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Sahito JH, Zhang H, Gishkori ZGN, Ma C, Wang Z, Ding D, Zhang X, Tang J. Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize. Int J Mol Sci 2024; 25:1918. [PMID: 38339196 PMCID: PMC10855973 DOI: 10.3390/ijms25031918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.
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Affiliation(s)
- Javed Hussain Sahito
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zeeshan Ghulam Nabi Gishkori
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhui Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhihao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
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Yang D, Li Y, Zhu M, Cui R, Gao J, Shu Y, Lu X, Zhang H, Zhang K. Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes (Basel) 2023; 14:2006. [PMID: 38002948 PMCID: PMC10671320 DOI: 10.3390/genes14112006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The FKBP (FK506-binding protein) gene family is an important member of the PPlase protease family and plays a vital role during the processes of plant growth and development. However, no studies of the FKBP gene family have been reported in cucumber. In this study, 19 FKBP genes were identified in cucumber, which were located on chromosomes 1, 3, 4, 6, and 7. Phylogenetic analysis divided the cucumber FKBP genes into three subgroups. The FKBP genes in the same subgroup exhibited similar structures and conserved motifs. The cis-acting elements analysis revealed that the promoters of cucumber FKBP genes contained hormone-, stress-, and development-related cis-acting elements. Synteny analysis of the FKBP genes among cucumber, Arabidopsis, and rice showed that 12 kinds of syntenic relationships were detected between cucumber and Arabidopsis FKBP genes, and 3 kinds of syntenic relationships were observed between cucumber and rice FKBP genes. The tissue-specific expression analysis showed that some FKBP genes were expressed in all tissues, while others were only highly expressed in part of the 10 types of tissues. The expression profile analysis of cucumber FKBP genes under 13 types of stresses showed that the CsaV3_1G007080 gene was differentially expressed under abiotic stresses (high temperature, NaCl, silicon, and photoperiod) and biotic stresses (downy mildew, green mottle mosaic virus, Fusarium wilt, phytophthora capsica, angular leaf spot, and root-knot nematode), which indicated that the CsaV3_1G007080 gene plays an important role in the growth and development of cucumber. The interaction protein analysis showed that most of the proteins in the FKBP gene family interacted with each other. The results of this study will lay the foundation for further research on the molecular biological functions of the cucumber FKBP gene family.
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Affiliation(s)
- Dekun Yang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yahui Li
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Mengdi Zhu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Rongjing Cui
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Jiong Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
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Zhang N, Feng S, Tian Y, Zhuang L, Cha G, Duan S, Li H, Nong X, Zhang Z, Tu X, Wang G. Identification, characterization and spatiotemporal expression analysis of the FKBP family genes in Locusta migratoria. Sci Rep 2023; 13:4048. [PMID: 36899085 PMCID: PMC10006077 DOI: 10.1038/s41598-023-30889-1] [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: 09/19/2022] [Accepted: 03/02/2023] [Indexed: 03/12/2023] Open
Abstract
FK506 binding proteins (FKBPs) are a highly-conserved group of proteins known to bind to FK506, an immunosuppressive drug. They play different physiological roles, including transcription regulation, protein folding, signal transduction and immunosuppression. A number of FKBP genes have been identified in eukaryotes; however, very little information about these genes has been reported in Locusta migratoria. Here, we identified and characterized 10 FKBP genes from L. migratoria. Phylogenetic analysis and comparison of domain architectures indicated that the LmFKBP family can be divided into two subfamilies and five subclasses. Developmental and tissue expression pattern analysis revealed that all LmFKBPs transcripts, including LmFKBP46, LmFKBP12, LmFKBP47, LmFKBP79, LmFKBP16, LmFKBP24, LmFKBP44b, LmFKBP53, were periodically expressed during different developmental stages and mainly expressed in the fat body, hemolymph, testis, and ovary. In brief, our work depicts a outline but panoramic picture of LmFKBP family in L. migratoria, and provides a solid foundation to further investigate the molecular functions of LmFKBPs.
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Affiliation(s)
- Neng Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observation and Experimental Station of Pests in Xilingol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, 026000, China
| | - Shiqian Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ye Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ling Zhuang
- Bayannur Forestry and Grassland Development Center, Bayannur, 015000, China
| | - Gan Cha
- Bayannur Forestry and Grassland Development Center, Bayannur, 015000, China
| | - Saiya Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongmei Li
- MARA-CABI Joint Laboratory for Bio-Safety, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Xiangqun Nong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zehua Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiongbing Tu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observation and Experimental Station of Pests in Xilingol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, 026000, China
| | - Guangjun Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Scientific Observation and Experimental Station of Pests in Xilingol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, 026000, China.
