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Fang H, Shan T, Gu H, Chen J, Qi Y, Li Y, Saeed M, Yuan J, Li P, Wang B. Identification and characterization of ACR gene family in maize for salt stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1381056. [PMID: 38745920 PMCID: PMC11091409 DOI: 10.3389/fpls.2024.1381056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Background Members of the ACR gene family are commonly involved in various physiological processes, including amino acid metabolism and stress responses. In recent decades, significant progress has been made in the study of ACR genes in plants. However, little is known about their characteristics and function in maize. Methods In this study, ACR genes were identified from the maize genome, and their molecular characteristics, gene structure, gene evolution, gene collinearity analysis, cis-acting elements were analyzed. qRT-PCR technology was used to verify the expression patterns of the ZmACR gene family in different tissues under salt stress. In addition, Ectopic expression technique of ZmACR5 in Arabidopsis thaliana was utilized to identify its role in response to salt stress. Results A total of 28 ZmACR genes were identified, and their molecular characteristics were extensively described. Two gene pairs arising from segmented replication events were detected in maize, and 18 collinear gene pairs were detected between maize and 3 other species. Through phylogenetic analysis, three subgroups were revealed, demonstrating distinct divergence between monocotyledonous and dicotyledonous plants. Analysis of ZmACR cis-acting elements revealed the optional involvement of ZmACR genes in light response, hormone response and stress resistance. Expression analysis of 8 ZmACR genes under salt treatment clearly revealed their role in the response to salt stress. Ectopic overexpression of ZmACR5 in Arabidopsis notably reduced salt tolerance compared to that of the wild type under salt treatment, suggesting that ZmACR5 has a negative role in the response to salt stress. Conclusion Taken together, these findings confirmed the involvement of ZmACR genes in regulating salt stress and contributed significantly to our understanding of the molecular function of ACR genes in maize, facilitating further research in this field.
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Affiliation(s)
- Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Tingyu Shan
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Haijing Gu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Junyu Chen
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yingxiao Qi
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yexiong Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Muhammad Saeed
- Department of Agricultural Sciences, Government College University, Faisalabad, Pakistan
| | | | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
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Wu C, Cai D, Li J, Lin Z, Wei W, Shan W, Chen J, Lu W, Su X, Kuang J. Banana MabHLH28 positively regulates the expression of softening-related genes to mediate fruit ripening independently or via cooperating with MaWRKY49/111. HORTICULTURE RESEARCH 2024; 11:uhae053. [PMID: 38706579 PMCID: PMC11069428 DOI: 10.1093/hr/uhae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/17/2024] [Indexed: 05/07/2024]
Abstract
Texture softening is a physiological indicator of fruit ripening, which eventually contributes to fruit quality and the consumer's acceptance. Despite great progress having been made in identification of the genes related to fruit softening, the upstream transcriptional regulatory pathways of these softening-related genes are not fully elucidated. Here, a novel bHLH gene, designated as MabHLH28, was identified because of its significant upregulation in banana fruit ripening. DAP-Seq analysis revealed that MabHLH28 bound to the core sequence of 'CAYGTG' presented in promoter regions of fruit softening-associated genes, such as the genes related to cell wall modification (MaPG3, MaPE1, MaPL5, MaPL8, MaEXP1, MaEXP2, MaEXPA2, and MaEXPA15) and starch degradation (MaGWD1 and MaLSF2), and these bindings were validated by EMSA and DLR assays. Transient overexpression and knockdown of MabHLH28 in banana fruit resulted in up- and down-regulation of softening-related genes, thereby hastening and postponing fruit ripening. Furthermore, overexpression of MabHLH28 in tomato accelerated the ripening process by elevating the accumulation of softening-associated genes. In addition, MabHLH28 showed interaction withMaWRKY49/111 and itself to form protein complexes, which could combinatorically strengthen the transcription of softening-associated genes. Taken together, our findings suggest that MabHLH28 mediates fruit softening by upregulating the expression of softening-related genes either alone or in combination with MaWRKY49/111.
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Affiliation(s)
- Chaojie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Danling Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zengxiang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xinguo Su
- Agronomy Dean, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Jianfei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Guo H, Tan J, Jiao Y, Huang B, Ma R, Ramakrishnan M, Qi G, Zhang Z. Genome-wide identification and expression analysis of the HAK/KUP/KT gene family in Moso bamboo. FRONTIERS IN PLANT SCIENCE 2024; 15:1331710. [PMID: 38595761 PMCID: PMC11002169 DOI: 10.3389/fpls.2024.1331710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/04/2024] [Indexed: 04/11/2024]
Abstract
The K+ uptake permease/high-affinity K+/K+ transporter (KUP/HAK/KT) family is the most prominent group of potassium (K+) transporters, playing a key role in K+ uptake, transport, plant growth and development, and stress tolerance. However, the presence and functions of the KUP/HAK/KT family in Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau), the fastest-growing plant, have not been studied. In this study, we identified 41 KUP/HAK/KT genes (PeHAKs) distributed across 18 chromosomal scaffolds of the Moso bamboo genome. PeHAK is a typical membrane protein with a conserved structural domain and motifs. Phylogenetic tree analysis classified PeHAKs into four distinct clusters, while collinearity analysis revealed gene duplications resulting from purifying selection, including both tandem and segmental duplications. Enrichment analysis of promoter cis-acting elements suggested their plausible role in abiotic stress response and hormone induction. Transcriptomic data and STEM analyses indicated that PeHAKs were involved in tissue and organ development, rapid growth, and responded to different abiotic stress conditions. Subcellular localization analysis demonstrated that PeHAKs are predominantly expressed at the cell membrane. In-situ PCR experiments confirmed that PeHAK was mainly expressed in the lateral root primordia. Furthermore, the involvement of PeHAKs in potassium ion transport was confirmed by studying the potassium ion transport properties of a yeast mutant. Additionally, through homology modeling, we revealed the structural properties of HAK as a transmembrane protein associated with potassium ion transport. This research provides a solid basis for understanding the classification, characterization, and functional analysis of the PeHAK family in Moso bamboo.
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Affiliation(s)
- Hui Guo
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Jiaqi Tan
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Yang Jiao
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bing Huang
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Ruifang Ma
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Guoning Qi
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhijun Zhang
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [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: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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Ahmed FF, Dola FS, Islam MSU, Zohra FT, Akter N, Rahman SM, Rauf Sarkar MA. Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley ( Hordeum vulgare L.). Genet Res (Camb) 2024; 2024:2924953. [PMID: 38444770 PMCID: PMC10914435 DOI: 10.1155/2024/2924953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/27/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are a significant subgroup of the receptor-like kinases (RLKs) protein family. They play crucial roles in plant growth, development, immune responses, signal transduction, and stress tolerance. However, the genome-wide identification and characterization of LecRLK genes and their regulatory elements have not been explored in a major cereal crop, barley (Hordeum vulgare L.). Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 LecRLK genes were identified in the barley genome (referred to as HvlecRLK) corresponding to the LecRLK genes of Arabidopsis thaliana. These putative HvlecRLK genes were classified into three groups: 62 G-type LecRLKs, 1 C-type LecRLK, and 50 L-type LecRLKs. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type HvlecRLK (96.8%), C-type HvlecRLK (100%), and L-type HvlecRLK (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of AtlecRLK. Notably, most of the HvlecRLKs (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that HvlecRLK gene pairs evolved through purifying selection and gene duplication was the major factor for the expansion of the HvlecRLK gene family. Exploration of gene ontology (GO) enrichment indicated that the identified HvlecRLK genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of HvlecRLK gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type HvleckRLK64 and HvleckRLK86. The promoter cis-acting regulatory element (CARE) analysis of barley identified a total of 75 CARE motifs responsive to light responsiveness (LR), tissue-specific (TS), hormone responsiveness (HR), and stress responsiveness (SR). The maximum number of CAREs was identified in HvleckRLK11 (25 for LR), HvleckRLK69 (17 for TS), and HvleckRLK80 (12 for HR). Additionally, HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110 were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 HvlecRLK genes and HvlecRLK13 was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 Arabidopsis STRING proteins. Our overall findings provide valuable information on the LecRLK gene family which might pave the way to advanced research on the functional mechanism of the candidate genes as well as to develop new barley cultivars in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Shohel Ul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Nasrin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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Mir Drikvand R, Sohrabi SM, Sohrabi SS, Samiei K. Molecular Identification and Characterization of Hevein Antimicrobial Peptide Genes in Two-Row and Six-Row Cultivars of Barley (Hordeum vulgare L.). Biochem Genet 2024:10.1007/s10528-024-10695-8. [PMID: 38386212 DOI: 10.1007/s10528-024-10695-8] [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: 09/29/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024]
Abstract
Heveins are one of the most important groups of plant antimicrobial peptides. So far, various roles in plant growth and development and in response to biotic and abiotic stresses have reported for heveins. The present study aimed to identify and characterize the hevein genes in two-row and six-row cultivars of barley. In total, thirteen hevein genes were identified in the genome of two-row and six-row cultivars of barley. The identified heveins were identical in two-row and six-row cultivars of barley and showed a high similarity with heveins from other plant species. The hevein coding sequences produced open reading frames (ORFs) ranged from 342 to 1002 bp. Most of the identified hevein genes were intronless, and the others had only one intron. The hevein ORFs produced proteins ranged from 113 to 333 amino acids. Search for conserved functional domains showed CBD and LYZ domains in barley heveins. All barley heveins comprised extracellular signal peptides ranged from 19 to 35 amino acids. The phylogenetic analysis divided barley heveins into two groups. The promoter analysis showed regulatory elements with different frequencies between two-row and six-row cultivars. These cis-acting elements included elements related to growth and development, hormone response, and environmental stresses. The expression analysis showed high expression level of heveins in root and reproductive organs of both two-row and six-row cultivars. The expression analysis also showed that barley heveins is induced by both biotic and abiotic stresses. The results of antimicrobial activity prediction showed the highest antimicrobial activity in CBD domain of barley heveins. The findings of the current study can improve our knowledge about the role of hevein genes in plant and can be used for future studies.
