)
- Yunsu Dai
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Yu Wang
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Liwang Zeng
- Key Laboratory of Applied Research on Tropical Crop Information Technology of Hainan Province, Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ruizong Jia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Linwen He
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Xueying Huang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Difa Liu
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haixu Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Shuai Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Ling Gao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Anping Guo
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Wei Xia
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
| | - Changmian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
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163
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Xu Z, Duan Y, Liu H, Xu M, Zhang Z, Xu L. Analysis of WAK Genes in Nine Cruciferous Species with a Focus on Brassica napus L. Int J Mol Sci 2023; 24:13601. [PMID: 37686407 PMCID: PMC10487794 DOI: 10.3390/ijms241713601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
The wall-associated kinase family contributes to plant cell elongation and pathogen recognition. Nine Cruciferous species were studied for identification and molecular evolution of the WAK gene family. Firstly, 178 WAK genes were identified. A phylogenetic tree was constructed of the Cruciferous WAK proteins into four categories, of which the Brassica rapa, Brassica oleracea and Brassica napus genes in the U's triangle were more closely related. The WAK gene family was unevenly distributed in B. napus chromosomal imaging, with the largest number of BnWAK genes located on chromosome C08. In the expression analysis, the expression patterns of the WAK gene family varied under different stress treatments, and some members of BnWAKs were significantly different under stress treatments. This study lays a foundation for further revealing the functional mechanisms of the WAK gene family in Brassica napus.
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Affiliation(s)
- Zishu Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yi Duan
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Perth, WA 6009, Australia
| | - Mingchao Xu
- Leshan Academy of Agricultural Sciences, Leshan 614000, China
| | - Zhi Zhang
- Leshan Academy of Agricultural Sciences, Leshan 614000, China
| | - Ling Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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164
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Duti IJ, Florian JR, Kittel AR, Amelung CD, Gray VP, Lampe KJ, Letteri RA. Peptide Stereocomplexation Orchestrates Supramolecular Assembly of Hydrogel Biomaterials. J Am Chem Soc 2023; 145:18468-18476. [PMID: 37566784 DOI: 10.1021/jacs.3c04872] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Stereocomplexation, or specific interactions among complementary stereoregular macromolecules, is burgeoning as an increasingly impactful design tool, exerting exquisite control of material structure and properties. Since stereocomplexation of polymers produces remarkable transformations in mechanics, morphology, and degradation, we sought to leverage stereocomplexation to tune these properties in peptide-based biomaterials. We found that blending the pentapeptides l- and d-KYFIL triggers dual mechanical and morphological transformations from stiff fibrous hydrogels into less stiff networks of plates, starkly contrasting prior reports that blending l- and d-peptides produces stiffer fibrous hydrogels than the individual constituents. The morphological transformation of KYFIL in phosphate-buffered saline from fibers that entangle into hydrogels to plates that cannot entangle explains the accompanying mechanical transformation. Moreover, the blends shield l-KYFIL from proteolytic degradation, producing materials with comparable proteolytic stability to d-KYFIL but with distinct 2D plate morphologies that in biomaterials may promote unique therapeutic release profiles and cell behavior. To confirm that these morphological, mechanical, and stability changes arise from differences in molecular packing as in polymer stereocomplexation, we acquired X-ray diffraction patterns, which showed l- and d-KYFIL to be amorphous and their blends to be crystalline. Stereocomplexation is particularly apparent in pure water, where l- and d-KYFIL are soluble random coils, and their blends form β-sheets and gel within minutes. Our results highlight the role of molecular details, such as peptide sequence, in determining the material properties resulting from stereocomplexation. Looking forward, the ability of stereocomplexation to orchestrate supramolecular assembly and tune application-critical properties champions stereochemistry as a compelling design consideration.
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Affiliation(s)
- Israt Jahan Duti
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Jonathan R Florian
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Anna R Kittel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Connor D Amelung
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Vincent P Gray
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Kyle J Lampe
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Rachel A Letteri
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
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165
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Nedvědová Š, De Stefano D, Walker O, Hologne M, Miele AE. Revisiting Schistosoma mansoni Micro-Exon Gene (MEG) Protein Family: A Tour into Conserved Motifs and Annotation. Biomolecules 2023; 13:1275. [PMID: 37759676 PMCID: PMC10526429 DOI: 10.3390/biom13091275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Genome sequencing of the human parasite Schistosoma mansoni revealed an interesting gene superfamily, called micro-exon gene (meg), that encodes secreted MEG proteins. The genes are composed of short exons (3-81 base pairs) regularly interspersed with long introns (up to 5 kbp). This article recollects 35 S. mansoni specific meg genes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment and propose a phylogenetic analysis. This work highlighted intriguing conserved patterns/motifs in the sequences of the highly variable MEG proteins. Based on the analyses, we were able to classify the verified MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs' common names and annotation in order to avoid duplication, to help the reproducibility of research results and to avoid possible misunderstandings.
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Affiliation(s)
- Štěpánka Nedvědová
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 16500 Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Davide De Stefano
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Olivier Walker
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Maggy Hologne
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Adriana Erica Miele
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
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166
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Hinsberger M, Becker-Kettern J, Jürgens-Wemheuer WM, Oertel J, Schulz-Schaeffer WJ. Development of an Enzyme-Linked Immunosorbent Assay (ELISA) for the Quantification of ARID1A in Tissue Lysates. Cancers (Basel) 2023; 15:4096. [PMID: 37627124 PMCID: PMC10452747 DOI: 10.3390/cancers15164096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
ARID1A is a subunit of the mammalian SWI/SNF complex, which is thought to regulate gene expression through restructuring chromatin structures. Its gene ARID1A is frequently mutated and ARID1A levels are lowered in several human cancers, especially gynecologic ones. A functional ARID1A loss may have prognostic or predictive value in terms of therapeutic strategies but has not been proposed based on a quantitative method. Hardly any literature is available on ARID1A levels in tumor samples. We developed an indirect enzyme-linked immunosorbent assay (ELISA) for ARID1A based on the current EMA and FDA criteria. We demonstrated that our ELISA provides the objective, accurate, and precise quantification of ARID1A concentrations in recombinant protein solutions, cell culture standards, and tissue lysates of tumors. A standard curve analysis yielded a 'goodness of fit' of R2 = 0.99. Standards measured on several plates and days achieved an inter-assay accuracy of 90.26% and an inter-assay precision with a coefficient of variation of 4.53%. When tumor lysates were prepared and measured multiple times, our method had an inter-assay precision with a coefficient of variation of 11.78%. We believe that our suggested method ensures a high reproducibility and can be used for a high sample throughput to determine the ARID1A concentration in different tumor entities. The application of our ELISA on various tumor and control tissues will allow us to explore whether quantitative ARID1A measurements in tumor samples are of predictive value.
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Affiliation(s)
- Manuel Hinsberger
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
| | - Julia Becker-Kettern
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
| | - Wiebke M. Jürgens-Wemheuer
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
| | - Joachim Oertel
- Department of Neurosurgery, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany;
| | - Walter J. Schulz-Schaeffer
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
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167
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Tang X, Hou Y, Jiang F, Lang H, Li J, Cheng J, Wang L, Liu X, Zhang H. Genome-wide characterization of SINA E3 ubiquitin ligase family members and their expression profiles in response to various abiotic stresses and hormones in kiwifruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107891. [PMID: 37459805 DOI: 10.1016/j.plaphy.2023.107891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/27/2023] [Accepted: 07/08/2023] [Indexed: 08/13/2023]
Abstract
SINA (Seven in absentia) proteins in the subtype of E3 ubiquitin ligase family have important functions in regulating the growth and development as well as in response to abiotic and biotic stresses in plants. However, the characteristics and possible functions of SINA family proteins in kiwifruit are not studied. In this research, a total number of 11 AcSINA genes in the kiwifruit genome were identified. Chromosome location and multiple sequence alignment analyses indicated that they were unevenly distributed on 10 chromosomes and all contained the typical N-terminal RING domain and C-terminal SINA domain. Phylogenetic, gene structure and collinear relationship analyses revealed that they were highly conserved with the same gene structure, and have gone through segmental duplication events. Expression pattern analyses demonstrated that all AcSINAs were ubiquitously expressed in roots, stems and leaves, and were responsive to different abiotic and plant hormone treatments with overlapped but distinct expression patterns. Further yeast two-hybrid and Arabidopsis transformation analyses demonstrated most AcSINAs interacted with itself or other AcSINA members to form homo- or heterodimers, and ectopic expression of AcSINA2 in Arabidopsis led to hypersensitive growth phenotype of transgenic seedlings to ABA treatment. Our results reveal that AcSINAs take part in the response to various abiotic stresses and hormones, and provide important information for the functional elucidation of AcSINAs in vine fruit plants.