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Suri A, Singh H, Kaur K, Kaachra A, Singh P. Genome-wide characterization of FK506-binding proteins, parvulins and phospho-tyrosyl phosphatase activators in wheat and their regulation by heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1053524. [PMID: 36589073 PMCID: PMC9797600 DOI: 10.3389/fpls.2022.1053524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Peptidyl-prolyl cis-trans isomerases (PPIases) are ubiquitous proteins which are essential for cis-trans isomerisation of peptide bonds preceding the proline residue. PPIases are categorized into four sub-families viz., cyclophilins, FK506-binding proteins (FKBPs), parvulins and protein phosphatase 2A phosphatase activators (PTPAs). Apart from catalysing the cis-trans isomerization, these proteins have also been implicated in diverse cellular functions. Though PPIases have been identified in several important crop plants, information on these proteins, except cyclophilins, is scanty in wheat. In order to understand the role of these genes in wheat, we carried out genome-wide identification using computational approaches. The present study resulted in identification of 71 FKBP (TaFKBP) 12 parvulin (TaPar) and 3 PTPA (TaPTPA) genes in hexaploid wheat genome, which are distributed on different chromosomes with uneven gene densities. The TaFKBP and TaPar proteins, besides PPIase domain, also contain additional domains, indicating functional diversification. In silico prediction also revealed that TaFKBPs are localized to ER, nucleus, chloroplast and cytoplasm, while the TaPars are confined to cytoplasm and nucleus. The TaPTPAs, on the contrary, appear to be present only in the cytoplasm. Evolutionary studies predicted that most of the TaFKBP, TaPar and TaPTPA genes in hexaploid wheat have been derived from their progenitor species, with some events of loss or gain. Syntenic analysis revealed the presence of many collinear blocks of TaFKBP genes in wheat and its sub-genome donors. qRT-PCR analysis demonstrated that expression of TaFKBP and TaPar genes is regulated differentially by heat stress, suggesting their likely involvement in thermotolerance. The findings of this study will provide basis for further functional characterization of these genes and their likely applications in crop improvement.
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Affiliation(s)
- Anantika Suri
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Anish Kaachra
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, HP, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat ( Triticum asetivum). Int J Mol Sci 2022; 23:ijms232314501. [PMID: 36498828 PMCID: PMC9739119 DOI: 10.3390/ijms232314501] [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: 10/17/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
FK506-binding protein (FKBP) genes have been found to play vital roles in plant development and abiotic stress responses. However, limited information is available about this gene family in wheat (Triticum aestivum L.). In this study, a total of 64 FKBP genes were identified in wheat via a genome-wide analysis involving a homologous search of the latest wheat genome data, which was unevenly distributed in 21 chromosomes, encoded 152 to 649 amino acids with molecular weights ranging from 16 kDa to 72 kDa, and was localized in the chloroplast, cytoplasm, nucleus, mitochondria, peroxisome and endoplasmic reticulum. Based on sequence alignment and phylogenetic analysis, 64 TaFKBPs were divided into four different groups or subfamilies, providing evidence of an evolutionary relationship with Aegilops tauschii, Brachypodium distachyon, Triticum dicoccoides, Arabidopsis thaliana and Oryza sativa. Hormone-related, abiotic stress-related and development-related cis-elements were preferentially presented in promoters of TaFKBPs. The expression levels of TaFKBP genes were investigated using transcriptome data from the WheatExp database, which exhibited tissue-specific expression patterns. Moreover, TaFKBPs responded to drought and heat stress, and nine of them were randomly selected for validation by qRT-PCR. Yeast cells expressing TaFKBP19-2B-2 or TaFKBP18-6B showed increased influence on drought stress, indicating their negative roles in drought tolerance. Collectively, our results provide valuable information about the FKBP gene family in wheat and contribute to further characterization of FKBPs during plant development and abiotic stress responses, especially in drought stress.