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Affiliation(s)
- Reza Mir Drikvand
- Department of Plant Genetics and Breeding, Islamic Azad University, Khorramabad Branch, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University, Ahvaz, Iran
| | - Seyed Sajad Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Kamran Samiei
- Department of Plant Genetics and Breeding, Islamic Azad University, Khorramabad Branch, Khorramabad, Iran
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van Es SW, Muñoz-Gasca A, Romero-Campero FJ, González-Grandío E, de Los Reyes P, Tarancón C, van Dijk ADJ, van Esse W, Pascual-García A, Angenent GC, Immink RGH, Cubas P. A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1. THE NEW PHYTOLOGIST 2024; 241:1193-1209. [PMID: 38009929 DOI: 10.1111/nph.19420] [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: 04/22/2023] [Accepted: 10/21/2023] [Indexed: 11/29/2023]
Abstract
The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::β-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.
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Affiliation(s)
- Sam W van Es
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Aitor Muñoz-Gasca
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Francisco J Romero-Campero
- Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Científicas, Ave. Américo Vespucio 49, 41092, Seville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Ave. Reina Mercedes s/n, 41012, Seville, Spain
| | - Eduardo González-Grandío
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro de Los Reyes
- Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Científicas, Ave. Américo Vespucio 49, 41092, Seville, Spain
| | - Carlos Tarancón
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Aalt D J van Dijk
- Bioinformatics, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Wilma van Esse
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Alberto Pascual-García
- Department of Systems Biology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Gerco C Angenent
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Richard G H Immink
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Pilar Cubas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
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8
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Hasan MN, Mosharaf MP, Uddin KS, Das KR, Sultana N, Noorunnahar M, Naim D, Mollah MNH. Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea ( Vigna unguiculata (L.) Walp.). BIOMED RESEARCH INTERNATIONAL 2023; 2023:8832406. [PMID: 38046903 PMCID: PMC10691899 DOI: 10.1155/2023/8832406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.
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Affiliation(s)
- Mohammad Nazmol Hasan
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Parvez Mosharaf
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Khandoker Saif Uddin
- Department of Quantitative Science (Statistics), International University of Business Agriculture and Technology (IUBAT), Uttara, Bangladesh
| | - Keya Rani Das
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nasrin Sultana
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mst. Noorunnahar
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
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Faysal Ahmed F, Dola FS, Zohra FT, Rahman SM, Konak JN, Sarkar MAR. Genome-wide identification, classification, and characterization of lectin gene superfamily in sweet orange (Citrus sinensis L.). PLoS One 2023; 18:e0294233. [PMID: 37956187 PMCID: PMC10642848 DOI: 10.1371/journal.pone.0294233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Lectins are sugar-binding proteins found abundantly in plants. Lectin superfamily members have diverse roles, including plant growth, development, cellular processes, stress responses, and defense against microbes. However, the genome-wide identification and functional analysis of lectin genes in sweet orange (Citrus sinensis L.) remain unexplored. Therefore, we used integrated bioinformatics approaches (IBA) for in-depth genome-wide identification, characterization, and regulatory factor analysis of sweet orange lectin genes. Through genome-wide comparative analysis, we identified a total of 141 lectin genes distributed across 10 distinct gene families such as 68 CsB-Lectin, 13 CsLysin Motif (LysM), 4 CsChitin-Bind1, 1 CsLec-C, 3 CsGal-B, 1 CsCalreticulin, 3 CsJacalin, 13 CsPhloem, 11 CsGal-Lec, and 24 CsLectinlegB.This classification relied on characteristic domain and phylogenetic analysis, showing significant homology with Arabidopsis thaliana's lectin gene families. A thorough analysis unveiled common similarities within specific groups and notable variations across different protein groups. Gene Ontology (GO) enrichment analysis highlighted the predicted genes' roles in diverse cellular components, metabolic processes, and stress-related regulation. Additionally, network analysis of lectin genes with transcription factors (TFs) identified pivotal regulators like ERF, MYB, NAC, WRKY, bHLH, bZIP, and TCP. The cis-acting regulatory elements (CAREs) found in sweet orange lectin genes showed their roles in crucial pathways, including light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and more. These findings will aid in the in-depth molecular examination of these potential genes and their regulatory elements, contributing to targeted enhancements of sweet orange species in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Department of Biochemistry and Molecular Biology, Faculty of LifeScience, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Cui Y, Cao Q, Li Y, He M, Liu X. Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5441-5457. [PMID: 37402253 DOI: 10.1093/jxb/erad248] [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: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
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Affiliation(s)
- Yue Cui
- College of Teacher Education, Molecular and Cellular Postdoctoral Research Station, Hebei Normal University, Shijiazhuang 050024, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiao Cao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mingqi He
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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11
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Nawade B, Bosamia TC, Lee JH, Jang JH, Lee OR. Genome-wide characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1216082. [PMID: 37745995 PMCID: PMC10514519 DOI: 10.3389/fpls.2023.1216082] [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: 05/03/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]
Abstract
The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified 14 genes from the DMP family in soybean (Glycine max) and characterized their physiochemical properties, subcellular location, gene structure, and promoter regions using bioinformatics tools. Additionally, their tissue-specific and stress-responsive expressions were analyzed using publicly available transcriptome data. Phylogenetic analysis of 198 DMPs from monocots and dicots revealed six clades, with clade-I encoding senescence-related AtDMP1/2 orthologues and clade-II including pollen-specific AtDMP8/9 orthologues. The largest clade, clade-III, predominantly included monocot DMPs, while monocot- and dicot-specific DMPs were assembled in clade-IV and clade-VI, respectively. Evolutionary analysis suggests that soybean GmDMPs underwent purifying selection during evolution. Using 68 transcriptome datasets, expression profiling revealed expression in diverse tissues and distinct responses to abiotic and biotic stresses. The genes Glyma.09G237500 and Glyma.18G098300 showed pistil-abundant expression by qPCR, suggesting they could be potential targets for female organ-mediated haploid induction. Furthermore, cis-acting regulatory elements primarily related to stress-, hormone-, and light-induced pathways regulate GmDMPs, which is consistent with their divergent expression and suggests involvement in growth and stress responses. Overall, our study provides a comprehensive report on the soybean GmDMP family and a framework for further biological functional analysis of DMP genes in soybean or other crops.
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Affiliation(s)
- Bhagwat Nawade
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Tejas C. Bosamia
- Plant Omics Division, Council of Scientific and Industrial Research-Central Salt and Marine Chemical Research Institute (CSIR-CSMCRI), Bhavnagar, Gujarat, India
| | - Jae Hyun Lee
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Jin Hoon Jang
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
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Huang LT, Liu CY, Li L, Han XS, Chen HW, Jiao CH, Sha AH. Genome-Wide Identification of bZIP Transcription Factors in Faba Bean Based on Transcriptome Analysis and Investigation of Their Function in Drought Response. PLANTS (BASEL, SWITZERLAND) 2023; 12:3041. [PMID: 37687286 PMCID: PMC10490193 DOI: 10.3390/plants12173041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Faba bean is an important cool-season edible legume crop that is constantly threatened by abiotic stresses such as drought. The basic leucine zipper (bZIP) gene family is one of the most abundant and diverse families of transcription factors in plants. It regulates plant growth and development and plays an important role in the response to biotic and abiotic stresses. In this study, we identified 18 members of the faba bean bZIP transcription factor family at the genome-wide level based on previous faba bean drought stress transcriptome sequencing data. A phylogenetic tree was constructed to group the 18 VfbZIP proteins into eight clades. Analysis of cis-acting elements in the promoter region suggested that these 18 VfbZIPs may be involved in regulating abiotic stress responses such as drought. Transcriptome data showed high expression of seven genes (VfbZIP1, VfbZIP2, VfbZIP5, VfbZIP7, VfbZIP15, VfbZIP17, and VfbZIP18) in the drought-tolerant cultivar under drought stress, in which VfbZIP1, VfbZIP2, and VfbZIP5 were consistently expressed as detected by quantitative real-time polymerase chain reaction (qRT-PCR) compared to the transcriptome data. Ectopic overexpression of the three VfbZIPs in tobacco, based on the potato Virus X (PVX) vector, revealed that VfbZIP5 enhanced the drought tolerance. Overexpressed VfbZIP5 in plants showed lower levels of proline (PRO), malondialdehyde (MDA), and peroxidase (POD) compared to those overexpressing an empty vector under 10 days of drought stress. Protein-protein interaction (PPI) analysis showed that VfbZIP5 interacted with seven proteins in faba bean, including VfbZIP7 and VfbZIP10. The results depict the importance of VfbZIPs in response to drought stress, and they would be useful for the improvement of drought tolerance.