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Affiliation(s)
- Xiaoli Tang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Yaqiong Hou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Fudong Jiang
- Yantai Academy of Agricultural Sciences, 26 West Gangcheng Avenue, Yantai, Shandong, 265559, China
| | - Hongshan Lang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Jianzhao Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Jieshan Cheng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Limin Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Xiaohua Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China.
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, 5 Qingdao Avenue, Yantai, 265503, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China.
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168
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Zheng Y, Young ND, Song J, Gasser RB. Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host-Parasite Interactions. Int J Mol Sci 2023; 24:12320. [PMID: 37569696 PMCID: PMC10418638 DOI: 10.3390/ijms241512320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Biodiversity within the animal kingdom is associated with extensive molecular diversity. The expansion of genomic, transcriptomic and proteomic data sets for invertebrate groups and species with unique biological traits necessitates reliable in silico tools for the accurate identification and annotation of molecules and molecular groups. However, conventional tools are inadequate for lesser-known organismal groups, such as eukaryotic pathogens (parasites), so that improved approaches are urgently needed. Here, we established a combined sequence- and structure-based workflow system to harness well-curated publicly available data sets and resources to identify, classify and annotate proteases and protease inhibitors of a highly pathogenic parasitic roundworm (nematode) of global relevance, called Haemonchus contortus (barber's pole worm). This workflow performed markedly better than conventional, sequence-based classification and annotation alone and allowed the first genome-wide characterisation of protease and protease inhibitor genes and gene products in this worm. In total, we identified 790 genes encoding 860 proteases and protease inhibitors representing 83 gene families. The proteins inferred included 280 metallo-, 145 cysteine, 142 serine, 121 aspartic and 81 "mixed" proteases as well as 91 protease inhibitors, all of which had marked physicochemical diversity and inferred involvements in >400 biological processes or pathways. A detailed investigation revealed a remarkable expansion of some protease or inhibitor gene families, which are likely linked to parasitism (e.g., host-parasite interactions, immunomodulation and blood-feeding) and exhibit stage- or sex-specific transcription profiles. This investigation provides a solid foundation for detailed explorations of the structures and functions of proteases and protease inhibitors of H. contortus and related nematodes, and it could assist in the discovery of new drug or vaccine targets against infections or diseases.
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Affiliation(s)
- Yuanting Zheng
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Neil D. Young
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, VIC 3800, Australia;
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Robin B. Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
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169
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Wu Y, Su SX, Wang T, Peng GH, He L, Long C, Li W. Identification and expression characteristics of NLP (NIN-like protein) gene family in pepper (Capsicum annuum L.). Mol Biol Rep 2023; 50:6655-6668. [PMID: 37358766 DOI: 10.1007/s11033-023-08587-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND Pepper (Capsicum annum L.) is the main crop in the vegetable industry. The growth and development of peppers are regulated by nitrate, but there is limited research on the molecular mechanisms of nitrate absorption and assimilation in peppers. A plant specific transcription factor NLP plays an important role in nitrate signal transduction. METHODS AND RESULTS In this study, a total of 7 NLP members were identified based on pepper genome data. Two nitrogen transport elements (GCN4) were found in the CaNLP5 promoter. In the phylogenetic tree, CaNLP members are divided into three branches, with pepper NLP and tomato NLP having the closest genetic relationship. The expression levels of CaNLP1, CaNLP3, and CaNLP4 are relatively high in the roots, stems, and leaves. The expression level of CaNLP7 gene is relatively high during the 5-7 days of pepper fruit color transformation. After various non-Biotic stress and hormone treatments, the expression of CaNLP1 was at a high level. The expression of CaNLP3 and CaNLP4 was down regulated in leaves, but up regulated in roots. Under conditions of nitrogen deficiency and sufficient nitrate, the expression patterns of NLP genes in pepper leaves and roots were determined. CONCLUSION These results provide important insights into the multiple functions of CaNLPs in regulating nitrate absorption and transport.
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Affiliation(s)
- Yuan Wu
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Industry Technology Research Academy of Pepper, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Shi-Xian Su
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Tao Wang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Industry Technology Research Academy of Pepper, Guizhou University, Guiyang, 550025, China
| | - Gui-Hua Peng
- Research Institute of Pepper, Zunyi, 563000, Guizhou Province, China
| | - Lei He
- Research Institute of Pepper, Zunyi, 563000, Guizhou Province, China
| | - Cha Long
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
- Industry Technology Research Academy of Pepper, Guizhou University, Guiyang, 550025, China.
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China.
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170
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Heinonen T, Flegel T, Müller H, Kehl A, Hundi S, Matiasek K, Fischer A, Donner J, Forman OP, Lohi H, Hytönen MK. A loss-of-function variant in canine GLRA1 associates with a neurological disorder resembling human hyperekplexia. Hum Genet 2023; 142:1221-1230. [PMID: 37222814 PMCID: PMC10449970 DOI: 10.1007/s00439-023-02571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
Hereditary hyperekplexia is a rare neuronal disorder characterized by an exaggerated startle response to sudden tactile or acoustic stimuli. In this study, we present a Miniature Australian Shepherd family showing clinical signs, which have genetic and phenotypic similarities with human hereditary hyperekplexia: episodes of muscle stiffness that could occasionally be triggered by acoustic stimuli. Whole genome sequence data analysis of two affected dogs revealed a 36-bp deletion spanning the exon-intron boundary in the glycine receptor alpha 1 (GLRA1) gene. Further validation in pedigree samples and an additional cohort of 127 Miniature Australian Shepherds, 45 Miniature American Shepherds and 74 Australian Shepherds demonstrated complete segregation of the variant with the disease, according to an autosomal recessive inheritance pattern. The protein encoded by GLRA1 is a subunit of the glycine receptor, which mediates postsynaptic inhibition in the brain stem and spinal cord. The canine GLRA1 deletion is located in the signal peptide and is predicted to cause exon skipping and subsequent premature stop codon resulting in a significant defect in glycine signaling. Variants in GLRA1 are known to cause hereditary hyperekplexia in humans; however, this is the first study to associate a variant in canine GLRA1 with the disorder, establishing a spontaneous large animal disease model for the human condition.
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Affiliation(s)
- Tiina Heinonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Thomas Flegel
- Department of Small Animals, Leipzig University, Leipzig, Germany
| | - Hanna Müller
- Tieraerztliches Fachzentrum Muehlhausen Dr. Ortmann & Dr. Stief, Muehlhausen/Thueringen, Germany
| | | | - Sruthi Hundi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Kaspar Matiasek
- Section of Clinical and Comparative Neuropathology, Institute of Veterinary Pathology, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Andrea Fischer
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Oliver P Forman
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Leicestershire, UK
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
- Folkhälsan Research Center, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
- Folkhälsan Research Center, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
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171
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Muñoz-Muñoz PLA, Mares-Alejandre RE, Meléndez-López SG, Ramos-Ibarra MA. Structural Insights into the Giardia lamblia Target of Rapamycin Homolog: A Bioinformatics Approach. Int J Mol Sci 2023; 24:11992. [PMID: 37569368 PMCID: PMC10418948 DOI: 10.3390/ijms241511992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
TOR proteins, also known as targets of rapamycin, are serine/threonine kinases involved in various signaling pathways that regulate cell growth. The protozoan parasite Giardia lamblia is the causative agent of giardiasis, a neglected infectious disease in humans. In this study, we used a bioinformatics approach to examine the structural features of GTOR, a G. lamblia TOR-like protein, and predict functional associations. Our findings confirmed that it shares significant similarities with functional TOR kinases, including a binding domain for the FKBP-rapamycin complex and a kinase domain resembling that of phosphatidylinositol 3-kinase-related kinases. In addition, it can form multiprotein complexes such as TORC1 and TORC2. These results provide valuable insights into the structure-function relationship of GTOR, highlighting its potential as a molecular target for controlling G. lamblia cell proliferation. Furthermore, our study represents a step toward rational drug design for specific anti-giardiasis therapeutic agents.
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Affiliation(s)
| | - Rosa E. Mares-Alejandre
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, Mexico; (P.L.A.M.-M.); (S.G.M.-L.); (M.A.R.-I.)
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172
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Liao G, Duan Y, Wang C, Zhuang Z, Wang H. Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis. Genes (Basel) 2023; 14:1416. [PMID: 37510318 PMCID: PMC10379382 DOI: 10.3390/genes14071416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.