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Liu M, Liu T, Lu J, Zhou Y, Liu S, Jiao P, Liu S, Qu J, Guan S, Ma Y. Characterization and Functional Analysis of ZmSWEET15a in Maize. DNA Cell Biol 2022; 41:564-574. [PMID: 35593918 PMCID: PMC9245729 DOI: 10.1089/dna.2021.1144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sugars will eventually be exported transporters (SWEETs) gene family is a new type of sugar transporters, which plays an important role in plant growth and development, physiological metabolism, and abiotic stress. In this study, we used quantitative real-time PCR to analyze the expression of ZmSWEET15a gene in different organs of maize and under different abiotic stresses. The results showed that ZmSWEET15a was expressed in roots, stems, leaves, and grains, with the highest expression level in leaves, which was highly correlated with leaf development. Under the treatment of polyethylene glycol (PEG), NaCl, H2O2, and abscisic acid stress, the expression of ZmSWEET15a was upregulated, while under the treatment of cold stress, the expression of ZmSWEET15a was inhibited. In sugar-specific experiments, we found that sucrose was the most effective carbon source for maize seed germination. The expression analysis of ZmSWEET15a in different carbon sources suggested that the expression of ZmSWEET15a was more likely to be induced by sucrose. Overexpression of ZmSWEET15a in maize plants could reduce the sucrose content in leaves and increase the sucrose content in grains. The heterologous expression of ZmSWEET15a in the yeast mutant strain SUSY7/ura indicated that ZmSWEET15a is a sucrose transporter and pH independent. This study provides new insight into sugar transport and carbohydrate partitioning in maize and other crops, and provide more genetic information for improving crop quality at the molecular level.
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Affiliation(s)
- Mengtong Liu
- Crop Genetics and Breeding Lines, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Tongyu Liu
- Crop Genetics and Breeding Lines, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Jianyu Lu
- Crop Genetics and Breeding Lines, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yangyang Zhou
- Crop Genetics and Breeding Lines, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Shubo Liu
- Crop Genetics and Breeding Lines, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Peng Jiao
- Crop Genetics and Breeding Lines, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Siyan Liu
- Department of Biotechnology, College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jing Qu
- Department of Biotechnology, College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Shuyan Guan
- Department of Biotechnology, College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Yiyong Ma
- Department of Biotechnology, College of Agronomy, Jilin Agricultural University, Changchun, China
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Shikha K, Shahi JP, Vinayan MT, Zaidi PH, Singh AK, Sinha B. Genome-wide association mapping in maize: status and prospects. 3 Biotech 2021; 11:244. [PMID: 33968587 PMCID: PMC8085158 DOI: 10.1007/s13205-021-02799-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02799-4.
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Affiliation(s)
- Kumari Shikha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - J. P. Shahi
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - M. T. Vinayan
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - P. H. Zaidi
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - A. K. Singh
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - B. Sinha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
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Cuello C, Baldy A, Brunaud V, Joets J, Delannoy E, Jacquemot MP, Botran L, Griveau Y, Guichard C, Soubigou-Taconnat L, Martin-Magniette ML, Leroy P, Méchin V, Reymond M, Coursol S. A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PLoS One 2019; 14:e0227011. [PMID: 31891625 PMCID: PMC6938352 DOI: 10.1371/journal.pone.0227011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.
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Affiliation(s)
- Clément Cuello
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aurélie Baldy
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Johann Joets
- Génétique Quantitative et Evolution—Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Marie-Pierre Jacquemot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Lucy Botran
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Yves Griveau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | | | - Valérie Méchin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Matthieu Reymond
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Sylvie Coursol
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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Waseem M, Ahmad F, Habib S, Gao Y, Li Z. Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.). Gene 2018; 678:143-154. [DOI: 10.1016/j.gene.2018.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/16/2018] [Accepted: 08/04/2018] [Indexed: 11/26/2022]
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10
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Dong Q, Mao K, Duan D, Zhao S, Wang Y, Wang Q, Huang D, Li C, Liu C, Gong X, Ma F. Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple. BMC Genomics 2018; 19:707. [PMID: 30253753 PMCID: PMC6156878 DOI: 10.1186/s12864-018-5097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 09/20/2018] [Indexed: 12/30/2022] Open
Abstract
Background The FK506-binding proteins (FKBPs) play diverse roles in numerous critical processes for plant growth, development, and abiotic stress responses. However, the FKBP gene family in the important fruit crop apple (Malus × domestica Borkh.) has not been studied as thoroughly as in other species. Our research objective was to investigate the mechanisms by which apple FKBPs enable apple plants to tolerate the effects of abiotic stresses. Results Using bioinformatics-based methods, RT-PCR, and qRT-PCR technologies, we identified 38 FKBP genes and cloned 16 of them in the apple genome. The phylogenetic analysis revealed three major groups within that family. The results from sequence alignments, 3-D structures, phylogenetics, and analyses of conserved domains indicated that apple FKBPs are highly and structurally conserved. Furthermore, genomics structure analysis showed that those genes are also highly and structurally conserved in several other species. Comprehensive qRT-PCR analysis found various expression patterns for MdFKBPs in different tissues and in plant responses to water-deficit and salt stresses. Based on the results from interaction network and co-expression analyses, we determined that the pairing in the MdFKBP62a/MdFKBP65a/b-mediated network is involved in water-deficit and salt-stress signaling, both of which are uniformly up-regulated through interactions with heat shock proteins in apple. Conclusions These results provide new insight for further study of FKBP genes and their functions in abiotic stress response and multiple metabolic and physiological processes in apple. Electronic supplementary material The online version of this article (10.1186/s12864-018-5097-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qinglong Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Dingyue Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yanpeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Qian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Dong Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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11