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Affiliation(s)
- Lin-Tao Huang
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China
| | - Chang-Yan Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Li Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Xue-Song Han
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Hong-Wei Chen
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Chun-Hai Jiao
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Ai-Hua Sha
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China
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Podder A, Ahmed FF, Suman MZH, Mim AY, Hasan K. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory element analyses in sunflower (Helianthus annuus). PLoS One 2023; 18:e0286994. [PMID: 37294803 PMCID: PMC10256174 DOI: 10.1371/journal.pone.0286994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/27/2023] [Indexed: 06/11/2023] Open
Abstract
RNA interference (RNAi) regulates a variety of eukaryotic gene expressions that are engaged in response to stress, growth, and the conservation of genomic stability during developmental phases. It is also intimately connected to the post-transcriptional gene silencing (PTGS) process and chromatin modification levels. The entire process of RNA interference (RNAi) pathway gene families mediates RNA silencing. The main factors of RNA silencing are the Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families. To the best of our knowledge, genome-wide identification of RNAi gene families like DCL, AGO, and RDR in sunflower (Helianthus annuus) has not yet been studied despite being discovered in some species. So, the goal of this study is to find the RNAi gene families like DCL, AGO, and RDR in sunflower based on bioinformatics approaches. Therefore, we accomplished an inclusive in silico investigation for genome-wide identification of RNAi pathway gene families DCL, AGO, and RDR through bioinformatics approaches such as (sequence homogeneity, phylogenetic relationship, gene structure, chromosomal localization, PPIs, GO, sub-cellular localization). In this study, we have identified five DCL (HaDCLs), fifteen AGO (HaAGOs), and ten RDR (HaRDRs) in the sunflower genome database corresponding to the RNAi genes of model plant Arabidopsis thaliana based on genome-wide analysis and a phylogenetic method. The analysis of the gene structure that contains exon-intron numbers, conserved domain, and motif composition analyses for all HaDCL, HaAGO, and HaRDR gene families indicated almost homogeneity among the same gene family. The protein-protein interaction (PPI) network analysis illustrated that there exists interconnection among identified three gene families. The analysis of the Gene Ontology (GO) enrichment showed that the detected genes directly contribute to the RNA gene-silencing and were involved in crucial pathways. It was observed that the cis-acting regulatory components connected to the identified genes were shown to be responsive to hormone, light, stress, and other functions. That was found in HaDCL, HaAGO, and HaRDR genes associated with the development and growth of plants. Finally, we are able to provide some essential information about the components of sunflower RNA silencing through our genome-wide comparison and integrated bioinformatics analysis, which open the door for further research into the functional mechanisms of the identified genes and their regulatory elements.
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Affiliation(s)
- Anamika Podder
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Zahid Hasan Suman
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Afsana Yeasmin Mim
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Khadiza Hasan
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
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Chakraborty S, Gangwar R, Zahra S, Poddar N, Singh A, Kumar S. Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes. Sci Rep 2023; 13:5914. [PMID: 37041245 PMCID: PMC10090146 DOI: 10.1038/s41598-023-33226-8] [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: 12/13/2022] [Accepted: 04/10/2023] [Indexed: 04/13/2023] Open
Abstract
Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.
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Affiliation(s)
- Srija Chakraborty
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rashmi Gangwar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shafaque Zahra
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nikita Poddar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Amarjeet Singh
- Stress Signalling Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Kaur H, Manchanda P, Kumar P, Dhall RK, Chhuneja P, Weng Y. Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.). Sci Rep 2023; 13:2403. [PMID: 36765113 PMCID: PMC9918540 DOI: 10.1038/s41598-023-29660-3] [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: 07/21/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon-intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.
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Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
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Jia Y, Yao M, He X, Xiong X, Guan M, Liu Z, Guan C, Qian L. Transcriptome and Regional Association Analyses Reveal the Effects of Oleosin Genes on the Accumulation of Oil Content in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2022; 11:3140. [PMID: 36432869 PMCID: PMC9698637 DOI: 10.3390/plants11223140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Rapeseed stores lipids in the form of oil bodies. Oil bodies in the seeds of higher plants are surrounded by oleosins. Adjusting oleosin protein levels can prevent the fusion of oil bodies and maintain oil body size during seed development. However, oil contents are affected by many factors, and studies on the complex molecular regulatory mechanisms underlying the variations in seed oil contents of B. napus are limited. In this study, a total of 53 BnOLEO (B. napus oleosin) genes were identified in the genome of B. napus through a genome-wide analysis. The promoter sequences of oleosin genes consisted of various light-, hormone-, and stress-related cis-acting elements, along with transcription factor (TF) binding sites, for 25 TF families in 53 BnOLEO genes. The differentially expressed oleosin genes between two high- and two low-oil-content accessions were explored. BnOLEO3-C09, BnOLEO4-A02, BnOLEO4-A09, BnOLEO2-C04, BnOLEO1-C01, and BnOLEO7-A03 showed higher expressions in the high-oil-content accessions than in low-oil-content accessions, at 25, 35, and 45 days after pollination (DAP) in two different environments. A regional association analysis of 50 re-sequenced rapeseed accessions was used to further analyze these six BnOLEO genes, and it revealed that the nucleotide variations in the BnOLEO1-C01 and BnOLEO7-A03 gene regions were related to the phenotypic variations in seed oil content. Moreover, a co-expression network analysis revealed that the BnOLEO genes were directly linked to lipid/fatty acid metabolism, TF, lipid transport, and carbohydrate genes, thus forming a molecular network involved in seed oil accumulation. These favorable haplotypes can be utilized in molecular marker-assisted selection in order to further improve seed oil contents in rapeseed.
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Guo L, Wang S, Nie Y, Shen Y, Ye X, Wu W. Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes. PLANT COMMUNICATIONS 2022; 3:100420. [PMID: 35949168 PMCID: PMC9700204 DOI: 10.1016/j.xplc.2022.100420] [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: 04/22/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 05/10/2023]
Abstract
Whole-genome duplication (WGD or polyploidization) has been suggested as a genetic contributor to angiosperm adaptation to environmental changes. However, many eudicot lineages did not undergo recent WGD (R-WGD) around and/or after the Cretaceous-Paleogene (K-Pg) boundary, times of severe environmental changes; how those plants survived has been largely ignored. Here, we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD: 12 R-WGD-containing plants (R-WGD-Y) and 10 R-WGD-lacking plants (R-WGD-N). Subsequently, we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation. The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF III and IX subfamilies through recurrent independent WGDs and tandem duplications (TDs) after the radiation of the plants. The expansions showed coincident enrichments in- times around and/or after the K-Pg boundary, when global cooling was a major environmental stressor. Consequently, convergent expansions and co-retentions of AP2/ERF III C-repeat binding factor (CBF) duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks. Moreover, promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code (G-box: CACGTG). We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF III and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes, and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.
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Affiliation(s)
- Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
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18
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Liu Z, Deng B, Yuan H, Zhang B, Liu J, Meng J, Chang M. Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis. Microb Cell Fact 2022; 21:216. [PMID: 36253826 PMCID: PMC9578197 DOI: 10.1186/s12934-022-01932-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. However, little is known about the transcriptional regulatory mechanisms of cellulose degradation. Results In this study, FfMYB15 that may regulate the expression of cellulase gene FfCEL6B in F. filiformis was identified. RNA interference (RNAi) showed that FfCEL6B positively regulated mycelial growth. Gene expression analyses indicated that the expression patterns of FfCEL6B and FfMYB15 in mycelia cultured on the 0.9% cellulose medium for different times were similar with a correlation coefficient of 0.953. Subcellular localization and transcriptional activity analyses implied that FfMYB15 was located in the nucleus and was a transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase assays demonstrated that FfMYB15 could bind and activate FfCEL6B promoter by recognizing MYB cis-acting element. Conclusions This study indicated that FfCEL6B played an active role in mycelial growth of F. filiformis and was regulated by FfMYB15. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01932-z.
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Affiliation(s)
- Zongqi Liu
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Bing Deng
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hui Yuan
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Benfeng Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Collaborative Innovation Center of Advancing Quality and Efficiency of Loess Plateau Edible Fungi, Taigu, 030801, Shanxi, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China. .,Collaborative Innovation Center of Advancing Quality and Efficiency of Loess Plateau Edible Fungi, Taigu, 030801, Shanxi, China.
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19
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Zhang A, Xu J, Xu X, Wu J, Li P, Wang B, Fang H. Genome-wide identification and characterization of the KCS gene family in sorghum ( Sorghum bicolor (L.) Moench). PeerJ 2022; 10:e14156. [PMID: 36225907 PMCID: PMC9549899 DOI: 10.7717/peerj.14156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/08/2022] [Indexed: 01/21/2023] Open
Abstract
The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0-1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of KCS family in sorghum and in response to abiotic stress.