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Affiliation(s)
- Guihua Liao
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Yu Duan
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Congcong Wang
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Zebin Zhuang
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Haishi Wang
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
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173
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Chen Q, Song Y, Liu K, Su C, Yu R, Li Y, Yang Y, Zhou B, Wang J, Hu G. Genome-Wide Identification and Functional Characterization of FAR1-RELATED SEQUENCE ( FRS) Family Members in Potato ( Solanum tuberosum). PLANTS (BASEL, SWITZERLAND) 2023; 12:2575. [PMID: 37447143 DOI: 10.3390/plants12132575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly understood in vegetative crops such as potato (Solanum tuberosum, St). In the present study, 20 putative StFRS proteins were identified in potato via genome-wide analysis. They were non-randomly localized to eight chromosomes and phylogenetic analysis classified them into six subgroups along with FRS proteins from Arabidopsis and tomato. Conserved protein motif, protein domain, and gene structure analyses supported the evolutionary relationships among the FRS proteins. Analysis of the cis-acting elements in the promoters and the expression profiles of StFRSs in various plant tissues and under different stress treatments revealed the spatiotemporal expression patterns and the potential roles of StFRSs in phytohormonal and stress responses. StFRSs were differentially expressed in the cultivar "Xisen 6", which is exposed to a variety of stresses. Hence, these genes may be critical in regulating abiotic stress. Elucidating the StFRS functions will lay theoretical and empirical foundations for the molecular breeding of potato varieties with high light use efficiency and stress resistance.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yang Song
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Chen Su
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Ying Li
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Yi Yang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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174
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Guo J, Yang Y, Wang T, Wang Y, Zhang X, Min D, Zhang X. Analysis of Raffinose Synthase Gene Family in Bread Wheat and Identification of Drought Resistance and Salt Tolerance Function of TaRS15-3B. Int J Mol Sci 2023; 24:11185. [PMID: 37446364 DOI: 10.3390/ijms241311185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Raffinose synthase (RS) plays a crucial role in plant growth and development, as well as in responses to biotic stresses and abiotic stresses, yet few studies have been conducted on its role in bread wheat. Therefore, in this study we screened and identified a family of bread wheat raffinose synthase genes based on bread wheat genome information and analyzed their physicochemical properties, phylogenetic evolutionary relationships, conserved structural domains, promoter cis-acting elements, and expression patterns. The BSMV-induced silencing of TaRS15-3B resulted in the bread wheat seedlings being susceptible to drought and salt stress and reduced the expression levels of stress-related and ROS-scavenging genes in bread wheat plants. This further affected the ability of bread wheat to cope with drought and salt stress. In conclusion, this study revealed that the RS gene family in bread wheat plays an important role in plant response to abiotic stresses and that the TaRS15-3B gene can improve the tolerance of transgenic bread wheat to drought and salt stresses, provide directions for the study of other RS gene families in bread wheat, and supply candidate genes for use in molecular breeding of bread wheat for stress resistance.
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Affiliation(s)
- Jiagui Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang 712100, China
| | - Yan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Tingting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang 712100, China
| | - Yizhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang 712100, China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang 712100, China
| | - Donghong Min
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Xiaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang 712100, China
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175
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Fox CR, Kedarinath K, Neal CJ, Sheiber J, Kolanthai E, Kumar U, Drake C, Seal S, Parks GD. Broad-Spectrum, Potent, and Durable Ceria Nanoparticles Inactivate RNA Virus Infectivity by Targeting Virion Surfaces and Disrupting Virus-Receptor Interactions. Molecules 2023; 28:5190. [PMID: 37446852 DOI: 10.3390/molecules28135190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
There is intense interest in developing long-lasting, potent, and broad-spectrum antiviral disinfectants. Ceria nanoparticles (CNPs) can undergo surface redox reactions (Ce3+ ↔ Ce4+) to generate ROS without requiring an external driving force. Here, we tested the mechanism behind our prior finding of potent inactivation of enveloped and non-enveloped RNA viruses by silver-modified CNPs, AgCNP1 and AgCNP2. Treatment of human respiratory viruses, coronavirus OC43 and parainfluenza virus type 5 (PIV5) with AgCNP1 and 2, respectively, prevented virus interactions with host cell receptors and resulted in virion aggregation. Rhinovirus 14 (RV14) mutants were selected to be resistant to inactivation by AgCNP2. Sequence analysis of the resistant virus genomes predicted two amino acid changes in surface-located residues D91V and F177L within capsid protein VP1. Consistent with the regenerative properties of CNPs, surface-applied AgCNP1 and 2 inactivated a wide range of structurally diverse viruses, including enveloped (OC43, SARS-CoV-2, and PIV5) and non-enveloped RNA viruses (RV14 and feline calicivirus; FCV). Remarkably, a single application of AgCNP1 and 2 potently inactivated up to four sequential rounds of virus challenge. Our results show broad-spectrum and long-lasting anti-viral activity of AgCNP nanoparticles, due to targeting of viral surface proteins to disrupt interactions with cellular receptors.
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Affiliation(s)
- Candace R Fox
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Kritika Kedarinath
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Craig J Neal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Jeremy Sheiber
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Udit Kumar
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | | | - Sudipta Seal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
- Nano Science Technology Center, University of Central Florida, Orlando, FL 32816, USA
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Griffith D Parks
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
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176
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Wang S, Sun X, Miao X, Mo F, Liu T, Chen Y. Genome-Wide Analysis and Expression Profiling of the Glutathione Peroxidase-like Enzyme Gene Family in Solanum tuberosum. Int J Mol Sci 2023; 24:11078. [PMID: 37446254 PMCID: PMC10342349 DOI: 10.3390/ijms241311078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Glutathione peroxidase-like enzyme is an important enzymatic antioxidant in plants. It is involved in scavenging reactive oxygen species, which can effectively prevent oxidative damage and improve resistance. GPXL has been studied in many plants but has not been reported in potatoes, the world's fourth-largest food crop. This study identified eight StGPXL genes in potatoes for the first time through genome-wide bioinformatics analysis and further studied the expression patterns of these genes using qRT-PCR. The results showed that the expression of StGPXL1 was significantly upregulated under high-temperature stress, indicating its involvement in potato defense against high-temperature stress, while the expression levels of StGPXL4 and StGPXL5 were significantly downregulated. The expression of StGPXL1, StGPXL2, StGPXL3, and StGPXL6 was significantly upregulated under drought stress, indicating their involvement in potato defense against drought stress. After MeJA hormone treatment, the expression level of StGPXL6 was significantly upregulated, indicating its involvement in the chemical defense mechanism of potatoes. The expression of all StGPXL genes is inhibited under biotic stress, which indicates that GPXL is a multifunctional gene family, which may endow plants with resistance to various stresses. This study will help deepen the understanding of the function of the potato GPXL gene family, provide comprehensive information for the further analysis of the molecular function of the potato GPXL gene family as well as a theoretical basis for potato molecular breeding.
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Affiliation(s)
| | | | | | | | | | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (S.W.); (X.S.); (X.M.); (F.M.); (T.L.)
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177
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Li H, Yang J, Ma R, An X, Pan F, Zhang S, Fu Y. Genome-wide identification and expression analysis of MYB gene family in Cajanus cajan and CcMYB107 improves plant drought tolerance. PHYSIOLOGIA PLANTARUM 2023; 175:e13954. [PMID: 37318225 DOI: 10.1111/ppl.13954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/16/2023]
Abstract
MYB transcription factor (TF) is one of the largest superfamilies that play a vital role in multiple plant biological processes. However, the MYB family has not been comprehensively identified and functionally verified in Cajanus cajan, which is the sixth most important legume crop. Here, 170 CcR2R3-MYBs were identified and divided into 43 functional subgroups. Segmental and tandem duplications and alternative splicing events were found and promoted the expansion of the CcR2R3-MYB gene family. Functional prediction results showed that CcR2R3-MYBs were mainly involved in secondary metabolism, cell fate and identity, developmental processes, and responses to abiotic stress. Cis-acting element analysis of promoters revealed that stress response elements were widespread in the above four functional branches, further suggesting CcR2R3-MYBs were extensively involved in abiotic stress response. The transcriptome data and qRT-PCR results indicated that most of the CcR2R3-MYB genes responded to various stresses, of which the expression of CcMYB107 was significantly induced by drought stress. Overexpression of CcMYB107 enhanced antioxidant enzyme activity and increased proline and lignin accumulation, thus improving the drought resistance of C. cajan. Furthermore, Overexpression of CcMYB107 up-regulated the expression of stress-related genes and lignin biosynthesis genes after drought stress. Our findings established a strong foundation for the investigation of biological function of CcR2R3-MYB TFs in C. cajan.