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Zeng J, Zhu X, Haider MS, Wang X, Zhang C, Wang C. Genome-Wide Identification and Analysis of the Type-B Authentic Response Regulator Gene Family in Peach (Prunus persica). Cytogenet Genome Res 2017; 151:41-49. [PMID: 28351057 DOI: 10.1159/000458170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
The type-B authentic response regulator (ARR-B) family members serve as DNA-binding transcriptional regulators, whose activities are probably regulated by phosphorylation/dephosphorylation, resulting in the rapid induction of type-A ARR genes. Type-B ARRs are believed to be involved in many biological processes, including cytokinin signaling, plant growth, and stress responses through a chaperone or by isomerization of proline residues during protein folding. The public availability of complete peach genome sequences allows the identification of 23 ARR-B genes by HMMER and blast analysis. Scaffold locations of these genes in the peach genome were determined, and the protein domain and motif organization of peach type-B ARRs were analyzed. The phylogenetic relationships between peach type-B ARRs were also assessed. The expression profiles of peach ARR-B genes revealed that most of the type-B ARRs showed high expression levels in tissues undergoing rapid cell division and may engage more cytokinins, like half-opened flowers, fruits at expansion stages, and young leaves. These findings not only contribute to a better understanding of the complex regulation of the peach ARR-B gene family, but also provide valuable information for future research in peach functional genomics.
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Affiliation(s)
- Jingjue Zeng
- College of Horticulture, Nanjing Agricultural University, Nanjing, PR China
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12
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Geisler M, Bailly A, Ivanchenko M. Master and servant: Regulation of auxin transporters by FKBPs and cyclophilins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:1-10. [PMID: 26940487 DOI: 10.1016/j.plantsci.2015.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 05/27/2023]
Abstract
Plant development and architecture are greatly influenced by the polar distribution of the essential hormone auxin. The directional influx and efflux of auxin from plant cells depends primarily on AUX1/LAX, PIN, and ABCB/PGP/MDR families of auxin transport proteins. The functional analysis of these proteins has progressed rapidly within the last decade thanks to the establishment of heterologous auxin transport systems. Heterologous co-expression allowed also for the testing of protein-protein interactions involved in the regulation of transporters and identified relationships with members of the FK506-Binding Protein (FKBP) and cyclophilin protein families, which are best known in non-plant systems as cellular receptors for the immunosuppressant drugs, FK506 and cyclosporin A, respectively. Current evidence that such interactions affect membrane trafficking, and potentially the activity of auxin transporters is reviewed. We also propose that FKBPs andcyclophilins might integrate the action of auxin transport inhibitors, such as NPA, on members of the ABCB and PIN family, respectively. Finally, we outline open questions that might be useful for further elucidation of the role of immunophilins as regulators (servants) of auxin transporters (masters).
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Affiliation(s)
- Markus Geisler
- University of Fribourg, Department of Biology-Plant Biology, CH-1700 Fribourg, Switzerland.
| | - Aurélien Bailly
- University of Zurich, Institute of Plant Biology, CH-8008 Zurich, Switzerland
| | - Maria Ivanchenko
- Oregon State University, Department of Botany and Plant Pathology, 2082 Cordley Hall, Corvallis, OR 97331, USA.
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13
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Gil-Quintana E, Lyon D, Staudinger C, Wienkoop S, González EM. Medicago truncatula and Glycine max: Different Drought Tolerance and Similar Local Response of the Root Nodule Proteome. J Proteome Res 2015; 14:5240-51. [PMID: 26503705 PMCID: PMC4673605 DOI: 10.1021/acs.jproteome.5b00617] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 12/14/2022]
Abstract
Legume crops present important agronomical and environmental advantages mainly due to their capacity to reduce atmospheric N2 to ammonium via symbiotic nitrogen fixation (SNF). This process is very sensitive to abiotic stresses such as drought, but the mechanism underlying this response is not fully understood. The goal of the current work is to compare the drought response of two legumes with high economic impact and research importance, Medicago truncatula and Glycine max, by characterizing their root nodule proteomes. Our results show that, although M. truncatula exhibits lower water potential values under drought conditions compared to G. max, SNF declined analogously in the two legumes. Both of their nodule proteomes are very similar, and comparable down-regulation responses in the diverse protein functional groups were identified (mainly proteins related to the metabolism of carbon, nitrogen, and sulfur). We suggest lipoxygenases and protein turnover as newly recognized players in SNF regulation. Partial drought conditions applied to a split-root system resulted in the local down-regulation of the entire proteome of drought-stressed nodules in both legumes. The high degree of similarity between both legume proteomes suggests that the vast amount of research conducted on M. truncatula could be applied to economically important legume crops, such as soybean.
