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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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Hu H, Dong B, Fan X, Wang M, Wang T, Liu Q. Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:11. [PMID: 36849744 PMCID: PMC9971424 DOI: 10.1186/s12284-023-00627-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice. But the effect is weak, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs contain remarkably different base compositions, and are under clearly differential selective constraints, with the former having higher GC content, and evolving relatively faster during evolution. In the group of SEGs, the variability in synonymous codon usage among genes is partially due to the variations in GC content, gene function, and gene expression level, which accounts for 22.03%, 5.99%, and 3.32% of the total codon usage variability, respectively. Therefore, mutational bias and natural selection should work on affecting the synonymous codon usage of SEGs in rice. These findings may deepen our knowledge for the mechanisms of origination, differentiation and regulation of SEGs in plants.
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Affiliation(s)
- Huan Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Boran Dong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Xiaoji Fan
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China
| | - Meixia Wang
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China
| | - Tingzhang Wang
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China.
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China.
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Figueiredo L, Santos RB, Figueiredo A. The grapevine aspartic protease gene family: characterization and expression modulation in response to Plasmopara viticola. JOURNAL OF PLANT RESEARCH 2022; 135:501-515. [PMID: 35426578 DOI: 10.1007/s10265-022-01390-z] [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: 12/31/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Grapevine aspartic proteases gene family is characterized and five VviAPs appear to be involved in grapevine defense against downy mildew. Grapevine (Vitis vinifera L.) is one of the most important crops worldwide. However, it is highly susceptible to the downy mildew disease caused by Plasmopara viticola (Berk. & Curt.) Berl. & De Toni. To minimize the use of fungicides used to control P. viticola, it is essential to gain a deeper comprehension on this pathosystem and proteases have gained particular interest in the past decade. Proteases were shown to actively participate in plant-pathogen interactions, not only in the processes that lead to plant cell death, stress responses and protein processing/degradation but also as components of the recognition and signalling pathways. The aim of this study was to identify and characterize the aspartic proteases (APs) involvement in grapevine defense against P. viticola. A genome-wide search and bioinformatics characterization of the V. vinifera AP gene family was conducted and a total of 81 APs proteins, coded by 65 genes, were found. VviAPs proteins can be divided into three categories, similar to those previously described for other plants. Twelve APs coding genes were selected, and expression analysis was conducted at several time-points after inoculation in both compatible and incompatible interactions. Five grapevine APs may be involved in grapevine tolerance against P. viticola. Our findings provide an overall understanding of the VviAPs gene family and establish better groundwork to further describe the roles of VviAPs in defense against P. viticola.
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Affiliation(s)
- Laura Figueiredo
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Rita B Santos
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Andreia Figueiredo
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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Cloning, Characterization, Expression Analysis, and Agglutination Studies of Novel Gene Encoding β-D-Galactose, N-Acetyl-D-Glucosamine and Lactose-Binding Lectin from Rice Bean (Vigna umbellata). Mol Biotechnol 2021; 64:293-310. [PMID: 34611825 DOI: 10.1007/s12033-021-00410-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Lectins are glycoproteins and known for their peculiar carbohydrate-binding activity and their insect-pest-resistant properties. Earlier we have published our research finding on novel gene encoding Bowman-Birk type protease inhibitor with insecticidal properties from rice bean. This paper presents first report on cloning, sequencing, and expression of RbL ORF of 843 bp encoding 280 amino acids long lectin precursor from rice bean (Vigna umbellata) seeds. Blast analysis revealed more than 90% similarity of RbL protein with Vigna aconitifolia and Vigna angularis lectins. Phylogenetic analysis also revealed a close relationship between RbL and other legume lectins. Sequence analysis of genomic DNA revealed intronless nature of RbL gene (GenBank accession No. MT043160). The isolated RbL ORF was expressed in E. coli BL-21(DE3) cells and maximum expression was recorded with 0.5 mM IPTG after 4 h incubation at 37 °C. Western blotting confirmed RbL protein expression in E. coli. Recombinant protein (His6-RbL) of ~ 35 kDa m.wt was purified using Ni-NTA affinity chromatography to the extent of 0.26 mg/ml. In silico analysis characterized RbL protein as acidic, stable, hydrophobic, and secretary protein with one signal peptide cleavage site (A26-A27) and four N-glycosylation sites. Template-based 3D model of RbL was structured using MODELLER tool and validated as good quality model. Structural analysis revealed dominance of β-pleated sheets and β-turns in RbL protein structure. β-D-galactose, N-acetyl-D-glucosamine, and lactose were predicted as putative ligands for RbL protein. Hydrogen bonding and hydrophobic forces were the major interactions between the predicted ligands and RbL protein. Agglutination and agglutination inhibition assays confirmed the binding specificity of RbL protein with the trypsinized rabbit erythrocytes and with the predicted ligands, respectively. Gene ontology analysis functionally annotated RbL protein as a plant defense protein. The novel information generated in the study is not mere pre-experimental findings but could also lay foundation for future research on exploring RbL gene and encoding protein for different biomedical and biotechnological applications.