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Affiliation(s)
- Hongquan Li
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, Harbin, China
| | - Jie Yang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, Harbin, China
| | - Ruijin Ma
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, Harbin, China
| | - Xiaoli An
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, Harbin, China
| | - Feng Pan
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, Harbin, China
| | - Su Zhang
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing, China
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178
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Dong X, Zhang K, Xun C, Chu T, Liang S, Zeng Y, Liu Z. Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World. Int J Mol Sci 2023; 24:10562. [PMID: 37445739 DOI: 10.3390/ijms241310562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or "transcriptional noise". However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids. The vigorous development of computational algorithms, ribosome profiling, and peptidome has facilitated the prediction and identification of many new SEPs. These SEPs were revealed to be involved in a wide range of basic biological processes, such as gene expression regulation, embryonic development, cellular metabolism, inflammation, and even carcinogenesis. To effectively understand the potential biological functions of SEPs, we discuss the history and development of the newly emerging research on sORFs and SEPs. In particular, we review a range of recently discovered bioinformatics tools for identifying, predicting, and validating SEPs as well as a variety of biochemical experiments for characterizing SEP functions. Lastly, this review underlines the challenges and future directions in identifying and validating sORFs and their encoded micropeptides, providing a significant reference for upcoming research on sORF-encoded peptides.
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Affiliation(s)
- Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Kun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Chengfeng Xun
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Tianqi Chu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Songping Liang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Yong Zeng
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zhonghua Liu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
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179
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Vendra VPR, Ostrowski C, Clark R, Dyba M, Tarasov SG, Hejtmancik JF. The Y46D Mutation Destabilizes Dense Packing of the Second Greek Key Pair of Human γC-Crystallin Causing Congenital Nuclear Cataracts. Biochemistry 2023; 62:1864-1877. [PMID: 37184593 PMCID: PMC10758276 DOI: 10.1021/acs.biochem.2c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The γ-crystallins are highly expressed structural lens proteins comprising four Greek key motifs arranged in two domains. Their globular structure and short-range spatial ordering are essential for lens transparency. Aromatic residues play a vital role in stabilizing Greek key folds by forming Greek key or non-Greek key pairs or tyrosine corners. We investigated the effects of the cataractogenic Y46D mutation in the second Greek key pair (Y46-Y51) of human γC-crystallin on its stability and aggregation. Wild-type and Y46D mutant human γC-crystallin were overexpressed in E. coli BL-21(DE3) PLysS cells, purified using ion-exchange and size-exclusion chromatography, and analyzed by fluorescence spectroscopy and circular dichroism spectroscopy. The Y46D mutation does not affect the γC-crystallin backbone conformation under benign conditions but alters the tryptophan microenvironment, exposing hydrophobic residues to the surface. The Y46D mutant undergoes a three-state transition under thermal stress with midpoints of 54.6 and 67.7 °C while the wild type shows a two-state transition with a midpoint of 77.6 °C. The Y46D mutant also shows a three-state transition under GuHCl stress with Cm values of 0.9 and 2.1 M while the wild type shows a two-state transition with a Cm of 2.4 M GuHCl. Mutant but not wild-type γC-crystallin forms light scattering particles upon heating at 65 °C. Overall, the Y46D CRYGS mutation leaves the protein fold intact under benign conditions but destabilizes the molecule by altering the tryptophan microenvironment and exposing hydrophobic residues to its surface, thus increasing its susceptibility to thermal and chemical stress with resultant self-aggregation, light scattering, and cataract.
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Affiliation(s)
- Venkata Pulla Rao Vendra
- Ophthalmic Molecular Genetics Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Christian Ostrowski
- Ophthalmic Molecular Genetics Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Rebecca Clark
- Ophthalmic Molecular Genetics Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Marzena Dyba
- Biophysics Resource in the Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702-4091, United States
| | - Sergey G Tarasov
- Biophysics Resource in the Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702-4091, United States
| | - J Fielding Hejtmancik
- Ophthalmic Molecular Genetics Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20852, United States
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180
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Schumann A, Cohn AR, Gaballa A, Wiedmann M. Escherichia coli B-Strains Are Intrinsically Resistant to Colistin and Not Suitable for Characterization and Identification of mcr Genes. Microbiol Spectr 2023; 11:e0089423. [PMID: 37199645 PMCID: PMC10269513 DOI: 10.1128/spectrum.00894-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi-, extensive, and pandrug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., in Escherichia coli) is a common approach, so far, no standard methods for heterologous expression and characterization of mcr genes exist. E. coli B-strains, designed for optimum protein expression, are frequently utilized. Here, we report that four E. coli B-strains are intrinsically resistant to colistin (MIC 8-16 μg/mL). The three tested B-strains that encode T7 RNA polymerase show growth defects when transformed with empty or mcr-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. E. coli SHuffle T7 express carrying empty pET17b also skips wells in colistin MIC assays in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in each pmrA and pmrB in all four E. coli B-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude that E. coli B-strains are not appropriate heterologous expression hosts for identification and characterization of mcr genes. IMPORTANCE Given the rise in multidrug, extensive drug, and pandrug resistance in bacteria and the increasing use of colistin to treat human infections, occurrence of mcr genes threatens human health, and characterization of these resistance genes becomes more important. We show that three commonly used heterologous expression strains are intrinsically resistant to colistin. This is important because these strains have previously been used to characterize and identify new mobile colistin resistance (mcr) genes. We also show that expression plasmids (i.e., pET17b) without inserts cause cell viability defects when carried by B-strains with T7 RNA polymerase and grown in the presence of IPTG. Our findings are important as they will facilitate improved selection of heterologous strains and plasmid combinations for characterizing AMR genes, which will be particularly important with a shift to Culture-independent diagnostic tests where bacterial isolates become increasingly less available for characterization.
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Affiliation(s)
- Anna Schumann
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York, USA
| | - Alexa R. Cohn
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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181
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Zheng Q, Zhao X, Huang Y, Zhang MM, He X, Ke S, Li Y, Zhang C, Ahmad S, Lan S, Li M, Liu ZJ. Genome-Wide Identification of the YABBY Gene Family in Dendrobium Orchids and Its Expression Patterns in Dendrobium chrysotoxum. Int J Mol Sci 2023; 24:10165. [PMID: 37373311 DOI: 10.3390/ijms241210165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. However, the relationships and specific functions of the YABBY genes in the Dendrobium species remain unknown. In this study, six DchYABBYs, nine DhuYABBYs, and nine DnoYABBYs were identified from the genome databases of the three Dendrobium species, which were unevenly distributed on five, eight, and nine chromosomes, respectively. The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. A sequence analysis showed that most of the YABBY proteins contained conserved C2C2 zinc-finger and YABBY domains, while a gene structure analysis revealed that 46% of the total YABBY genes contained seven exons and six introns. All the YABBY genes harbored a large number of Methyl Jasmonate responsive elements, as well as anaerobic induction cis-acting elements in the promoter regions. Through a collinearity analysis, one, two, and two segmental duplicated gene pairs were identified in the D. chrysotoxum, D. huoshanense, and D. nobile genomes, respectively. The Ka/Ks values of these five gene pairs were lower than 0.5, indicating that the Dendrobium YABBY genes underwent negative selection. In addition, an expression analysis revealed that DchYABBY2 plays a role in ovary and early-stage petal development, while DchYABBY5 is essential for lip development and DchYABBY6 is crucial for early sepal formation. DchYABBY1 primarily regulates sepals during blooming. Furthermore, there is the potential involvement of DchYABBY2 and DchYABBY5 in gynostemium development. The results of a comprehensive genome-wide study would provide significant clues for future functional investigations and pattern analyses of YABBY genes in different flower parts during flower development in the Dendrobium species.