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Affiliation(s)
- Erena Gil-Quintana
- Department
of Environmental Sciences, Public University
of Navarra, E-31006 Pamplona, Spain
| | - David Lyon
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Christiana Staudinger
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Stefanie Wienkoop
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Esther M. González
- Department
of Environmental Sciences, Public University
of Navarra, E-31006 Pamplona, Spain
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14
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Ziogas V, Tanou G, Belghazi M, Filippou P, Fotopoulos V, Grigorios D, Molassiotis A. Roles of sodium hydrosulfide and sodium nitroprusside as priming molecules during drought acclimation in citrus plants. PLANT MOLECULAR BIOLOGY 2015; 89:433-50. [PMID: 26404728 DOI: 10.1007/s11103-015-0379-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/31/2015] [Indexed: 05/04/2023]
Abstract
Emerging evidence suggests that the gaseous molecules hydrogen sulfide (H2S) and nitric oxide (NO) enhances plant acclimation to stress; however, the underlying mechanism remains unclear. In this work, we explored if pretreatment of citrus roots with NaHS (a H2S donor) or sodium nitroprusside (SNP, a NO donor) for 2 days (d) could elicit long-lasting priming effects to subsequent exposure to PEG-associated drought stress for 21 d following a 5 d acclimation period. Detailed physiological study documented that both pretreatments primed plants against drought stress. Analysis of the level of nitrite, NOx, S-nitrosoglutahione reductase, Tyr-nitration and S-nitrosylation along with the expression of genes involved in NO-generation suggested that the nitrosative status of leaves and roots was altered by NaHS and SNP. Using a proteomic approach we characterized S-nitrosylated proteins in citrus leaves exposed to chemical treatments, including well known and novel S-nitrosylated targets. Mass spectrometry analysis also enabled the identification of 42 differentially expressed proteins in PEG alone-treated plants. Several PEG-responsive proteins were down-regulated, especially photosynthetic proteins. Finally, the identification of specific proteins that were regulated by NaHS and SNP under PEG conditions provides novel insight into long-term drought priming in plants and in a fruit crop such as citrus in particular.
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Affiliation(s)
- Vasileios Ziogas
- Faculty of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloníki, Greece
| | - Georgia Tanou
- Faculty of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloníki, Greece
| | - Maya Belghazi
- Faculty of Medicine, Proteomics Analysis Center (CAPM), 13916, Marseilles, France
| | - Panagiota Filippou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3036, Limassol, Cyprus
| | - Vasileios Fotopoulos
- Faculty of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloníki, Greece
| | - Diamantidis Grigorios
- Faculty of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloníki, Greece
| | - Athanassios Molassiotis
- Faculty of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloníki, Greece.
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15
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Gong F, Yang L, Tai F, Hu X, Wang W. "Omics" of maize stress response for sustainable food production: opportunities and challenges. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:714-32. [PMID: 25401749 DOI: 10.1089/omi.2014.0125] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Maize originated in the highlands of Mexico approximately 8700 years ago and is one of the most commonly grown cereal crops worldwide, followed by wheat and rice. Abiotic stresses (primarily drought, salinity, and high and low temperatures), together with biotic stresses (primarily fungi, viruses, and pests), negatively affect maize growth, development, and eventually production. To understand the response of maize to abiotic and biotic stresses and its mechanism of stress tolerance, high-throughput omics approaches have been used in maize stress studies. Integrated omics approaches are crucial for dissecting the temporal and spatial system-level changes that occur in maize under various stresses. In this comprehensive analysis, we review the primary types of stresses that threaten sustainable maize production; underscore the recent advances in maize stress omics, especially proteomics; and discuss the opportunities, challenges, and future directions of maize stress omics, with a view to sustainable food production. The knowledge gained from studying maize stress omics is instrumental for improving maize to cope with various stresses and to meet the food demands of the exponentially growing global population. Omics systems science offers actionable potential solutions for sustainable food production, and we present maize as a notable case study.