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Mihálik D, Lančaričová A, Mrkvová M, Kaňuková Š, Moravčíková J, Glasa M, Šubr Z, Predajňa L, Hančinský R, Grešíková S, Havrlentová M, Hauptvogel P, Kraic J. Diacylglycerol Acetyltransferase Gene Isolated from Euonymus europaeus L. Altered Lipid Metabolism in Transgenic Plant towards the Production of Acetylated Triacylglycerols. Life (Basel) 2020; 10:life10090205. [PMID: 32947896 PMCID: PMC7554731 DOI: 10.3390/life10090205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022] Open
Abstract
Euonymus species from the Celastraceae family are considered as a source of unusual genes modifying the oil content and fatty acid composition of vegetable oils. Due to the possession of genes encoding enzyme diacylglycerol acetyltransferase (DAcT), Euonymus plants can synthesize and accumulate acetylated triacyglycerols. The gene from Euonymus europaeus (EeDAcT) encoding the DAcT was identified, isolated, characterized, and modified for cloning and genetic transformation of plants. This gene has a unique nucleotide sequence and amino acid composition, different from orthologous genes from other Euonymus species. Nucleotide sequence of original EeDAcT gene was modified, cloned into transformation vector, and introduced into tobacco plants. Overexpression of EeDAcT gene was confirmed, and transgenic host plants produced and accumulated acetylated triacylglycerols (TAGs) in immature seeds. Individual transgenic plants showed difference in amounts of synthesized acetylTAGs and also in fatty acid composition of acetylTAGs.
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Affiliation(s)
- Daniel Mihálik
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 92168 Piešt’any, Slovakia; (D.M.); (A.L.); (M.H.); (P.H.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Andrea Lančaričová
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 92168 Piešt’any, Slovakia; (D.M.); (A.L.); (M.H.); (P.H.)
| | - Michaela Mrkvová
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Šarlota Kaňuková
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Jana Moravčíková
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Miroslav Glasa
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (Z.Š.); (L.P.)
| | - Zdeno Šubr
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (Z.Š.); (L.P.)
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (Z.Š.); (L.P.)
| | - Richard Hančinský
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Simona Grešíková
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Michaela Havrlentová
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 92168 Piešt’any, Slovakia; (D.M.); (A.L.); (M.H.); (P.H.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
| | - Pavol Hauptvogel
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 92168 Piešt’any, Slovakia; (D.M.); (A.L.); (M.H.); (P.H.)
| | - Ján Kraic
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 92168 Piešt’any, Slovakia; (D.M.); (A.L.); (M.H.); (P.H.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (Š.K.); (J.M.); (M.G.); (R.H.); (S.G.)
- Correspondence:
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Chen T, Meng D, Liu X, Cheng X, Wang H, Jin Q, Xu X, Cao Y, Cai Y. RIGD: A Database for Intronless Genes in the Rosaceae. Front Genet 2020; 11:868. [PMID: 32849839 PMCID: PMC7426402 DOI: 10.3389/fgene.2020.00868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 07/16/2020] [Indexed: 11/13/2022] Open
Abstract
Most eukaryotic genes are interrupted by one or more introns, and only prokaryotic genomes are composed of mainly single-exon genes without introns. Due to the absence of introns, intronless genes in eukaryotes have become important materials for comparative genomics and evolutionary biology. There is currently no cohesive database that collects intronless genes in plants into a single database, although many databases on exons and introns exist. In this study, we constructed the Rosaceae Intronless Genes Database (RIGD), a user-friendly web interface to explore and collect information on intronless genes from different plants. Six Rosaceae species, Pyrus bretschneideri, Pyrus communis, Malus domestica, Prunus persica, Prunus mume, and Fragaria vesca, are included in the current release of the RIGD. Sequence data and gene annotation were collected from different databases and integrated. The main purpose of this study is to provide gene sequence data. In addition, attribute analysis, functional annotations, subcellular localization prediction, and GO analysis are reported. The RIGD allows users to browse, search, and download data with ease. Blast and comparative analyses are also provided through this online database, which is available at http://www.rigdb.cn/.