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Affiliation(s)
- Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Minghe Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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182
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Zhao X, Zhang M, He X, Zheng Q, Huang Y, Li Y, Ahmad S, Liu D, Lan S, Liu Z. Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Three Orchids. Int J Mol Sci 2023; 24:10039. [PMID: 37373185 DOI: 10.3390/ijms241210039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 05/29/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and functions of the SPLs in the Orchidaceae. In this study, Cymbidium goeringii Rchb. f., Dendrobium chrysotoxum Lindl., and Gastrodia elata BI. were used as research objects. The SPL gene family of these orchids was analyzed on a genome-wide scale, and their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns were studied. Transcriptome and qRT-PCR methods were combined to investigate the regulatory effect of SPLs on the development of flower organs during the flowering process (bud, initial bloom, and full bloom). This study identifies a total of 43 SPLs from C. goeringii (16), D. chrysotoxum (17), and G. elata (10) and divides them into eight subfamilies according to the phylogenetic tree. Most SPL proteins contained conserved SBP domains and complex gene structures; half of the genes had introns longer than 10 kb. The largest number and variety of cis-acting elements associated with light reactions were enriched, accounting for about 45% of the total (444/985); 13/43 SPLs contain response elements of miRNA156. GO enrichment analysis showed that the functions of most SPLs were mainly enriched in the development of plant flower organs and stems. In addition, expression patterns and qRT-PCR analysis suggested the involvement of SPL genes in the regulation of flower organ development in orchids. There was little change in the expression of the CgoSPL in C. goeringii, but DchSPL9 and GelSPL2 showed significant expression during the flowering process of D. chrysotoxum and G. elata, respectively. In summary, this paper provides a reference for exploring the regulation of the SPL gene family in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengmeng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingkun Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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183
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Bag P, Shutova T, Shevela D, Lihavainen J, Nanda S, Ivanov AG, Messinger J, Jansson S. Flavodiiron-mediated O 2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring. Nat Commun 2023; 14:3210. [PMID: 37270605 DOI: 10.1038/s41467-023-38938-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023] Open
Abstract
Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.
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Affiliation(s)
- Pushan Bag
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, UK
| | - Tatyana Shutova
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, Umeå, Sweden
| | - Jenna Lihavainen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sanchali Nanda
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Alexander G Ivanov
- Department of Biology, University of Western Ontario, London, ON, Canada
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Johannes Messinger
- Department of Chemistry, Chemical Biological Centre, Umeå University, Umeå, Sweden
- Department of Chemistry-Ångström laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden.
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Palumbo F, Draga S, Magon G, Gabelli G, Vannozzi A, Farinati S, Scariolo F, Lucchin M, Barcaccia G. MIK2 is a candidate gene of the S-locus for sporophytic self-incompatibility in chicory ( Cichorium intybus, Asteraceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1204538. [PMID: 37332702 PMCID: PMC10272723 DOI: 10.3389/fpls.2023.1204538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
The Cichorium genus offers a unique opportunity to study the sporophytic self-incompatibility (SSI) system, being composed of species characterized by highly efficient self-incompatibility (e.g., C. intybus) and complete self-compatibility (e.g., C. endivia). To this end, the chicory genome was used to map seven previously identified SSI locus-associated markers. The region containing the S-locus was therefore restricted to an ~4 M bp window on chromosome 5. Among the genes predicted in this region, MDIS1 INTERACTING RECEPTOR LIKE KINASE 2 (ciMIK2) was particularly promising as a candidate for SSI. Its ortholog in Arabidopsis (atMIK2) is involved in pollen-stigma recognition reactions, and its protein structure is similar to that of S-receptor kinase (SRK), a key component of the SSI system in the Brassica genus. The amplification and sequencing of MIK2 in chicory and endive accessions revealed two contrasting scenarios. In C. endivia, MIK2 was fully conserved even when comparing different botanical varieties (i.e., smooth and curly endive). In C. intybus, 387 polymorphic positions and 3 INDELs were identified when comparing accessions of different biotypes all belonging to the same botanical variety (i.e., radicchio). The polymorphism distribution throughout the gene was uneven, with hypervariable domains preferentially localized in the LRR-rich extracellular region, putatively identified as the receptor domain. The gene was hypothesized to be under positive selection, as the nonsynonymous mutations were more than double the synonymous ones (dN/dS = 2.17). An analogous situation was observed when analyzing the first 500 bp of the MIK2 promoter: no SNPs were observed among the endive samples, whereas 44 SNPs and 6 INDELs were detected among the chicory samples. Further analyses are needed to confirm the role of MIK2 in SSI and to demonstrate whether the 23 species-specific nonsynonymous SNPs in the CDS and/or the species-specific 10 bp-INDEL found in a CCAAT box region of the promoter are responsible for the contrasting sexual behaviors of chicory and endive.
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185
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Qi Z, Xu Y, Dong B, Pi X, Zhang Q, Wang D, Wang Z. Molecular characterization, structural and expression analysis of twelve CXC chemokines and eight CXC chemokine receptors in largemouth bass (Micropterus salmoides). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 143:104673. [PMID: 36858298 DOI: 10.1016/j.dci.2023.104673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
The chemokine-receptor system plays important roles in the leukocyte trafficking, inflammation, immune cell differentiation, cancer and other biological processes. In the present study, the sequence features, structures and expression patterns of twelve CXC chemokine ligands (CXCL8a.1, CXCL8a.2, CXCL8b.1, CXCL8b.2, CXCL12a, CXCL12b, CXCL13.1, CXCL13.2, CXCL14, CXCL18a, CXCL18b and CXCL19) and eight CXC chemokine receptors (CXCR1, CXCR2, CXCR3.1, CXCR3.2, CXCR3.3, CXCR4a, CXCR4b and CXCR5) of largemouth bass (Micropterus salmoides) were analyzed. All the CXCLs and CXCRs of largemouth bass shared high sequence identities with their teleost counterparts and possessed conserved motifs and structures of CXCLs and CXCRs family. Realtime qPCR revealed that these CXCLs and CXCRs were ubiquitously expressed in all examined tissues, with high expression levels in the immune-related tissues (spleen, head kidney, and gill). Following lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (polyI:C) stimulations, most of these CXCLs and CXCRs were significantly up-regulated in spleen. In addition, the potential interacted molecules of these CXCLs and CXCRs were analyzed by protein-protein interaction network analysis. To the best of our knowledge, this is the first study that in detail analyzes the CXCLs and CXCRs of largemouth bass. Our results provide valuable basis for study the function and mechanism of chemokine-receptor system in largemouth bass.
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Affiliation(s)
- Zhitao Qi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, China.
| | - Yang Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Biao Dong
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, China
| | - Xiangyu Pi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, China
| | - Qihuan Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, China
| | - Dezhong Wang
- Sheyang Kangyu Aquatic Products Technology Co., Ltd, Yancheng, Jiangsu Province, 224300, China
| | - Zisheng Wang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, China
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186
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Wang Y, Wang X, Luo Y, Zhang J, Lin Y, Wu J, Zeng B, Liu L, Yan P, Liang J, Guo H, Jin L, Tang Q, Long K, Li M. Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon. PLoS Genet 2023; 19:e1010746. [PMID: 37289658 PMCID: PMC10249823 DOI: 10.1371/journal.pgen.1010746] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 04/14/2023] [Indexed: 06/10/2023] Open
Abstract
Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to feed newborn squabs. Nonetheless, the transcriptomic dynamics and role in the rapid transition of core crop functions during 'lactation' remain largely unexplored. Here, we generated a de novo pigeon genome assembly to construct a high resolution spatio-temporal transcriptomic landscape of the crop epithelium across the entire breeding stage. This multi-omics analysis identified a set of 'lactation'-related genes involved in lipid and protein metabolism, which contribute to the rapid functional transitions in the crop. Analysis of in situ high-throughput chromatin conformation capture (Hi-C) sequencing revealed extensive reorganization of promoter-enhancer interactions linked to the dynamic expression of these 'lactation'-related genes between stages. Moreover, their expression is spatially localized in specific epithelial layers, and can be correlated with phenotypic changes in the crop. These results illustrate the preferential de novo synthesis of 'milk' lipids and proteins in the crop, and provides candidate enhancer loci for further investigation of the regulatory elements controlling pigeon 'lactation'.