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Affiliation(s)
- Aixia Zhang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jingjing Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Xin Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, Jiangsu, China
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
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20
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Evangelene Christy SM, Arun V. Isolation, cloning and functional analysis of a putative constitutive promoter of E3 ubiquitin- protein ligase RF4 from Coleus amboinicus Lour. Biotechnol Appl Biochem 2022; 70:746-760. [PMID: 35931417 DOI: 10.1002/bab.2395] [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: 03/07/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022]
Abstract
Promoter is a region in the genome sequence located upstream of the transcription start site comprising cis acting elements, which initiates and regulates the transcription of an associated gene. As the need for genetically engineered plants has widened, the requirement to develop methods to optimize the control of transgene expression has also increased. Therefore, analyzing the functionality of the promoter is very important in understanding the target gene expression. The widespread use of viral constitutive promoters (Cauliflower mosaic virus - CaMV35) has raised concerns about the safety and containment of the transgene in the environment. Hence isolation and characterization of novel promoters using fast and efficient genetic engineering tools is the need of the hour. The present study, for the first time, describes the isolation and characterization of a novel constitutive promoter driving Ubiquitin E3 ligase from the plant Coleus amboinicus, a perennial herb, of Lamiaceae family. The functionality of the isolated promoter was demonstrated using the β Glucuronidase as a reporter in tobacco var Petit havana. Development of blue color in the tobacco leaves indicated the presence of a functional promoter. We describe for the first time the isolation and characterization of E3 ubiquitin- protein ligase RF4 promoter from Coleus amboinicus Lour. In silico analysis revealed the presence of core promoter elements and other responsive elements in the promoter. The functionality of the promoter was demonstrated in tobacco leaf discs via GUS staining. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- S M Evangelene Christy
- Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - V Arun
- Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
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21
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Light regulates chlorophyll biosynthesis via ELIP1 during the storage of Chinese cabbage. Sci Rep 2022; 12:11098. [PMID: 35773334 PMCID: PMC9247097 DOI: 10.1038/s41598-022-15451-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/23/2022] [Indexed: 11/08/2022] Open
Abstract
Chlorophyll loss is a major problem during green vegetable storage. However, the molecular mechanism is still unclear. In this study, a 21 days of storage experiments showed chlorophyll content was higher in light-stored Chinese cabbage (Brassica chinensis L.) leaves than those in dark-stored samples. Transcriptome analyses were performed on these samples to determine the effects of light. Among 311 differentially expressed genes (DEGs), early light-induced protein 1 (ELIP1) was identified as the main control gene for chlorophyll synthesis. Tissues and subcellular localization indicated that ELIP1 was localized in the nucleus. Motifs structure analyses, chromatin immunoprecipitation (ChIP) assays, luciferase reporter assays, and overexpression experiments demonstrated that ELIP1 regulated the expressions of genomes uncoupled 4 (GUN4), Glutamyl-tRNA reductase family protein (HEMA1), and Mg-protoporphyrin IX methyltransferase (CHLM) by binding to G-box-like motifs and affected chlorophyll biosynthesis during the storage of Chinese cabbage. It is a possible common tetrapyrrole biosynthetic pathway for chlorophylls, hemes, and bilin pigments in photosynthetic organisms. Our research also revealed that white light can be used as a regulatory factor to improve the storage ability and extent shelf life of Chinese cabbage.
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22
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Liu X, Wu R, Bulley SM, Zhong C, Li D. Kiwifruit MYBS1-like and GBF3 transcription factors influence l-ascorbic acid biosynthesis by activating transcription of GDP-L-galactose phosphorylase 3. THE NEW PHYTOLOGIST 2022; 234:1782-1800. [PMID: 35288947 PMCID: PMC9325054 DOI: 10.1111/nph.18097] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/23/2022] [Indexed: 05/04/2023]
Abstract
Plant-derived Vitamin C (l-ascorbic acid (AsA)) is crucial for human health and wellbeing and thus increasing AsA content is of interest to plant breeders. In plants GDP-l-galactose phosphorylase (GGP) is a key biosynthetic control step and here evidence is presented for two new transcriptional activators of GGP. AsA measurement, transcriptomics, transient expression, hormone application, gene editing, yeast 1/2-hybrid, and electromobility shift assay (EMSA) methods were used to identify two positively regulating transcription factors. AceGGP3 was identified as the most highly expressed GGP in Actinidia eriantha fruit, which has high fruit AsA. A gene encoding a 1R-subtype myeloblastosis (MYB) protein, AceMYBS1, was found to bind the AceGGP3 promoter and activate its expression. Overexpression and gene-editing show AceMYBS1 effectively increases AsA accumulation. The bZIP transcription factor AceGBF3 (a G-box binding factor), also was shown to increase AsA content, and was confirmed to interact with AceMYBS1. Co-expression experiments showed that AceMYBS1 and AceGBF3 additively promoted AceGGP3 expression. Furthermore, AceMYBS1, but not GBF3, was repressed by abscisic acid, resulting in reduced AceGGP3 expression and accumulation of AsA. This study sheds new light on the roles of MYBS1 homologues and ABA in modulating AsA synthesis, and adds to the understanding of mechanisms underlying AsA accumulation.
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Affiliation(s)
- Xiaoying Liu
- Wuhan Botanical GardenChinese Academy of SciencesJiufeng 1 RoadWuhan430074HubeiChina
- College of Life SciencesUniversity of Chinese Academy of Sciences19A Yuquan RoadBeijing100049China
| | - Rongmei Wu
- The New Zealand Institute for Plant and Food Research Limited120 Mt Albert Road, Mt AlbertAuckland1025New Zealand
| | - Sean M. Bulley
- The New Zealand Institute for Plant and Food Research Limited412 No 1 Rd, RD2Te Puke3182New Zealand
| | - Caihong Zhong
- Wuhan Botanical GardenChinese Academy of SciencesJiufeng 1 RoadWuhan430074HubeiChina
- College of Life SciencesUniversity of Chinese Academy of Sciences19A Yuquan RoadBeijing100049China
| | - Dawei Li
- Wuhan Botanical GardenChinese Academy of SciencesJiufeng 1 RoadWuhan430074HubeiChina
- College of Life SciencesUniversity of Chinese Academy of Sciences19A Yuquan RoadBeijing100049China
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23
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Han X, Wang X, Shen C, Mo Y, Tian R, Mao L, Luo Z, Yang H. Exogenous ABA promotes aroma biosynthesis of postharvest kiwifruit after low-temperature storage. PLANTA 2022; 255:82. [PMID: 35257207 DOI: 10.1007/s00425-022-03855-w] [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: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Exogenous ABA played a positive role in the accumulation and biosynthesis of aroma components of postharvest kiwifruit after low-temperature storage, especially the esters production during ripening. Low-temperature storage (LTS) generally affects the aroma formation associated with the decrease in aroma quality in kiwifruit. In this work, abscisic acid (ABA) treatment after LTS increased the production of aroma components in postharvest kiwifruit and enhanced the related enzyme activity, especially alcohol acyltransferase (AAT), branched amino acid transaminase (BCAT) and hydroperoxide lyase (HPL). Corresponding to the enzyme activity, the gene expression of AchnAAT, AchnADH, AchnBCAT and AchnHPL was significantly up-regulated by ABA. The principal component analysis further illustrated the differences in aroma components between ABA and the control. The positive correlation of aroma accumulation with the expression levels of AchnPDC and AchnLOX and the enzyme activities of BCAT and pyruvate decarboxylase (PDC) was also revealed by correlation analysis. In addition, the promoter sequences of the key genes involved in aroma biosynthesis contained multiple cis-elements (ABRE and G-box) of ABA-responsive proteins. Combining the transcriptome sequencing data, the promoting role of ABA signaling in the regulation of aroma biosynthesis of postharvest kiwifruit after LTS was discussed. This study would provide a reference for improving aroma quality of postharvest kiwifruit after LTS, as well the molecular mechanism of kiwifruit aroma fading after LTS.
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Affiliation(s)
- Xueyuan Han
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Xiaoyu Wang
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Chi Shen
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Yiwei Mo
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Rungang Tian
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Huanyi Yang
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China.
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Sehrish S, Sumbal W, Xie M, Zhao C, Zuo R, Gao F, Liu S. Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L. Int J Mol Sci 2022; 23:ijms23041936. [PMID: 35216050 PMCID: PMC8879272 DOI: 10.3390/ijms23041936] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022] Open
Abstract
SET domain group encoding proteins function as histone lysine methyltransferases. These proteins are involved in various biological processes, including plant development and adaption to the environment by modifying the chromatin structures. So far, the SET domain genes (SDGs) have not been systematically investigated in Brassica napus (B. napus). In the current study, through genome-wide analysis, a total of 122 SDGs were identified in the B. napus genome. These BnSDGs were subdivided into seven (I-VII) classes based on phylogeny analysis, domain configurations, and motif distribution. Segmental duplication was involved in the evolution of this family, and the duplicated genes were under strong purifying selection. The promoter sequence of BnSDGs consisted of various growth, hormones, and stress-related cis-acting elements along with transcription factor binding sites (TFBSs) for 20 TF families in 59 of the 122 BnSDGs. The gene ontology (GO) analysis revealed that BnSDGs were closely associated with histone and non-histone methylation and metal binding capacity localized mostly in the nucleus. The in silico expression analysis at four developmental stages in leaf, stem root, floral organ, silique, and seed tissues showed a broad range of tissue and stage-specific expression pattern. The expression analysis under four abiotic stresses (dehydration, cold, ABA, and salinity) also provided evidence for the importance of BnSDGs in stress environments. Based on expression analysis, we performed reverse transcription-quantitative PCR for 15 target BnSDGs in eight tissues (young leaf, mature leaf, root, stem, carpel, stamen, sepal, and petals). Our results were in accordance with the in silico expression data, suggesting the importance of these genes in plant development. In conclusion, this study lays a foundation for future functional studies on SDGs in B. napus.