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Affiliation(s)
- Fangping Gong
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Science, Henan Agricultural University , Zhengzhou, China
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16
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Maniatsi S, Farmaki T, Abatzopoulos TJ. The study of fkbp and ubiquitin reveals interesting aspects of Artemia stress history. Comp Biochem Physiol B Biochem Mol Biol 2015; 186:8-19. [DOI: 10.1016/j.cbpb.2015.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/22/2015] [Accepted: 04/01/2015] [Indexed: 01/17/2023]
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17
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Leng X, Han J, Wang X, Zhao M, Sun X, Wang C, Fang J. Characterization of a Calmodulin-binding Transcription Factor from Strawberry (Fragaria × ananassa). THE PLANT GENOME 2015; 8:eplantgenome2014.08.0039. [PMID: 33228307 DOI: 10.3835/plantgenome2014.08.0039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 06/11/2023]
Abstract
Calmodulin-binding transcription activator (CAMTA) is a calmodulin-binding transcription factor that has a broad range of functions from sensory mechanisms to regulating many growth and developmental processes. In this study, we isolated four strawberry CAMTA (FaCAMTA) genes using HMMER and BLAST analysis. The chromosome scaffold locations of these CAMTA genes in the strawberry genome were determined and the protein domain and motif organization [CG-1, transcription factor immunoglobulin, ankyrin (ANK) repeats, calmodulin-binding IQ motif) of FaCAMTAs were also assessed. All FaCAMTAs were predicted to be Ca- and calmodulin-binding proteins. The expression profiles of FaCAMTA genes were measured in different tissues and revealed distinct FaCAMTA gene expression patterns under heat, cold, and salt stress. These data not only contribute to a better understanding of the complex regulation of the FaCAMTA gene family but also provide evidence supporting the role of CAMTAs in multiple signaling pathways involved in stress responses. This investigation can provide useful information for further study.
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Affiliation(s)
- Xiangpeng Leng
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Jian Han
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and the Chinese Academy of Sciences, P.O. Box1435, No.1 Qianhu Houcun, Zhongshanmen Wai, Nanjing, 210014, P.R. China
| | - Mizhen Zhao
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Zhongling St. 50, Nanjing, 210014, P.R. China
| | - Xin Sun
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
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18
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Akkasaeng C, Tantisuwichwong N, Ngamhui NO, Roytrakul S, Jogloy S, Pathanothai A. Changes in Protein Expression in Peanut Leaves in the Response to Progressive Water Stress. Pak J Biol Sci 2015; 18:19-26. [PMID: 26353412 DOI: 10.3923/pjbs.2015.19.26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This investigation was carried out at the Department of Plant Science and Agricultural Resources, Khon Kaen University in the rainy season of 2011. The objective of this study was to identify proteins in leaves of drought-susceptible peanut plants when regulated by progressive water stresses. The drought-susceptible peanut plants of Khon Kaen 4 cultivar were grown in pots under controlled environment. At day 30 after seed emergence, the plants were subjected to stress conditions for 5 and 6 days. The results showed that withheld water supply for 5 and 6 days gave moderately and severely water stresses, respectively. Under moderate water stress conditions, two up-regulated and eight down-regulated proteins were attained. The up-regulated proteins were striated fibre assembling and flap endonuclease 1. The down-regulated proteins were peptidyl-prolyl cis-trans isomerase FKBP4, tRNA(Ile)-lysidine synthase, chloroplastic, chloroplastic thioredoxin F-type, cytidinedeaminase 7, ALF domain class transcription factor, nudix hydrolase 8, pentatricopeptide repeat super-family protein, putative and ribulose-1,5-bisphosphate carboxylase/oxygenase, a large sub-unit. Under severe water stress conditions, two proteins, i.e., tRNA(Ile) lysidine synthase, chloroplastic and ALF domain class transcription factor did not change their relative abundance significantly where it indicated drought acclimation. The remaining proteins displayed significant changes and the changes were the same as those found in the peanut leaves when deprived water for 5 days. Up-regulated proteins are responsible for alleviating oxidative damages to plant genome and mediating plants responsive to the environmental factors in providing mechanical support, barriers and a rapid transport route. Down-regulated proteins were associated with drought susceptibility of the Khon Kaen 4 peanut plants.