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Affiliation(s)
- Yujie Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yi Luo
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiaman Zhang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yu Lin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jie Wu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lei Liu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Peiqi Yan
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiyuan Liang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
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187
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Thind AC, Mota CM, Gonçalves APN, Sha J, Wohlschlegel JA, Mineo TWP, Bradley PJ. The Toxoplasma gondii effector GRA83 modulates the host's innate immune response to regulate parasite infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543158. [PMID: 37398161 PMCID: PMC10312501 DOI: 10.1101/2023.05.31.543158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Toxoplasma gondii 's propensity to infect its host and cause disease is highly dependent on its ability to modulate host cell functions. One of the strategies the parasite uses to accomplish this is via the export of effector proteins from the secretory dense granules. Dense granule (GRA) proteins are known to play roles in nutrient acquisition, host cell cycle manipulation, and immune regulation. Here, we characterize a novel dense granule protein named GRA83, which localizes to the parasitophorous vacuole in tachyzoites and bradyzoites. Disruption of GRA83 results in increased virulence, weight loss, and parasitemia during the acute infection, as well as a marked increase in the cyst burden during the chronic infection. This increased parasitemia was associated with an accumulation of inflammatory infiltrates in tissues in both the acute and chronic infection. Murine macrophages infected with Δ gra83 tachyzoites produced less interleukin-12 (IL-12) in vitro , which was confirmed with reduced IL-12 and interferon gamma (IFN-γ) in vivo . This dysregulation of cytokines correlates with reduced nuclear translocation of the p65 subunit of the NF-κB complex. While GRA15 similarly regulates NF-κB, infection with Δ gra83/ Δ gra15 parasites did not further reduce p65 translocation to the host cell nucleus, suggesting these GRAs function in converging pathways. We also used proximity labelling experiments to reveal candidate GRA83 interacting T. gondii derived partners. Taken together, this work reveals a novel effector that stimulates the innate immune response, enabling the host to limit parasite burden. Importance Toxoplasma gondii poses a significant public health concern as it is recognized as one of the leading foodborne pathogens in the United States. Infection with the parasite can cause congenital defects in neonates, life-threatening complications in immunosuppressed patients, and ocular disease. Specialized secretory organelles, including the dense granules, play an important role in the parasite's ability to efficiently invade and regulate components of the host's infection response machinery to limit parasite clearance and establish an acute infection. Toxoplasma' s ability to avoid early clearance, while also successfully infecting the host long enough to establish a persistent chronic infection, is crucial in allowing for its transmission to a new host. While multiple GRAs directly modulate host signaling pathways, they do so in various ways highlighting the parasite's diverse arsenal of effectors that govern infection. Understanding how parasite-derived effectors harness host functions to evade defenses yet ensure a robust infection are important for understanding the complexity of the pathogen's tightly regulated infection. In this study, we characterize a novel secreted protein named GRA83 that stimulates the host cell's response to limit infection.
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188
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Jing X, Deng N, Shalmani A. Characterization of Malectin/Malectin-like Receptor-like Kinase Family Members in Foxtail Millet ( Setaria italica L.). Life (Basel) 2023; 13:1302. [PMID: 37374087 DOI: 10.3390/life13061302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Plant malectin/malectin-like receptor-like kinases (MRLKs) play crucial roles throughout the life course of plants. Here, we identified 23 SiMRLK genes from foxtail millet. All the SiMRLK genes were named according to the chromosomal distribution of the SiMRLKs in the foxtail millet genome and grouped into five subfamilies based on phylogenetic relationships and structural features. Synteny analysis indicated that gene duplication events may take part in the evolution of SiMRLK genes in foxtail millet. The expression profiles of 23 SiMRLK genes under abiotic stresses and hormonal applications were evaluated through qRT-PCR. The expression of SiMRLK1, SiMRLK3, SiMRLK7 and SiMRLK19 were significantly affected by drought, salt and cold stresses. Exogenous ABA, SA, GA and MeJA also obviously changed the transcription levels of SiMRLK1, SiMRLK3, SiMRLK7 and SiMRLK19. These results signified that the transcriptional patterns of SiMRLKs showed diversity and complexity in response to abiotic stresses and hormonal applications in foxtail millet.
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Affiliation(s)
- Xiuqing Jing
- Department of Biology, Taiyuan Normal University, Jinzhong 030619, China
- College of Life Science, Shanxi University, Taiyuan 030006, China
| | - Ning Deng
- Department of Biology, Taiyuan Normal University, Jinzhong 030619, China
| | - Abdullah Shalmani
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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189
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Chen J, Wan H, Zhu W, Dai X, Yu Y, Zeng C. Identification and Expression Analysis of the Isopentenyl Transferase (IPT) Gene Family under Lack of Nitrogen Stress in Oilseed ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112166. [PMID: 37299144 DOI: 10.3390/plants12112166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 06/12/2023]
Abstract
BnIPT gene family members in Brassica napus and analyzing their expression under different exogenous hormones and abiotic stress treatments to provide a theoretical basis for clarifying their functions and molecular genetic mechanisms in nitrogen deficiency stress tolerance of B. napus. Using the Arabidopsis IPT protein as the seed sequence, combined with the IPT protein domain PF01715, 26 members of the BnIPT gene family were identified from the whole genome of the rape variety ZS11. Additionally, the physicochemical properties and structures, phylogenetic relationships, synteny relationships, protein-protein interaction network, and gene ontology enrichment were analyzed. Based on transcriptome data, the expression patterns of the BnIPT gene under different exogenous hormone and abiotic stress treatments were analyzed. We used the qPCR method to identify the relative expression level of BnIPT genes that may be related to the stress resistance of rapeseed in transcriptome analysis under normal nitrogen (N: 6 mmol·L-1) and nitrogen deficiency (N: 0) conditions and analyzed its effect on rapeseed under nitrogen deficiency stress role in tolerance. In response to nitrogen deficiency signals, the BnIPT gene showed a trend of up-regulation in shoots and down-regulation in roots, indicating that it may affect the process of nitrogen transport and redistribution to enhance the stress resistance of rapeseed to respond to the nitrogen deficiency stress. This study provides a theoretical basis for clarifying the function and molecular genetic mechanism of the BnIPT gene family in nitrogen deficiency stress tolerance in rape.
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Affiliation(s)
- Jingdong Chen
- College of Life Science, Jianghan University, Wuhan 430056, China
| | - Heping Wan
- College of Life Science, Jianghan University, Wuhan 430056, China
| | - Wenhui Zhu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xigang Dai
- College of Life Science, Jianghan University, Wuhan 430056, China
| | - Yi Yu
- College of Life Science, Jianghan University, Wuhan 430056, China
| | - Changli Zeng
- College of Life Science, Jianghan University, Wuhan 430056, China
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190
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Pei M, Xie X, Peng B, Chen X, Chen Y, Li Y, Wang Z, Lu G. Identification and Expression Analysis of Phosphatidylinositol Transfer Proteins Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112122. [PMID: 37299101 DOI: 10.3390/plants12112122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
The family of phosphatidylinositol transfer proteins (PITPs) is able to bind specific lipids to carry out various biological functions throughout different stages of plant life. But the function of PITPs in rice plant is unclear. In this study, 30 PITPs were identified from rice genome, which showed differences in physicochemical properties, gene structure, conservation domains, and subcellular localization. The promoter region of the OsPITPs genes included at least one type of hormone response element, such as methyl jasmonate (Me JA) and salicylic acid (SA). Furthermore, the expression level of OsML-1, OsSEC14-3, OsSEC14-4, OsSEC14-15, and OsSEC14-19 genes were significantly affected by infection of rice blast fungus Magnaporthe oryzae. Based on these findings, it is possible that OsPITPs may be involved in rice innate immunity in response to M. oryzae infection through the Me JA and SA pathway.
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Affiliation(s)
- Mengtian Pei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuze Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baoyi Peng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinchi Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yixuan Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ya Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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191
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Sun Y, Jia X, Yang Z, Fu Q, Yang H, Xu X. Genome-Wide Identification of PEBP Gene Family in Solanum lycopersicum. Int J Mol Sci 2023; 24:ijms24119185. [PMID: 37298136 DOI: 10.3390/ijms24119185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The PEBP gene family is crucial for the growth and development of plants, the transition between vegetative and reproductive growth, the response to light, the production of florigen, and the reaction to several abiotic stressors. The PEBP gene family has been found in numerous species, but the SLPEBP gene family has not yet received a thorough bioinformatics investigation, and the members of this gene family are currently unknown. In this study, bioinformatics was used to identify 12 members of the SLPEBP gene family in tomato and localize them on the chromosomes. The physicochemical characteristics of the proteins encoded by members of the SLPEBP gene family were also examined, along with their intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements. In parallel, a phylogenetic tree was built and the collinear relationships of the PEBP gene family among tomato, potato, pepper, and Arabidopsis were examined. The expression of 12 genes in different tissues and organs of tomato was analyzed using transcriptomic data. It was also hypothesized that SLPEBP3, SLPEBP5, SLPEBP6, SLPEBP8, SLPEBP9, and SLPEBP10 might be related to tomato flowering and that SLPEBP2, SLPEBP3, SLPEBP7, and SLPEBP11 might be related to ovary development based on the tissue-specific expression analysis of SLPEBP gene family members at five different stages during flower bud formation to fruit set. This article's goal is to offer suggestions and research directions for further study of tomato PEBP gene family members.