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Han X, Wei X, Lu W, Wu Q, Mao L, Luo Z. Transcriptional regulation of KCS gene by bZIP29 and MYB70 transcription factors during ABA-stimulated wound suberization of kiwifruit (Actinidia deliciosa). BMC PLANT BIOLOGY 2022; 22:23. [PMID: 34998386 PMCID: PMC8742354 DOI: 10.1186/s12870-021-03407-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/09/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Our previous study has demonstrated that the transcription of AchnKCS involved in suberin biosynthesis was up-regulated by exogenous abscisic acid (ABA) during the wound suberization of kiwifruit, but the regulatory mechanism has not been fully elucidated. RESULTS Through subcellular localization analysis in this work, AchnbZIP29 and AchnMYB70 transcription factors were observed to be localized in the nucleus. Yeast one-hybrid and dual-luciferase assay proved the transcriptional activation of AchnMYB70 and transcriptional suppression of AchnbZIP29 on AchnKCS promoter. Furthermore, the transcription level of AchnMYB70 was enhanced by ABA during wound suberization of kiwifruit, but AchnbZIP29 transcription was reduced by ABA. CONCLUSIONS Therefore, it was believed that ABA enhanced the transcriptional activation of AchnMYB70 on AchnKCS by increasing AchnMYB70 expression. On the contrary, ABA relieved the inhibitory effect of AchnbZIP29 on transcription of AchnKCS by inhibiting AchnbZIP29 expression. These results gave further insight into the molecular regulatory network of ABA in wound suberization of kiwifruit.
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Affiliation(s)
- Xueyuan Han
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Xiaopeng Wei
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan, China
| | - Wenjing Lu
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiong Wu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China.
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China.
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
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Liu Z, Xiong T, Zhao Y, Qiu B, Chen H, Kang X, Yang J. Genome-wide characterization and analysis of Golden 2-Like transcription factors related to leaf chlorophyll synthesis in diploid and triploid Eucalyptus urophylla. FRONTIERS IN PLANT SCIENCE 2022; 13:952877. [PMID: 35968152 PMCID: PMC9366356 DOI: 10.3389/fpls.2022.952877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 05/02/2023]
Abstract
Golden 2-Like (GLK) transcription factors play a crucial role in chloroplast development and chlorophyll synthesis in many plant taxa. To date, no systematic analysis of GLK transcription factors in tree species has been conducted. In this study, 40 EgrGLK genes in the Eucalyptus grandis genome were identified and divided into seven groups based on the gene structure and motif composition. The EgrGLK genes were mapped to 11 chromosomes and the distribution of genes on chromosome was uneven. Phylogenetic analysis of GLK proteins between E. grandis and other species provided information for the high evolutionary conservation of GLK genes among different species. Prediction of cis-regulatory elements indicated that the EgrGLK genes were involved in development, light response, and hormone response. Based on the finding that the content of chlorophyll in mature leaves was the highest, and leaf chlorophyll content of triploid Eucalyptus urophylla was higher than that of the diploid control, EgrGLK expression pattern in leaves of triploid and diploid E. urophylla was examined by means of transcriptome analysis. Differential expression of EgrGLK genes in leaves of E. urophylla of different ploidies was consistent with the trend in chlorophyll content. To further explore the relationship between EgrGLK expression and chlorophyll synthesis, co-expression networks were generated, which indicated that EgrGLK genes may have a positive regulatory relationship with chlorophyll synthesis. In addition, three EgrGLK genes that may play an important role in chlorophyll synthesis were identified in the co-expression networks. And the prediction of miRNAs targeting EgrGLK genes showed that miRNAs might play an important role in the regulation of EgrGLK gene expression. This research provides valuable information for further functional characterization of GLK genes in Eucalyptus.
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Affiliation(s)
- Zhao Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Tao Xiong
- Guangxi Dongmen Forest Farm, Chongzuo, China
| | | | - Bingfa Qiu
- Guangxi Dongmen Forest Farm, Chongzuo, China
| | - Hao Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Xiangyang Kang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Jun Yang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- *Correspondence: Jun Yang,
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Dhatterwal P, Mehrotra S, Miller AJ, Mehrotra R. Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops. PLANT MOLECULAR BIOLOGY 2021; 107:451-475. [PMID: 34674117 DOI: 10.1007/s11103-021-01193-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India
| | - Anthony J Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India.
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Ahmed FF, Hossen MI, Sarkar MAR, Konak JN, Zohra FT, Shoyeb M, Mondal S. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata). PLoS One 2021; 16:e0256873. [PMID: 34473743 PMCID: PMC8412350 DOI: 10.1371/journal.pone.0256873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
RNA silencing is mediated through RNA interference (RNAi) pathway gene families, i.e., Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) and their cis-acting regulatory elements. The RNAi pathway is also directly connected with the post-transcriptional gene silencing (PTGS) mechanism, and the pathway controls eukaryotic gene regulation during growth, development, and stress response. Nevertheless, genome-wide identification of RNAi pathway gene families such as DCL, AGO, and RDR and their regulatory network analyses related to transcription factors have not been studied in many fruit crop species, including banana (Musa acuminata). In this study, we studied in silico genome-wide identification and characterization of DCL, AGO, and RDR genes in bananas thoroughly via integrated bioinformatics approaches. A genome-wide analysis identified 3 MaDCL, 13 MaAGO, and 5 MaRDR candidate genes based on multiple sequence alignment and phylogenetic tree related to the RNAi pathway in banana genomes. These genes correspond to the Arabidopsis thaliana RNAi silencing genes. The analysis of the conserved domain, motif, and gene structure (exon-intron numbers) for MaDCL, MaAGO, and MaRDR genes showed higher homogeneity within the same gene family. The Gene Ontology (GO) enrichment analysis exhibited that the identified RNAi genes could be involved in RNA silencing and associated metabolic pathways. A number of important transcription factors (TFs), e.g., ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, were identified by network and sub-network analyses between TFs and candidate RNAi gene families. Furthermore, the cis-acting regulatory elements related to light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions were identified in candidate MaDCL, MaAGO, and MaRDR genes. These genome-wide analyses of these RNAi gene families provide valuable information related to RNA silencing, which would shed light on further characterization of RNAi genes, their regulatory elements, and functional roles, which might be helpful for banana improvement in the breeding program.
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Affiliation(s)
- Fee Faysal Ahmed
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
- * E-mail:
| | - Md. Imran Hossen
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Faculty of Biological Science and Technology, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Faculty of Life Science, Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Fatema Tuz Zohra
- Faculty of Agriculture, Laboratory of Fruit Science, Saga University, Honjo-machi, Saga, Japan
| | - Md. Shoyeb
- Faculty of Biological Science and Technology, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Samiran Mondal
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
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Xie Q, Xu J, Huang K, Su Y, Tong J, Huang Z, Huang C, Wei M, Lin W, Xiao L. Dynamic formation and transcriptional regulation mediated by phytohormones during chalkiness formation in rice. BMC PLANT BIOLOGY 2021; 21:308. [PMID: 34193032 PMCID: PMC8247166 DOI: 10.1186/s12870-021-03109-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/21/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) Chalkiness, the opaque part in the kernel endosperm formed by loosely piled starch and protein bodies. Chalkiness is a complex quantitative trait regulated by multiple genes and various environmental factors. Phytohormones play important roles in the regulation of chalkiness formation but the underlying molecular mechanism is still unclear at present. RESULTS In this research, Xiangzaoxian24 (X24, pure line of indica rice with high-chalkiness) and its origin parents Xiangzaoxian11 (X11, female parent, pure line of indica rice with high-chalkiness) and Xiangzaoxian7 (X7, male parent, pure line of indica rice with low-chalkiness) were used as materials. The phenotype, physiological and biochemical traits combined with transcriptome analysis were conducted to illustrate the dynamic process and transcriptional regulation of rice chalkiness formation. Impressively, phytohormonal contents and multiple phytohormonal signals were significantly different in chalky caryopsis, suggesting the involvement of phytohormones, particularly ABA and auxin, in the regulation of rice chalkiness formation, through the interaction of multiple transcription factors and their downstream regulators. CONCLUSION These results indicated that chalkiness formation is a dynamic process associated with multiple genes, forming a complex regulatory network in which phytohormones play important roles. These results provided informative clues for illustrating the regulatory mechanisms of chalkiness formation in rice.
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Affiliation(s)
- Qin Xie
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jinke Xu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
| | - Ke Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
| | - Yi Su
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
| | - Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Chao Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Manlin Wei
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
| | - Wanhuang Lin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China.
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China.