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19
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Plant immunophilins: a review of their structure-function relationship. Biochim Biophys Acta Gen Subj 2014; 1850:2145-58. [PMID: 25529299 DOI: 10.1016/j.bbagen.2014.12.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 01/02/2023]
Abstract
BACKGROUND Originally discovered as receptors for immunosuppressive drugs, immunophilins consist of two major groups, FK506 binding proteins (FKBPs) and cyclosporin A binding proteins (cyclophilins, CYPs). Many members in both FKBP and CYP families are peptidyl prolyl isomerases that are involved in protein folding processes, though they share little sequence homology. It is not surprising to find immunophilins in all organisms examined so far, including viruses, bacteria, fungi, plants and animals, as protein folding represents a common process in all living systems. SCOPE OF REVIEW Studies on plant immunophilins have revealed new functions beyond protein folding and new structural properties beyond that of typical PPIases. This review focuses on the structural and functional diversity of plant FKBPs and CYPs. MAJOR CONCLUSIONS The differences in sequence, structure as well as subcellular localization, have added on to the diversity of this family of molecular chaperones. In particular, the large number of immunophilins present in the thylakoid lumen of the photosynthetic organelle, promises to deliver insights into the regulation of photosynthesis, a unique feature of plant systems. However, very little structural information and functional data are available for plant immunophilins. GENERAL SIGNIFICANCE Studies on the structure and function of plant immunophilins are important in understanding their role in plant biology. By reviewing the structural and functional properties of some immunophilins that represent the emerging area of research in plant biology, we hope to increase the interest of researchers in pursuing further research in this area. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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20
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Zhang Y, Han J, Liu D, Wen X, Li Y, Tao R, Peng Y, Fang J, Wang C. Genome-wide identification and analysis of FK506-binding protein gene family in peach (Prunus persica). Gene 2014; 536:416-24. [PMID: 24342662 DOI: 10.1016/j.gene.2013.10.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/23/2013] [Accepted: 10/28/2013] [Indexed: 10/25/2022]
Abstract
The FKBP protein family has prolyl isomerase activity and is related in function to cyclophilins. FKBPs are known to be involved in many biological processes including hormone signaling, plant growth, and stress responses through a chaperone or an isomerization of proline residues during protein folding. The availability of complete peach genome sequences allowed the identification of 21 FKBP genes by HMMER and BLAST analyses. Scaffold locations of these FKBP genes in the peach genome were determined and the protein domain and motif organization of peach FKBPs were analyzed. The phylogenetic relationships between peach FKBPs were also assessed. The expression profiles of peach FKBP gene results revealed that most peach FKBPs were expressed in all tissues, while a few peach FKBPs were specifically expressed in some of the tissues. This data could contribute to better understanding of the complex regulation of the peach FKBP gene family, and also provide valuable information for further research in peach functional genomics.
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Affiliation(s)
- Yanping Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xicheng Wen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ran Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongbin Peng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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21
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Leng X, Liu D, Zhao M, Sun X, Li Y, Mu Q, Zhu X, Li P, Fang J. Genome-wide identification and analysis of FK506-binding protein family gene family in strawberry (Fragaria × ananassa). Gene 2013; 534:390-9. [PMID: 24230972 DOI: 10.1016/j.gene.2013.08.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 01/03/2023]
Abstract
The FK506 binding proteins (FKBPs) are abundant and ubiquitous proteins belonging to the large peptidyl-prolylcis-trans isomerase superfamily. FKBPs are known to be involved in many biological processes including hormone signaling, plant growth, and stress responses through a chaperone or an isomerization of proline residues during protein folding. The availability of complete strawberry genome sequences allowed the identification of 23 FKBP genes by HMMER and blast analysis. Chromosome scaffold locations of these FKBP genes in the strawberry genome were determined and the protein domain and motif organization of FaFKBPs analyzed. The phylogenetic relationships between strawberry FKBPs were also assessed. The expression profiles of FaFKBPs genes results revealed that most FaFKBPs were expressed in all tissues, while a few FaFKBPs were specifically expressed in some of the tissues. These data not only contribute to some better understanding of the complex regulation of the strawberry FKBP gene family, but also provide valuable information for further research in strawberry functional genomics.
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Affiliation(s)
- Xiangpeng Leng
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China
| | - Dan Liu
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China
| | - Mizhen Zhao
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, PR China
| | - Xin Sun
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China
| | - Yu Li
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China
| | - Qian Mu
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China
| | - Pengyu Li
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China.
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing 210095, PR China.
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22
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Whole genome identification and analysis of FK506-binding protein family genes in grapevine (Vitis vinifera L.). Mol Biol Rep 2012; 40:4015-31. [PMID: 23269629 DOI: 10.1007/s11033-012-2480-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
In plant and animal species FK506-binding protein (FKBP) family genes are important conserved genes and it is defined as the receptors of FK506 and rapamycin, where they work as PPIase and protein folding chaperones. FKBP have been isolated from Arabidopsis thaliana, Oryza sativa, and Zea mays. In grape, twenty-three genes containing the FK506-binding domain (FKBP_C) were first time identified by HMMER and blast research, they were classified into three groups and 17 out of the 23 genes were located on 11 chromosomes (Chr1, 3, 5, 7, 8, 14, 15, 16, 17, 18, and 19). The predicted gene expression pattern and semi-quantitative RT-PCR results revealed that five VvFKBPs were expressed in all tissues, while seven VvFKBPs were expressed only in some of the tissues, and the remaining VvFKBPs were not expressed in leaf, stem, inflorescences, flowers, and a mixture of fruit tissues (small, medium and big-sized fruits). Most of the VvFKBPs in grapevine 'Summer Black' were similar to those predicted one in 'Pinot Noir' except for VvFKBP16-4 and VvFKBPa. VvFKBP12, FaFKBP12 and PpFKBP12 were cloned from 'Summer Black', 'Sweet Charlie' and 'Xiahui 6'. Protein structure analysis confirmed that homologous genes have some differences during the process of protein structure construction. In this study, we characterized and verified 23 FKBP family genes in grapevine (Vitis vinifera L.) as well as their sub-cellular and chromosome location. The successful cloning of CDS regions and protein structural analysis of VvFKBP12, FaFKBP12, and PpFKBP12 can provide useful information for further study.