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Affiliation(s)
- Yimeng Sun
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Xinyi Jia
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Zhenru Yang
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Qingjun Fu
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Huanhuan Yang
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Xiangyang Xu
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
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192
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Liu Y, Wang M, Huang Y, Zhu P, Qian G, Zhang Y, Li L. Genome-Wide Identification and Analysis of R2R3-MYB Genes Response to Saline-Alkali Stress in Quinoa. Int J Mol Sci 2023; 24:ijms24119132. [PMID: 37298082 DOI: 10.3390/ijms24119132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Soil saline-alkalization inhibits plant growth and development and seriously affects crop yields. Over their long-term evolution, plants have formed complex stress response systems to maintain species continuity. R2R3-MYB transcription factors are one of the largest transcription factor families in plants, widely involved in plant growth and development, metabolism, and stress response. Quinoa (Chenopodium quinoa Willd.), as a crop with high nutritional value, is tolerant to various biotic and abiotic stress. In this study, we identified 65 R2R3-MYB genes in quinoa, which are divided into 26 subfamilies. In addition, we analyzed the evolutionary relationships, protein physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of CqR2R3-MYB family members. To investigate the roles of CqR2R3-MYB transcription factors in abiotic stress response, we performed transcriptome analysis to figure out the expression file of CqR2R3-MYB genes under saline-alkali stress. The results indicate that the expression of the six CqMYB2R genes was altered significantly in quinoa leaves that had undergone saline-alkali stress. Subcellular localization and transcriptional activation activity analysis revealed that CqMYB2R09, CqMYB2R16, CqMYB2R25, and CqMYB2R62, whose Arabidopsis homologues are involved in salt stress response, are localized in the nucleus and exhibit transcriptional activation activity. Our study provides basic information and effective clues for further functional investigation of CqR2R3-MYB transcription factors in quinoa.
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Affiliation(s)
- Yuqi Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Mingyu Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Yongshun Huang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Guangtao Qian
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Yiming Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lixin Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
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193
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Chen J, Han P, Liu X, Wang X. Characterization of Japanese flounder (Paralichthys olivaceus) STAT members: An immune-related gene family involved in Edwardsiella tarda and temperature stress. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108818. [PMID: 37201733 DOI: 10.1016/j.fsi.2023.108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
The signal transducer and activator of transcription (STAT) family members are not only the transcriptional activators, but also play important roles in regulating inflammatory response. Some members have been reported to be involved in innate bacterial and antiviral immunity in aquatic organisms. However, no systematic research on STATs has been found in teleost. In this present study, we characterized six STAT genes in Japanese flounder based on bioinformatics methods, namely PoSTAT1, PoSTAT2, PoSTAT3, PoSTAT4, PoSTAT5 and PoSTAT6. The phylogenetic analysis of STATs in fish indicated that STATs were highly conserved and revealed an absence of STAT5 in a few species. Further analysis of gene structures and motifs showed STAT proteins shared a similar structure and probably had similar functionality in Japanese flounder. The expression profiles of different development stages and tissues demonstrated that PoSTATs exhibited specificity in temporality and spatiality as well as PoSTAT4 was highly expressed in gill. The transcriptome data analysis of E. tarda and temperature stress showed that PoSTAT1 and PoSTAT2 were more respective to these two kinds of stress. In addition, the results also demonstrated that these PoSTATs might regulate immune response in different ways, manifested by up-regulation in E. tarda infection and down-regulation in temperature stress. In a word, this systematic analysis of PoSTATs would provide valuable information about the phylogenetic relationship of STATs in fish species and help understand the role of STAT genes in the immune response of Japanese flounder.
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Affiliation(s)
- Jianming Chen
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
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194
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Yu A, Zou H, Li P, Yao X, Zhou Z, Gu X, Sun R, Liu A. Genomic characterization of the NAC transcription factors, directed at understanding their functions involved in endocarp lignification of iron walnut ( Juglans sigillata Dode). Front Genet 2023; 14:1168142. [PMID: 37229193 PMCID: PMC10203416 DOI: 10.3389/fgene.2023.1168142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
The NAC (NAM, ATAF1/2, and CUC2) transcription factors (TF), one of the largest plant-specific gene families, play important roles in the regulation of plant growth and development, stress response and disease resistance. In particular, several NAC TFs have been identified as master regulators of secondary cell wall (SCW) biosynthesis. Iron walnut (Juglans sigillata Dode), an economically important nut and oilseed tree, has been widely planted in the southwest China. The thick and high lignified shell derived endocarp tissues, however, brings troubles in processing processes of products in industry. It is indispensable to dissect the molecular mechanism of thick endocarp formation for further genetic improvement of iron walnut. In the present study, based on genome reference of iron walnut, 117 NAC genes, in total, were identified and characterized in silico, which involves only computational analysis to provide insight into gene function and regulation. We found that the amino acids encoded by these NAC genes varied from 103 to 1,264 in length, and conserved motif numbers ranged from 2 to 10. The JsiNAC genes were unevenly distributed across the genome of 16 chromosomes, and 96 of these genes were identified as segmental duplication genes. Furthermore, 117 JsiNAC genes were divided into 14 subfamilies (A-N) according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana and common walnut (Juglans regia). Furthermore, tissue-specific expression pattern analysis demonstrated that a majority of NAC genes were constitutively expressed in five different tissues (bud, root, fruit, endocarp, and stem xylem), while a total of 19 genes were specifically expressed in endocarp, and most of them also showed high and specific expression levels in the middle and late stages during iron walnut endocarp development. Our result provided a new insight into the gene structure and function of JsiNACs in iron walnut, and identified key candidate JsiNAC genes involved in endocarp development, probably providing mechanistic insight into shell thickness formation across nut species.
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195
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Ilyas M, Ali I, Nasser Binjawhar D, Ullah S, Eldin SM, Ali B, Iqbal R, Bokhari SHA, Mahmood T. Molecular Characterization of Germin-like Protein Genes in Zea mays ( ZmGLPs) Using Various In Silico Approaches. ACS OMEGA 2023; 8:16327-16344. [PMID: 37179620 PMCID: PMC10173433 DOI: 10.1021/acsomega.3c01104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
Germin (GER) and germin-like proteins (GLPs) play an important role in various plant processes. Zea mays contains 26 germin-like protein genes (ZmGLPs) located on chromosomes 2, 4, and 10; most of which are functionally unexplored. The present study aimed to characterize all ZmGLPs using the latest computational tools. All of them were studied at a physicochemical, subcellular, structural, and functional level, and their expression was predicted in plant development, against biotic and abiotic stresses using various in silico approaches. Overall, ZmGLPs showed greater similarity in their physicochemical properties, domain architecture, and structure, mostly localized in the cytoplasmic or extracellular regions. Phylogenetically, they have a narrow genetic background with a recent history of gene duplication events on chromosome 4. Functional analysis revealed novel enzymatic activities of phosphoglycolate phosphatase, adenosylhomocysteinase, phosphoglycolate phosphatase-like, osmotin/thaumatin-like, and acetohydroxy acid isomeroreductase largely mediated by disulfide bonding. Expression analysis revealed their crucial role in the root, root tips, crown root, elongation and maturation zones, radicle, and cortex with the highest expression being observed during germination and at the maturity levels. Further, ZmGLPs showed strong expression against biotic (Aspergillus flavus, Colletotrichum graminicola, Cercospora zeina, Fusarium verticillioides, and Fusarium virguliforme) while limited expression was noted against abiotic stresses. Concisely, our results provide a platform for additional functional exploration of the ZmGLP genes against various environmental stresses.
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Affiliation(s)
- Muhammad Ilyas
- Department
of Botany, Kohsar University Murree, Murree 19679, Punjab, Pakistan
| | - Iftikhar Ali
- Centre
for Plant Science and Biodiversity, University
of Swat, Charbagh 19120, Pakistan
- Department
of Genetics and Development, Columbia University
Irving Medical Center, New York, New York 10032, United States
| | - Dalal Nasser Binjawhar
- Department
of Chemistry, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Sami Ullah
- Department
of Forestry & Range Management, Kohsar
University Murree, Murree 19679, Pakistan
| | - Sayed M Eldin
- Center
of
Research, Faculty of Engineering, Future
University in Egypt, New Cairo 11835, Egypt
| | - Baber Ali
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Rashid Iqbal
- Department
of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Syed Habib Ali Bokhari
- Department
of Biosciences, CUI, Islamabad, Pakistan; Faculty of Biomedical and
Life Sciences, Kohsar University Murree, Murree 19679, Pakistan
| | - Tariq Mahmood
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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196
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Jin X, Hou X, Wang X, Zhang M, Chen J, Song M, Zhang J, Zheng H, Chang W, Lou H. Characterization of an allosteric inhibitor of fungal-specific C-24 sterol methyltransferase to treat Candida albicans infections. Cell Chem Biol 2023; 30:553-568.e7. [PMID: 37160123 DOI: 10.1016/j.chembiol.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/02/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023]
Abstract
Filamentation is an important virulence factor of the pathogenic fungus Candida albicans. The abolition of Candida albicans hyphal formation by disrupting sterol synthesis is an important concept for the development of antifungal drugs with high safety. Here, we conduct a high-throughput screen using a C. albicans strain expressing green fluorescent protein-labeled Dpp3 to identify anti-hypha agents by interfering with ergosterol synthesis. The antipyrine derivative H55 is characterized to have minimal cytotoxicity and potent inhibition of C. albicans hyphal formation in multiple cultural conditions. H55 monotherapy exhibits therapeutic efficacy in mouse models of azole-resistant candidiasis. H55 treatment increases the accumulation of zymosterol, the substrate of C-24 sterol methyltransferase (Erg6). The results of enzyme assays, photoaffinity labeling, molecular simulation, mutagenesis, and cellular thermal shift assays support H55 as an allosteric inhibitor of Erg6. Collectively, H55, an inhibitor of the fungal-specific enzyme Erg6, holds potential to treat C. albicans infections.