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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Feng G, Han J, Yang Z, Liu Q, Shuai Y, Xu X, Nie G, Huang L, Liu W, Zhang X. Genome-wide identification, phylogenetic analysis, and expression analysis of the SPL gene family in orchardgrass (Dactylis glomerata L.). Genomics 2021; 113:2413-2425. [PMID: 34058273 DOI: 10.1016/j.ygeno.2021.05.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
SPL (SQUAMOSA promoter binding protein-like) is a plant-specific transcription factor family that contains the conserved SBP domain, which plays a vital role in the vegetative-to-reproductive phase transition, flowering development and regulation, tillering/branching, and stress responses. Although the SPL family has been identified and characterized in various plant species, limited information about it has been obtained in orchardgrass, which is a critical forage crop worldwide. In this study, 17 putative DgSPL genes were identified among seven chromosomes, and seven groups that share similar gene structures and conserved motifs were determined by phylogenetic analysis. Of these, eight genes have potential target sites for miR156. cis-Element and gene ontology annotation analysis indicated DgSPLs may be involved in regulating development and abiotic stress responses. The expression patterns of eight DgSPL genes at five developmental stages, in five tissues, and under three stress conditions were determined by RNA-seq and qRT-PCR. These assays indicated DgSPLs are involved in vegetative-to-reproductive phase transition, floral development, and stress responses. The transient expression analysis in tobacco and heterologous expression assays in yeast indicated that miR156-targeted DG1G01828.1 and DG0G01071.1 are nucleus-localized proteins, that may respond to drought, salt, and heat stress. Our study represents the first systematic analysis of the SPL family in orchardgrass. This research provides a comprehensive assessment of the DgSPL family, which lays the foundation for further examination of the role of miR156/DgSPL in regulating development and stress responses in forages grasses.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Qiuxu Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yang Shuai
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Zhao X, Zeng X, Lin N, Yu S, Fernie AR, Zhao J. CsbZIP1-CsMYB12 mediates the production of bitter-tasting flavonols in tea plants (Camellia sinensis) through a coordinated activator-repressor network. HORTICULTURE RESEARCH 2021; 8:110. [PMID: 33931627 PMCID: PMC8087823 DOI: 10.1038/s41438-021-00545-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 05/02/2023]
Abstract
Under high light conditions or UV radiation, tea plant leaves produce more flavonols, which contribute to the bitter taste of tea; however, neither the flavonol biosynthesis pathways nor the regulation of their production are well understood. Intriguingly, tea leaf flavonols are enhanced by UV-B but reduced by shading treatment. CsFLS, CsUGT78A14, CsMYB12, and CsbZIP1 were upregulated by UV-B radiation and downregulated by shading. CsMYB12 and CsbZIP1 bound to the promoters of CsFLS and CsUGT78A14, respectively, and activated their expression individually. CsbZIP1 positively regulated CsMYB12 and interacted with CsMYB12, which specifically activated flavonol biosynthesis. Meanwhile, CsPIF3 and two MYB repressor genes, CsMYB4 and CsMYB7, displayed expression patterns opposite to that of CsMYB12. CsMYB4 and CsMYB7 bound to CsFLS and CsUGT78A14 and repressed their CsMYB12-activated expression. While CsbZIP1 and CsMYB12 regulated neither CsMYB4 nor CsMYB7, CsMYB12 interacted with CsbZIP1, CsMYB4, and CsMYB7, but CsbZIP1 did not physically interact with CsMYB4 or CsMYB7. Finally, CsPIF3 bound to and activated CsMYB7 under shading to repress flavonol biosynthesis. These combined results suggest that UV activation and shading repression of flavonol biosynthesis in tea leaves are coordinated through a complex network involving CsbZIP1 and CsPIF3 as positive MYB activators and negative MYB repressors, respectively. The study thus provides insight into the regulatory mechanism underlying the production of bitter-tasting flavonols in tea plants.
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Affiliation(s)
- Xuecheng Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 230036, Hefei, China
| | - Xiangsheng Zeng
- College of Agronomy, Anhui Agricultural University, 230036, Hefei, China
| | - Ning Lin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 230036, Hefei, China
| | - Shuwei Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 230036, Hefei, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 230036, Hefei, China.
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Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice ( Oryza sativa L.). PLANTS 2021; 10:plants10040716. [PMID: 33917162 PMCID: PMC8067883 DOI: 10.3390/plants10040716] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Rice is an important grain that is the staple food for most of the world's population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.
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Chen Q, Song Q, Yang X, Han H, Zhang X, Liao Y, Zhang W, Ye J, Cheng S, Xu F. Characterization of a novel levopimaradiene synthase gene responsible for the biosynthesis of terpene trilactones in Ginkgo biloba. PLANT SIGNALING & BEHAVIOR 2021; 16:1885906. [PMID: 33570442 PMCID: PMC7971208 DOI: 10.1080/15592324.2021.1885906] [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: 12/15/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Terpene trilactones (TTLs) are the main medicinal compounds of Ginkgo biloba. Levopimaradiene synthase (LPS) is the crucial enzyme that catalyzes TTLs biosynthesis in G. biloba. In this study, a novel LPS gene (designated as GbLPS2) was cloned from G. biloba leaves. The open reading frame of GbLPS2 gene was 2520 bp in length, encoding a predicted polypeptide of 840 amino acids. Phylogenetic analysis revealed that the GbLPS2 was highly homologous with reported LPS proteins in other plants. On the basis of the genomic DNA (gDNA) template, a 4308 bp gDNA sequence of GbLPS2 and a 913 bp promoter sequence were amplified. Cis-acting elements in promoter analysis indicated that GbLPS2 could be regulated by methyl jasmonate (MeJA) and abscisic acid (ABA). Tissue-specific expression analysis revealed that GbLPS2 was mainly expressed in roots and ovulate strobilus. MeJA treatment could significantly induce the expression level of GbLPS2 and increase the content of TTLs. This study illustrates the structure and the tissue-specific expression pattern of GbLPS2 and demonstrates that exogenous hormones regulated the expression of GbLPS2 and TTL content in G. biloba. Our results provide a target gene for the enhancement of TTL content in G. biloba via genetic engineering.
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Affiliation(s)
- Qiangwen Chen
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Qiling Song
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Huan Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Xian Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Shuiyuan Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato ( Solanum lycopersicum). Genes (Basel) 2021; 12:genes12030417. [PMID: 33799396 PMCID: PMC7998346 DOI: 10.3390/genes12030417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/23/2022] Open
Abstract
F-box genes play an important role in the growth and development of plants, but there are few studies on its role in a plant’s response to abiotic stresses. In order to further study the functions of F-box genes in tomato (Solanum lycopersicum, Sl), a total of 139 F-box genes were identified in the whole genome of tomato using bioinformatics methods, and the basic information, transcript structure, conserved motif, cis-elements, chromosomal location, gene evolution, phylogenetic relationship, expression patterns and the expression under cold stress, drought stress, jasmonic acid (JA) treatment and salicylic acid (SA) treatment were analyzed. The results showed that SlFBX genes were distributed on 12 chromosomes of tomato and were prone to TD (tandem duplication) at the ends of chromosomes. WGD (whole genome duplication), TD, PD (proximal duplication) and TRD (transposed duplication) modes seem play an important role in the expansion and evolution of tomato SlFBX genes. The most recent divergence occurred 1.3042 million years ago, between SlFBX89 and SlFBX103. The cis-elements in SlFBX genes’ promoter regions were mainly responded to phytohormone and abiotic stress. Expression analysis based on transcriptome data and qRT-PCR (Real-time quantitative PCR) analysis of SlFBX genes showed that most SlFBX genes were differentially expressed under abiotic stress. SlFBX24 was significantly up-regulated at 12 h under cold stress. This study reported the SlFBX gene family of tomato for the first time, providing a theoretical basis for the detailed study of SlFBX genes in the future, especially the function of SlFBX genes under abiotic stress.
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Garmash EV, Belykh ES, Velegzhaninov IO. The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts of ALTERNATIVE OXIDASE1a under high intensity light. PLANT SIGNALING & BEHAVIOR 2021; 16:1864962. [PMID: 33369529 PMCID: PMC7889022 DOI: 10.1080/15592324.2020.1864962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We compared the expression of mitochondrial alternative oxidase (AOX) and other non-phosphorylating respiratory components (NPhPs) in wild type and AOX1a transgenic Arabidopsis thaliana following short-term transfer of plants to higher irradiance conditions to gain more insight into the mechanisms of AOX functioning under light. The AOX1a overexpressing line (XX-2) showed the highest amount of AOX1a transcripts and AOX1A synthesis during the entire experiment, and many NPhPs genes were down-regulated after 6-8 h under the higher light conditions. Antisense AS-12 plants displayed a compensatory effect, typically after 8 h of exposure to higher irradiance, by up-regulating their expression of the majority of genes encoding AOX and other respiratory components. In addition, AS-12 plants displayed 'overcompensation effects' prior to their transfer to high light conditions, i.e., they showed a higher expression level of certain genes. As a result, the ROS content in AS-12, as in XX-2, was consistently lower than in the wild type. All NPhPs genes share, in common with AOX1a, light- and stress-related cis-acting regulatory elements (CAREs) in their promoters. However, the expression of respiratory genes does not always depend on the level of AOX1a expression. This suggests the presence of multiple combinations of signaling pathways in gene induction. Based on our results, we outline possible directions for future research.
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Affiliation(s)
- Elena V. Garmash
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
- CONTACT Elena V. Garmash Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena S. Belykh
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Ilya O. Velegzhaninov
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
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Mosharaf MP, Rahman H, Ahsan MA, Akond Z, Ahmed FF, Islam MM, Moni MA, Mollah MNH. In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.). PLoS One 2020; 15:e0228233. [PMID: 33347517 PMCID: PMC7751981 DOI: 10.1371/journal.pone.0228233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.
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Affiliation(s)
- Md. Parvez Mosharaf
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Hafizur Rahman
- Department of Microbiology, Rajshahi Institute of Biosciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Asif Ahsan
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Zobaer Akond
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh
- Agricultural Statistics and ICT Division, Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh
| | - Fee Faysal Ahmed
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Mazharul Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Ali Moni
- The University of Sydney, Sydney Medical School, School of Medical Sciences, Discipline of Biomedical Science, Sydney, New South Wales, Australia
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- * E-mail:
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Rezaee S, Ahmadizadeh M, Heidari P. Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice. PLANTS 2020; 9:plants9020233. [PMID: 32054112 PMCID: PMC7076550 DOI: 10.3390/plants9020233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 11/16/2022]
Abstract
Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.