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Affiliation(s)
- Tianzhe Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Xin Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
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Shou Y, Zhu Y, Ding Y. Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages. BMC PLANT BIOLOGY 2020; 20:229. [PMID: 32448144 PMCID: PMC7245953 DOI: 10.1186/s12870-020-02439-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 05/10/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND The vegetative growth is an important stage for plants when they conduct photosynthesis, accumulate and collect all resources needed and prepare for reproduction stage. Bamboo is one of the fastest growing plant species. The rapid growth of Phyllostachys edulis results from the expansion of intercalary meristem at the basal part of nodes, which are differentiated from the apical meristem of rhizome lateral buds. However, little is known about the major signaling pathways and players involved during this rapid development stage of bamboo. To study this question, we adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. RESULTS We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation. CONCLUSION Significant changes occur in various signaling pathways during the development of rhizome lateral buds. It is crucial to understand how these changes are translated to Phyllostachys edulis fast growth. These results expand our knowledge on the Moso bamboo internodes fast growth and provide research basis for further study.
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Affiliation(s)
- Yuting Shou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Yihua Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
- Bamboo Research Institute, Nanjing ForestryUniversity, Nanjing, 210037 Jiangsu China
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Begum Y, Mondal SK. Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species. J Biomol Struct Dyn 2020; 39:2387-2414. [PMID: 32292132 DOI: 10.1080/07391102.2020.1748717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-II), University of Calcutta, Kolkata, West Bengal, India
| | - Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
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Nagasawa T, Kawaguchi M, Yano T, Isoyama S, Yasumasu S, Okabe M. Translocation of promoter-conserved hatching enzyme genes with intron-loss provides a new insight in the role of retrocopy during teleostean evolution. Sci Rep 2019; 9:2448. [PMID: 30792427 PMCID: PMC6385490 DOI: 10.1038/s41598-019-38693-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/17/2018] [Indexed: 11/12/2022] Open
Abstract
The hatcing enzyme gene (HE) encodes a protease that is indispensable for the hatching process and is conserved during vertebrate evolution. During teleostean evolution, it is known that HE experienced a drastic transfiguration of gene structure, namely, losing all of its introns. However, these facts are contradiction with each other, since intron-less genes typically lose their original promoter because of duplication via mature mRNA, called retrocopy. Here, using a comparative genomic assay, we showed that HEs have changed their genomic location several times, with the evolutionary timings of these translocations being identical to those of intron-loss. We further showed that HEs maintain the promoter sequence upstream of them after translocation. Therefore, teleostean HEs are unique genes which have changed intra- (exon-intron) and extra-genomic structure (genomic loci) several times, although their indispensability for the reproductive process of hatching implies that HE genes are translocated by retrocopy with their promoter sequence.
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Affiliation(s)
- Tatsuki Nagasawa
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Research Fellow of the Japan Society for the Promotion of Science (JSPS), Tokyo, 102-0083, Japan.,Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Tohru Yano
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Sho Isoyama
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
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Abstract
SUPPRESSOR OF PHYB-4#5DOMINANT (sob5-D) was previously identified as a suppressor of the phyB-4 long-hypocotyl phenotype in Arabidopsis thaliana. Overexpression of SOB5 conferred dwarf phenotypes similar to those observed in plants containing elevated levels of cytokinin (CK) nucleotides and nucleosides. Two SOB-FIVE- LIKE (SOFL) proteins, AtSOFL1 and AtSOFL2, which are more similar at the protein level to each other than they are to SOB5, conferred similar phenotypes to the sob5-D mutant when overexpressed. We used protein sequences of founding SOFL gene family members to perform database searches and identified a total of 289 SOFL homologs in genomes of 89 angiosperm species. Phylogenetic analysis results implied that the SOFL gene family emerged during the expansion of angiosperms and later evolved into four distinct clades. Among the newly identified gene family members are four previously unreported Arabidopsis SOFLs. Multiple sequence alignment of the 289 SOFL protein sequences revealed two highly conserved domains; SOFL-A and SOFL-B. We used overexpression and site-directed mutagenesis studies to demonstrate that SOFL domains are necessary for SOB5 and AtSOFL1’s overexpression phenotypes. Examination of the subcellular localization patterns of founding Arabidopsis thaliana SOFLs suggested they may be localized in the cytoplasm and/or the nucleus. Overall, we report that SOFLs are a plant-specific gene family characterized by two conserved domains that are important for function.