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Affiliation(s)
- Xueyang Jin
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Xuben Hou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Xue Wang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Ming Zhang
- Institute of Medical Science, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jinyao Chen
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Minghui Song
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Jiaozhen Zhang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Hongbo Zheng
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Wenqiang Chang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.
| | - Hongxiang Lou
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.
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197
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Wang J, Liu S, Ren P, Jia F, Kang F, Wang R, Xue R, Yan X, Huang L. A novel protein elicitor (PeSy1) from Saccharothrix yanglingensis induces plant resistance and interacts with a receptor-like cytoplasmic kinase in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2023; 24:436-451. [PMID: 36872468 PMCID: PMC10098051 DOI: 10.1111/mpp.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/28/2022] [Accepted: 01/30/2023] [Indexed: 05/03/2023]
Abstract
Previously, we reported a rare actinomycete Saccharothrix yanglingensis Hhs.015 with strong biocontrol ability, which can colonize plant tissues and induce resistance, but the key elicitor and immune mechanisms were unclear. In this study, a novel protein elicitor screened from the genome of Hhs.015, PeSy1 (protein elicitor of S. yanglingensis 1), could induce a strong hypersensitive response (HR) and resistance in plants. The PeSy1 gene encodes an 11 kDa protein with 109 amino acids that is conserved in Saccharothrix species. PeSy1-His recombinant protein induced early defence events such as a cellular reactive oxygen species burst, callose deposition, and the activation of defence hormone signalling pathways, which enhanced Nicotiana benthamiana resistance to Sclerotinia sclerotiorum and Phytophthora capsici, and Solanum lycopersicum resistance to Pseudomonas syringae pv. tomato DC3000. Through pull-down and mass spectrometry, candidate proteins that interacted with PeSy1 were obtained from N. benthamiana. We confirmed the interaction between receptor-like cytoplasmic kinase RSy1 (Response to PeSy1) and PeSy1 using co-immunoprecipitation, bimolecular fluorescence complementation, and microscale thermophoresis. PeSy1 treatment promoted up-regulation of marker genes in pattern-triggered immunity. The cell death it elicited was dependent on the co-receptors NbBAK1 and NbSOBIR1, suggesting that PeSy1 acts as a microbe-associated molecular pattern from Hhs.015. Additionally, RSy1 positively regulated PeSy1-induced plants resistant to S. sclerotiorum. In conclusion, our results demonstrated a novel receptor-like cytoplasmic kinase in the plant perception of microbe-associated molecular patterns, and the potential of PeSy1 in induced resistance provided a new strategy for biological control of actinomycetes in agricultural diseases.
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Affiliation(s)
- Jianxun Wang
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Shang Liu
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Peng Ren
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Fengguo Jia
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Feng Kang
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Ruolin Wang
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Renzheng Xue
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Xia Yan
- College of Life ScienceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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198
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Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler PR, Golby P, Adnew B, Gagneux S, Aseffa A, Gordon SV, Comas I, Young DB, Waddell SJ, Larrouy-Maumus G, Berg S. Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom 2023; 9:mgen001011. [PMID: 37171244 PMCID: PMC10272862 DOI: 10.1099/mgen.0.001011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/07/2023] [Indexed: 05/13/2023] Open
Abstract
Lineage 7 (L7) emerged in the phylogeny of the Mycobacterium tuberculosis complex (MTBC) subsequent to the branching of 'ancient' lineage 1 and prior to the Eurasian dispersal of 'modern' lineages 2, 3 and 4. In contrast to the major MTBC lineages, the current epidemiology suggests that prevalence of L7 is highly confined to the Ethiopian population, or when identified outside of Ethiopia, it has mainly been in patients of Ethiopian origin. To search for microbiological factors that may contribute to its restricted distribution, we compared the genome of L7 to the genomes of globally dispersed MTBC lineages. The frequency of predicted functional mutations in L7 was similar to that documented in other lineages. These include mutations characteristic of modern lineages - such as constitutive expression of nitrate reductase - as well as mutations in the VirS locus that are commonly found in ancient lineages. We also identified and characterized multiple lineage-specific mutations in L7 in biosynthesis pathways of cell wall lipids, including confirmed deficiency of methoxy-mycolic acids due to a stop-gain mutation in the mmaA3 gene that encodes a methoxy-mycolic acid synthase. We show that the abolished biosynthesis of methoxy-mycolates of L7 alters the cell structure and colony morphology on selected growth media and impacts biofilm formation. The loss of these mycolic acid moieties may change the host-pathogen dynamic for L7 isolates, explaining the limited geographical distribution of L7 and contributing to further understanding the spread of MTBC lineages across the globe.
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Affiliation(s)
- Elena Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daire Cantillon
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
- Present address: Department of Tropical Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Carlos Madrazo
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Graham Rose
- Francis Crick Institute, London, UK
- Present address: North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK
| | | | - Paul Golby
- Animal and Plant Health Agency, Weybridge, UK
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Iñaki Comas
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Douglas B. Young
- Francis Crick Institute, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Simon J. Waddell
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Stefan Berg
- Animal and Plant Health Agency, Weybridge, UK
- Present address: Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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199
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Cai P, Liu S, Zhang D, Xing H, Han M, Liu D, Gong L, Hu QN. SynBioTools: a one-stop facility for searching and selecting synthetic biology tools. BMC Bioinformatics 2023; 24:152. [PMID: 37069545 PMCID: PMC10111727 DOI: 10.1186/s12859-023-05281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. RESULTS We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. CONCLUSIONS SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.
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Affiliation(s)
- Pengli Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sheng Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dachuan Zhang
- Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - Huadong Xing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengying Han
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dongliang Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Linlin Gong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qian-Nan Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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200
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Li K, Wei Y, Wang Y, Tan B, Chen S, Li H. Genome-Wide Identification of LBD Genes in Foxtail Millet ( Setaria italica) and Functional Characterization of SiLBD21. Int J Mol Sci 2023; 24:ijms24087110. [PMID: 37108274 PMCID: PMC10138450 DOI: 10.3390/ijms24087110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
Plant-specific lateral organ boundaries domain (LBD) proteins play important roles in plant growth and development. Foxtail millet (Setaria italica) is one new C4 model crop. However, the functions of foxtail millet LBD genes are unknown. In this study, a genome-wide identification of foxtail millet LBD genes and a systematical analysis were conducted. A total of 33 SiLBD genes were identified. They are unevenly distributed on nine chromosomes. Among these SiLBD genes, six segmental duplication pairs were detected. The thirty-three encoded SiLBD proteins could be classified into two classes and seven clades. Members in the same clade have similar gene structure and motif composition. Forty-seven kinds of cis-elements were found in the putative promoters, and they are related to development/growth, hormone, and abiotic stress response, respectively. Meanwhile, the expression pattern was investigated. Most SiLBD genes are expressed in different tissues, while several genes are mainly expressed in one or two kinds of tissues. In addition, most SiLBD genes respond to different abiotic stresses. Furthermore, the function of SiLBD21, which is mainly expressed in roots, was characterized by ectopic expression in Arabidopsis and rice. Compared to controls, transgenic plants generated shorter primary roots and more lateral roots, indicating the function of SiLBD21 in root development. Overall, our study laid the foundation for further functional elucidation of SiLBD genes.
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Affiliation(s)
- Kunjie Li
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yaning Wei
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yimin Wang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Bin Tan
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Shoukun Chen
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Haifeng Li
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
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