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Yang Y, Yu TF, Ma J, Chen J, Zhou YB, Chen M, Ma YZ, Wei WL, Xu ZS. The Soybean bZIP Transcription Factor Gene GmbZIP2 Confers Drought and Salt Resistances in Transgenic Plants. Int J Mol Sci 2020; 21:E670. [PMID: 31968543 PMCID: PMC7013997 DOI: 10.3390/ijms21020670] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 12/16/2022] Open
Abstract
Abiotic stresses, such as drought and salt, are major environmental stresses, affecting plant growth and crop productivity. Plant bZIP transcription factors (bZIPs) confer stress resistances in harsh environments and play important roles in each phase of plant growth processes. In this research, 15 soybean bZIP family members were identified from drought-induced de novo transcriptomic sequences of soybean, which were unevenly distributed across 12 soybean chromosomes. Promoter analysis showed that these 15 genes were rich in ABRE, MYB and MYC cis-acting elements which were reported to be involved in abiotic stress responses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that 15 GmbZIP genes could be induced by drought and salt stress. GmbZIP2 was significantly upregulated under stress conditions and thus was selected for further study. Subcellular localization analysis revealed that the GmbZIP2 protein was located in the cell nucleus. qRT-PCR results show that GmbZIP2 can be induced by multiple stresses. The overexpression of GmbZIP2 in Arabidopsis and soybean hairy roots could improve plant resistance to drought and salt stresses. The result of differential expression gene analysis shows that the overexpression of GmbZIP2 in soybean hairy roots could enhance the expression of the stress responsive genes GmMYB48, GmWD40, GmDHN15, GmGST1 and GmLEA. These results indicate that soybean bZIPs played pivotal roles in plant resistance to abiotic stresses.
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Affiliation(s)
- Yan Yang
- College of Agriculture, Yangtze University, Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China;
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Tai-Fei Yu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China;
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Wen-Liang Wei
- College of Agriculture, Yangtze University, Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China;
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (T.-F.Y.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
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Novel endogenous promoters for genetic engineering of the marine microalga Nannochloropsis gaditana CCMP526. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Li Y, Liu W, Zhong H, Zhang HL, Xia Y. Redox-sensitive bZIP68 plays a role in balancing stress tolerance with growth in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:768-783. [PMID: 31348568 DOI: 10.1111/tpj.14476] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/06/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Perturbation of the cellular redox state by stress conditions is sensed by redox-sensitive proteins so that the cell can physiologically respond to stressors. However, the mechanisms linking sensing to response remain poorly understood in plants. Here we report that the transcription factor bZIP68 underwent in vivo oxidation in Arabidopsis cells under oxidative stress which is dependent on its redox-sensitive Cys320 residue. bZIP68 is primarily localized to the nucleus under normal growth conditions in Arabidopsis seedlings. Oxidative stress reduces its accumulation in the nucleus and increases its cytosolic localization. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed that bZIP68 primarily binds to promoter regions containing the core G-box (CACGTG) or G-box-like motif of the genes involved in abiotic and biotic stress responses, photosynthesis, biosynthetic processes, and transcriptional regulation. The bzip68 mutant displayed slower growth under normal conditions but enhanced tolerance to oxidative stress. The results from the ChIP-seq and phenotypic and transcriptome comparison between the bzip68 mutant and wildtype indicate that bZIP68 normally suppresses expression of stress tolerance genes and promotes expression of growth-related genes, whereas its inactivation enhances stress tolerance but suppresses growth. bZIP68 might balance stress tolerance with growth through the extent of its oxidative inactivation according to the environment.
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Affiliation(s)
- Yimin Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- College of Pharmacy, Shaanxi Qinling Application and Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Wuzhen Liu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Huan Zhong
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Hai-Lei Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- State Key Laboratory of Agricultural Biotechnology, Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong
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Identification and Functional Characterization of a Soybean ( Glycine max) Thioesterase that Acts on Intermediates of Fatty Acid Biosynthesis. PLANTS 2019; 8:plants8100397. [PMID: 31597241 PMCID: PMC6843456 DOI: 10.3390/plants8100397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/21/2019] [Accepted: 10/02/2019] [Indexed: 11/16/2022]
Abstract
(1) Background: Plants possess many acyl-acyl carrier protein (acyl-ACP) thioesterases (TEs) with unique specificity. One such TE is methylketone synthase 2 (MKS2), an enzyme with a single-hotdog-fold structure found in several tomato species that hydrolyzes 3-ketoacyl-ACPs to give free 3-ketoacids. (2) Methods: In this study, we identified and characterized a tomato MKS2 homolog gene, namely, GmMKS2, in the genome of soybean (Glycine max). (3) Results: GmMKS2 underwent alternative splicing to produce three alternative transcripts, but only one encodes a protein with thioesterase activity when recombinantly expressed in Escherichia coli. Heterologous expression of the main transcript of GmMKS2, GmMKS2-X2, in E. coli generated various types of fatty acids, including 3-ketoacids-with 3-ketotetradecenoic acid (14:1) being the most abundant-cis-Δ5-dodecanoic acid, and 3-hydroxyacids, suggesting that GmMKS2 acts as an acyl-ACP thioesterase. In plants, the GmMKS2-X2 transcript level was found to be higher in the roots compared to other examined organs. In silico analysis revealed that there is a substantial enrichment of putative cis-regulatory elements related to disease-resistance responses and abiotic stress responses in the promoter of this gene. (4) Conclusions: GmMKS2 showed broad substrate specificities toward a wide range of acyl-ACPs that varied in terms of chain length, oxidation state, and saturation degree. Our results suggest that GmMKS2 might have a stress-related physiological function in G. max.
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Han X, Mao L, Lu W, Wei X, Ying T, Luo Z. Positive Regulation of the Transcription of AchnKCS by a bZIP Transcription Factor in Response to ABA-Stimulated Suberization of Kiwifruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7390-7398. [PMID: 31244202 DOI: 10.1021/acs.jafc.9b01609] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Wound-induced suberization is an essentially protective healing process for wounded fruit to reduce water loss and microbial infection. It has been demonstrated that abscisic acid (ABA) could promote wound suberization, but the molecular mechanism of ABA regulation remains little known. In this study, the transcript level of Achn030011 (designated as AchnKCS), coding a β-ketoacyl-coenzyme A synthase (KCS) involved in suberin biosynthesis, was found to be significantly upregulated by ABA in wounded kiwifruit. A bZIP transcription factor (Achn270881), a possible downstream transcription factor in the ABA signaling pathway, was screened and designated as AchnbZIP12 according to its homology with related Arabidopsis transcription factors. A yeast one-hybrid assay demonstrated that AchnbZIP12 could interact with the AchnKCS promoter. Furthermore, significant trans-activation of AchnbZIP12 on AchnKCS was verified. The transcript level of AchnbZIP12 was also upregulated upon treatment with ABA. These results imply that AchnbZIP12 acts as a positive regulator in ABA-mediated AchnKCS transcription during wound suberization of kiwifruit.
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Affiliation(s)
- Xueyuan Han
- School of Life Sciences , Shaoxing University , Shaoxing , Zhejiang Province 312000 , People's Republic of China
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
- Ningbo Research Institute , Zhejiang University , Ningbo 315100 , People's Republic of China
| | - Wenjing Lu
- Institute of Food Science , Zhejiang Academy of Agricultural Sciences , Hangzhou 310021 , People's Republic of China
| | - Xiaopeng Wei
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
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Bello BK, Hou Y, Zhao J, Jiao G, Wu Y, Li Z, Wang Y, Tong X, Wang W, Yuan W, Wei X, Zhang J. NF-YB1-YC12-bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1222-1235. [PMID: 30552799 PMCID: PMC6576074 DOI: 10.1111/pbi.13048] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 05/14/2023]
Abstract
Identification of seed development regulatory genes is the key for the genetic improvement in rice grain quality. NF-Ys are the important transcription factors, but their roles in rice grain quality control and the underlying molecular mechanism remain largely unknown. Here, we report the functional characterization a rice NF-Y heterotrimer complex NF-YB1-YC12-bHLH144, which is formed by the binding of NF-YB1 to NF-YC12 and then bHLH144 in a sequential order. Knock-out of each of the complex genes resulted in alteration of grain qualities in all the mutants as well as reduced grain size in crnf-yb1 and crnf-yc12. RNA-seq analysis identified 1496 genes that were commonly regulated by NF-YB1 and NF-YC12, including the key granule-bound starch synthase gene Wx. NF-YC12 and bHLH144 maintain NF-YB1 stability from the degradation mediated by ubiquitin/26S proteasome, while NF-YB1 directly binds to the 'G-box' domain of Wx promoter and activates Wx transcription, hence to regulate rice grain quality. Finally, we revealed a novel grain quality regulatory pathway controlled by NF-YB1-YC12-bHLH144 complex, which has great potential for rice genetic improvement.