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Karali D, Oxley D, Runions J, Ktistakis N, Farmaki T. The Arabidopsis thaliana immunophilin ROF1 directly interacts with PI(3)P and PI(3,5)P2 and affects germination under osmotic stress. PLoS One 2012; 7:e48241. [PMID: 23133621 PMCID: PMC3487907 DOI: 10.1371/journal.pone.0048241] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 09/21/2012] [Indexed: 01/03/2023] Open
Abstract
A direct interaction of the Arabidopsis thaliana immunophilin ROF1 with phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-bisphosphate was identified using a phosphatidylinositol-phosphate affinity chromatography of cell suspension extracts, combined with a mass spectrometry (nano LC ESI-MS/MS) analysis. The first FK506 binding domain was shown sufficient to bind to both phosphatidylinositol-phosphate stereoisomers. GFP-tagged ROF1 under the control of a 35S promoter was localised in the cytoplasm and the cell periphery of Nicotiana tabacum leaf explants. Immunofluorescence microscopy of Arabidopsis thaliana root tips verified its cytoplasmic localization and membrane association and showed ROF1 localization in the elongation zone which was expanded to the meristematic zone in plants grown on high salt media. Endogenous ROF1 was shown to accumulate in response to high salt treatment in Arabidopsis thaliana young leaves as well as in seedlings germinated on high salt media (0.15 and 0.2 M NaCl) at both an mRNA and protein level. Plants over-expressing ROF1, (WSROF1OE), exhibited enhanced germination under salinity stress which was significantly reduced in the rof1(-) knock out mutants and abolished in the double mutants of ROF1 and of its interacting homologue ROF2 (WSrof1(-)/2(-)). Our results show that ROF1 plays an important role in the osmotic/salt stress responses of germinating Arabidopsis thaliana seedlings and suggest its involvement in salinity stress responses through a phosphatidylinositol-phosphate related protein quality control pathway.
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Affiliation(s)
- Debora Karali
- Institute of Applied Biosciences, Centre for Research and Technology – Hellas, Thermi, Thessaloniki, Greece
| | - David Oxley
- The Mass Spectrometry Group, Babraham Institute, Cambridge, United Kingdom
| | - John Runions
- School of Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | | | - Theodora Farmaki
- Institute of Applied Biosciences, Centre for Research and Technology – Hellas, Thermi, Thessaloniki, Greece
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Gollan PJ, Bhave M, Aro EM. The FKBP families of higher plants: Exploring the structures and functions of protein interaction specialists. FEBS Lett 2012; 586:3539-47. [PMID: 22982859 DOI: 10.1016/j.febslet.2012.09.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 08/31/2012] [Accepted: 09/03/2012] [Indexed: 01/24/2023]
Abstract
The FK506-binding proteins (FKBPs) are known both as the receptors for immunosuppressant drugs and as prolyl isomerase (PPIase) enzymes that catalyse rotation of prolyl bonds. FKBPs are characterised by the inclusion of at least one FK506-binding domain (FKBd), the receptor site for proline and the active site for PPIase catalysis. The FKBPs form large and diverse families in most organisms, with the largest FKBP families occurring in higher plants. Plant FKBPs are molecular chaperones that interact with specific protein partners to regulate a diversity of cellular processes. Recent studies have found that plant FKBPs operate in intricate and coordinated mechanisms for regulating stress response and development processes, and discoveries of new interaction partners expand their cellular influences to gene expression and photosynthetic adaptations. This review presents an examination of the molecular and structural features and functional roles of the higher plant FKBP family within the context of these recent findings, and discusses the significance of domain conservation and variation for the development of a diverse, versatile and complex chaperone family.
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Affiliation(s)
- Peter J Gollan
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, P.O. Box 218, Hawthorn, VIC 3122, Australia.
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