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Uhrig RG, Moorhead G. AtSLP2 is an intronless protein phosphatase that co-expresses with intronless mitochondrial pentatricopeptide repeat (PPR) and tetratricopeptide (TPR) protein encoding genes. PLANT SIGNALING & BEHAVIOR 2017; 12:e1307493. [PMID: 28350216 PMCID: PMC5437834 DOI: 10.1080/15592324.2017.1307493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 06/06/2023]
Abstract
Shewanella-like PPP family phosphatases (SLPs) are a unique lineage of eukaryote PPP-family phosphatases of bacterial origin which are not found in metazoans. 1,2 Their absence in metazoans is marked by their ancient bacterial origins and presence in plants. 1 Recently, we found that the SLP2 phosphatase ortholog of Arabidopsis thaliana localized to the mitochondrial intermembrane space (IMS) where it was determined to be activated by mitochondrial intermembrane space protein 40 (MIA40) to regulate seed germination. 3 Through examination of atslp2 knockout (accelerated germination) and 35S::AtSLP2 over-expressing (delayed germination) plants it was found that AtSLP2 influences Arabidopsis thaliana germination rates via gibberellic acid (GA) biosynthesis. 3 However, the exact mechanism by which this occurs remains unresolved. To identify potential partners of AtSLP2 in regulating germination through GA, we undertook a gene co-expression network analysis using RNA-sequencing data available through Genevestigator ( https://genevestigator.com/gv/ ).
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Affiliation(s)
- R. Glen Uhrig
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Group of Plant Biotechnology, Department of Biology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Greg Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Figueiredo J, Costa GJ, Maia M, Paulo OS, Malhó R, Sousa Silva M, Figueiredo A. Revisiting Vitis vinifera Subtilase Gene Family: A Possible Role in Grapevine Resistance against Plasmopara viticola. FRONTIERS IN PLANT SCIENCE 2016; 7:1783. [PMID: 27933087 PMCID: PMC5122586 DOI: 10.3389/fpls.2016.01783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/11/2016] [Indexed: 05/08/2023]
Abstract
Subtilisin-like proteases, also known as subtilases, are a very diverse family of serine peptidases present in many organisms. In grapevine, there are hints of the involvement of subtilases in defense mechanisms, but their role is not yet understood. The first characterization of the subtilase gene family was performed in 2014. However, simultaneously, the grapevine genome was re-annotated and several sequences were re-annotated or retrieved. We have performed a re-characterization of this family in grapevine and identified 82 genes coding for 97 putative proteins, as result of alternative splicing. All the subtilases identified present the characteristic S8 peptidase domain and the majority of them also have a pro-domain I9 inhibitor, a protease-associated (PA) domain, and a signal peptide for targeting to the secretory pathway. Phylogenetic studies revealed six subtilase groups denominated VvSBT1 to VvSBT6. As several evidences have highlighted the participation of plant subtilases in response to biotic stimulus, we have investigated subtilase participation in grapevine resistance to Plasmopara viticola, the causative agent of downy mildew. Fourteen grapevine subtilases presenting either high homology to P69C from tomato, SBT3.3 from Arabidopsis thaliana or located near the Resistance to P. viticola (RPV) locus were selected. Expression studies were conducted in the grapevine-P. viticola pathosystem with resistant and susceptible cultivars. Our results may indicate that some of grapevine subtilisins are potentially participating in the defense response against this biotrophic oomycete.
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Affiliation(s)
- Joana Figueiredo
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Gonçalo J. Costa
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Marisa Maia
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Rui Malhó
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Andreia Figueiredo
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
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Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res 2016; 45:1015-1020. [PMID: 27742820 PMCID: PMC5210635 DOI: 10.1093/nar/gkw935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Roger Thilmony
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA .,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
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