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Affiliation(s)
| | - Yuxuan Hou
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Juan Zhao
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guiai Jiao
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yawen Wu
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhiyong Li
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yifeng Wang
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xiaohong Tong
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Wei Wang
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Wenya Yuan
- State Key Lab of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio‐ResourcesHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei UniversityWuhanChina
| | - Xiangjin Wei
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jian Zhang
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
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El Sarraf N, Gurel F, Tufan F, McGuffin LJ. Characterisation of HvVIP1 and expression profile analysis of stress response regulators in barley under Agrobacterium and Fusarium infections. PLoS One 2019; 14:e0218120. [PMID: 31199821 PMCID: PMC6570034 DOI: 10.1371/journal.pone.0218120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/27/2019] [Indexed: 01/23/2023] Open
Abstract
Arabidopsis thaliana's VirE2-Interacting Protein 1 (VIP1) interacts with Agrobacterium tumefaciens VirE2 protein and regulates stress responses and plant immunity signaling occurring downstream of the Mitogen-Activated Protein Kinase (MPK3) signal transduction pathway. In this study, a full-length cDNA of 972bp encoding HvVIP1 was obtained from barley (Hordeum vulgare L.) leaves. A corresponding 323 amino acid poly-peptide was shown to carry the conserved bZIP (Basic Leucine Zipper) domain within its 157th and 223rd amino acid residue. 13 non-synonymous SNPs were spotted within the HvVIP1 bZIP domain sequence when compared with AtVIP1. Moreover, minor differences in the bZIP domain locations and lengths were noted when comparing Arabidopsis thaliana and Hordeum vulgare VIP1 proteins through the 3D models, structural domain predictions and disorder prediction profiling. The expression of HvVIP1 was stable in barley tissues infected by pathogen (whether Agrobacterium tumefaciens or Fusarium culmorum), but was induced at specific time points. We found a strong correlation between the transcript accumulation of HvVIP1 and barley PR- genes HvPR1, HvPR4 and HvPR10, but not with HvPR3 and HvPR5, probably due to low induction of those particular genes. In addition, a gene encoding for a member of the barley MAPK family, HvMPK1, showed significantly higher expression after pathogenic infection of barley cells. Collectively, our results might suggest that early expression of PR genes upon infection in barley cells play a pivotal role in the Agrobacterium-resistance of this plant.
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Affiliation(s)
- Nadia El Sarraf
- Department of Agriculture and Food Engineering, University of Balamand, Koura, Lebanon
- * E-mail:
| | - Filiz Gurel
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Feyza Tufan
- Institute of Science, Program of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Liam J. McGuffin
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, United Kingdom
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Sircar S, Parekh N. Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach. PLoS One 2019; 14:e0216068. [PMID: 31059518 PMCID: PMC6502313 DOI: 10.1371/journal.pone.0216068] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress. RESULTS Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as 'seed' genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions. CONCLUSION Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.
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Affiliation(s)
- Sanchari Sircar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
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Zhang N, McHale LK, Finer JJ. Changes to the core and flanking sequences of G-box elements lead to increases and decreases in gene expression in both native and synthetic soybean promoters. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:724-735. [PMID: 30191675 PMCID: PMC6419578 DOI: 10.1111/pbi.13010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/05/2018] [Accepted: 08/31/2018] [Indexed: 05/22/2023]
Abstract
Cis-regulatory elements in promoters are major determinants of binding specificity of transcription factors (TFs) for transcriptional regulation. To improve our understanding of how these short DNA sequences regulate gene expression, synthetic promoters consisting of both classical (CACGTG) and variant G-box core sequences along with different flanking sequences derived from the promoters of three different highly expressing soybean genes, were constructed and used to regulate a green fluorescent protein (gfp) gene. Use of the classical 6-bp G-box provided information on the base level of GFP expression while modifications to the 2-4 flanking bases on either side of the G-box influenced the intensity of gene expression in both transiently transformed lima bean cotyledons and stably transformed soybean hairy roots. The proximal 2-bp sequences on either flank of the G-box significantly affected G-box activity, while the distal 2-bp flanking nucleotides also influenced gene expression albeit with a decreasing effect. Manipulation of the upstream 2- to 4-bp flanking sequence of a G-box variant (GACGTG), found in the proximal region of a relatively weak soybean glycinin promoter, significantly enhanced promoter activity using both transient and stable expression assays, if the G-box variant was first converted into a classical G-box (CACGTG). In addition to increasing our understanding of regulatory element composition and structure, this study shows that minimal targeted changes in native promoter sequences can lead to enhanced gene expression, and suggests that genome editing of the promoter region can result in useful and predictable changes in native gene expression.
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Affiliation(s)
- Ning Zhang
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOHUSA
- Present address:
Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Leah K. McHale
- Department of Horticulture and Crop ScienceThe Ohio State UniversityColumbusOHUSA
| | - John J. Finer
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOHUSA
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Analysis of genes encoding seed storage proteins (SSPs) in chickpea (Cicer arietinum L.) reveals co-expressing transcription factors and a seed-specific promoter. Funct Integr Genomics 2018; 19:373-390. [PMID: 30560463 DOI: 10.1007/s10142-018-0650-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/27/2022]
Abstract
Improvement of the quality and quantity of chickpea seed protein can be greatly facilitated by an understanding of the genic organization and the genetic architecture of the genes encoding seed storage proteins (SSPs). The aim of this study was to provide a comprehensive analysis of the chickpea SSP genes, putative co-expressing transcription factors (TFs), and to identify a seed-specific SSP gene promoter. A genome-wide identification of SSP genes in chickpea led to the identification of 21 non-redundant SSP encoding genes located on 6 chromosomes. Phylogenetic analysis grouped SSP genes into 3 subgroups where members within the same clade demonstrated similar motif composition and intron-exon organization. Tandem duplications were identified to be the major contributors to the expansion of the SSP gene family in chickpea. Co-expression analysis revealed 14 TFs having expression profiles similar to the SSP genes that included members of important TF families that are known to regulate seed development. Expression analysis of SSP genes and TFs revealed significantly higher expression in late stages of seed development as well as in high seed protein content (HPC) genotypes. In silico analysis of the promoter regions of the SSP encoding genes revealed several seed-specific cis-regulatory elements such as RY repeats, ACGT motifs, CAANTG, and GCN4. A candidate promoter was analyzed for seed specificity by generating stable transgenics in Arabidopsis. Overall, this study provides a useful resource to explore the regulatory networks involved in SSP synthesis and/or accumulation for utilization in developing nutritionally improved chickpea genotypes.
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Kong W, Ding L, Cheng J, Wang B. Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa. RICE (NEW YORK, N.Y.) 2018; 11:52. [PMID: 30209707 PMCID: PMC6135729 DOI: 10.1186/s12284-018-0243-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Complex co-regulatory networks in plants may elicit responses during pathogen infections. A number of genes are activated when these responses take place. Identification of these genes would shed new light on understanding the mechanisms of rice response to pathogen infections and the elucidation of crosstalk among diverse signaling networks in rice disease resistance/susceptibility. RESULTS Here we report the identification of genes with pathogen-inducible cis-regulatory elements (PICEs) (AS-1, G-box, GCC-box, and H-box) in the promoter regions in rice. Our results showed that a set of 882 rice genes contained these four elements in their promoter regions. Of these genes, 190 encode disease resistance/susceptibility related proteins, and 70 encode transcription factors. Analyses of the available microarray data demonstrated that 357 transcripts were differentially expressed after pathogen infections. 48 out of 53 differentially expressed transcription factors are up-regulated or down-regulated by more than 1.1-fold in response to pathogen infections. Analyses of the public mRNA-Seq data showed that 327 transcripts were differently expressed after pathogen infections. A total of 100 up-regulated genes and 37 down-regulated genes were found in common between the microarray and mRNA-Seq data. CONCLUSIONS We report here a set of rice genes that contain the four PICEs, i.e., AS-1, G-box, GCC-box, and H-box, in their promoter regions, of which, 53.5% were up- or down-regulated when pathogens attack. The PICEs in the gene promoters are critical for rice response to pathogen infections. They are also useful markers for identification of rice genes involved in response to pathogen infections.
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Affiliation(s)
- Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Li Ding
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jia Cheng
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Bin Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Ashwini N, Sajeevan RS, Udayakumar M, Nataraja KN. Identification of splice variant of OsGBF1 in Oryza sativa ssp. indica genotypes under salinity stress. 3 Biotech 2018; 8:345. [PMID: 30073130 DOI: 10.1007/s13205-018-1370-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
G-box-binding factors are plant transcription factors, involved in a wide range of biological processes including abiotic stress responses. In this study, we analyzed the expression of OsGBF1 during salt stress in two contrasting Oryza sativa spp. indica genotypes, Rasi and Tellahamsa. Two-day-old seedlings were exposed to NaCl stress under two different conditions. One set was exposed to 100 mM NaCl before transferring to 250 mM (induction stress), while another set was transferred directly to 250 mM (shock stress). During early induction stress, OsGBF1 was up-regulated in Rasi when compared to Tellahamsa. We cloned full-length OsGBF1 from these two genotypes, and analyzed the sequences. Our analysis indicated the presence of transcript variants, which are designated as OsGBF1a and 1b. OsGBF1b variant retained introns, which lead to the generation of premature termination codon. OsGBF1b transcript levels were not significantly different at 12-h of induction stress in Tellahamsa and Rasi. At 24-h of shock stress, OsGBF1b was up-regulated in both genotypes and the transcript was more in Rasi. Since, OsGBF1a and 1b are predicted to be splice variants, we examined expression pattern of OsSKIP, a splicing factor and component of the spliceosome. In induction stress, OsSKIP was up-regulated at 12- and 24-h in Rasi when compared to Tellahamsa. On the contrary, at 24-h shock stress, OsSKIP was down-regulated in Rasi when compared to Tellahamsa. It is possible that OsSKIP expression was increased in Rasi during induction stress for accurate splicing that could aid in tolerance. This is the first report on OsGBF1 splice variant and the variant could have specific functions linked to stress tolerance in rice.
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Affiliation(s)
- Narasimha Ashwini
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
| | - Radha Sivarajan Sajeevan
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
- 2Present Address: National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore, 560 065 India
| | - Makarala Udayakumar
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
| | - Karaba N Nataraja
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
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