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Singh H, Kaur K, Singh M, Kaur G, Singh P. Plant Cyclophilins: Multifaceted Proteins With Versatile Roles. FRONTIERS IN PLANT SCIENCE 2020; 11:585212. [PMID: 33193535 PMCID: PMC7641896 DOI: 10.3389/fpls.2020.585212] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.
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Affiliation(s)
- Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- William Harvey Heart Centre, Queen Mary University of London, London, United Kingdom
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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Weng Y, Ge L, Jia S, Mao P, Ma X. Cyclophilin AtROC1 S58F confers Arabidopsis cold tolerance by modulating jasmonic acid signaling and antioxidant metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 152:81-89. [PMID: 32388423 DOI: 10.1016/j.plaphy.2020.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/31/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Cyclophilins (CYPs), a class of proteins with a conserved peptidyl-prolyl cis-trans isomerase domain, are widely involved in the regulation of plant growth and development, as well as in the response to abiotic stresses including cold. In our previous study, we identified an Arabidopsis gain-of-function mutant ROC1S58F with enhanced cold-tolerance and enhanced expression of jasmonic acid (JA) and oxidative stress responsive genes. Here, we show the underlying molecular mechanisms for the improved cold tolerance observed in the ROC1S58F mutant. Compared to the WT, the ROC1S58F mutant showed an increased survival rates and a reduced level of electrolyte leakage and endogenous JA content under the freezing treatment. Correspondingly, the JA biosynthesis genes (AtAOC1 and AtOPR3) and signaling genes (AtJAZ5, AtJAZ10 and AtMYB15) are down-regulated in the ROC1S58F mutant compared with the WT. Moreover, both the transcripts and activities of the ROS-scavenging enzymes (SOD/POD/MDHAR) increased in cold-stressed ROC1S58F mutant, which might mitigate the ROS-induced oxidative stress and contribute to the mutant freezing tolerance. Taken together, our findings indicate that AtROC1S58F confers Arabidopsis freezing tolerance by modulating JA signaling and antioxidant metabolism jointly. This research thus provides a molecular mechanism for AtROC1S58F-conferred freezing resistance in Arabidopsis and offers guidance for crop breeding towards an improved cold tolerance.
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Affiliation(s)
- Yinyin Weng
- College of Grassland Science and Technology, China Agricultural University, Beijing, 10093, China; Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Lingqiao Ge
- College of Grassland Science and Technology, China Agricultural University, Beijing, 10093, China; Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, 10093, China; Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Peisheng Mao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 10093, China; Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Xiqing Ma
- College of Grassland Science and Technology, China Agricultural University, Beijing, 10093, China; Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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Ge L, Zhang K, Cao X, Weng Y, Liu B, Mao P, Ma X. Sequence characteristics of Medicago truncatula cyclophilin family members and function analysis of MsCYP20-3B involved in axillary shoot development. Mol Biol Rep 2019; 47:907-919. [PMID: 31741262 DOI: 10.1007/s11033-019-05183-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/05/2019] [Indexed: 12/25/2022]
Abstract
Cyclophilins (CYPs) belonging to the immunophilin family are present in all organisms and widely distributed in various cells associated with the activity of peptidyl-prolyl cis/trans isomerase. Plant CYPs are members of a multi-gene family and are involved in a series of biological processes. However, little is known about their structure, evolution, developmental expression and functional analysis in Medicago truncatula. In this study, a total of 33 CYP genes were identified and found to be unevenly distributed on eight chromosomes. Among them, 21 are single-domain and 12 are multi-domain proteins, and most were predicted to be localized in the cytosol, nucleus or chloroplast. Phylogenetic and gene structure analysis revealed seven segmental gene pairs, indicating that segmental duplication probably made a large contribution to the expansion of MtCYP gene family. Furthermore, gene expression analysis revealed that about 10 MtCYP genes (were) highly expressed involved in vegetative and reproduction tissues in M. truncatula, and MsCYP20-3B was mainly upregulated in stems, leaves and flower buds in alfalfa (Medicago sativa). Overexpression of MsCYP20-3B was shown to regulate axillary shoot development associated with higher jasmonic acid and abscisic acid contents in M. truncatula. Our study suggests the importance of the CYP genes family in development, reproduction and stress responses, and provides a reference for future studies and application of CYP genes for alfalfa genetic improvement.
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Affiliation(s)
- Lingqiao Ge
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xiaohui Cao
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yinyin Weng
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Bei Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Peisheng Mao
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.,Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xiqing Ma
- College of Grassland Science and Technology, China Agricultural University, Beijing, China. .,Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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Yan H, Zhou B, He W, Nie Y, Li Y. Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa 'Tsuda'. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1223-1232. [PMID: 32291012 DOI: 10.1071/fp18029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 07/02/2018] [Indexed: 05/20/2023]
Abstract
ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa 'Tsuda'. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old 'Tsuda' turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of 'Tsuda' turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.
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Affiliation(s)
- Haifang Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Bo Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Wei He
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yuzhe Nie
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yuhua Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
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iTRAQ-based analysis of the Arabidopsis proteome reveals insights into the potential mechanisms of anthocyanin accumulation regulation in response to phosphate deficiency. J Proteomics 2018; 184:39-53. [PMID: 29920325 DOI: 10.1016/j.jprot.2018.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 01/18/2023]
Abstract
Phosphate (Pi) deficiency significantly limits plant growth in natural and agricultural systems. Accumulation of anthocyanins in shoots is a common response of Arabidopsis thaliana to Pi deficiency. To elucidate the mechanisms underlying Pi deficiency-induced anthocyanin accumulation, we employed a proteomic approach based on isobaric tags for relative and absolute quantification (iTRAQ) to investigate protein expression profiles of Arabidopsis thaliana seedlings subjected to Pi deficiency for 7 days. In total, 5,106 proteins were identified, of which 156 displayed significant changes in abundance upon Pi deficiency. Bioinformatics analysis indicated that flavonoid biosynthesis was the most significantly elevated metabolic process under Pi deficiency. We further examined the potential role of the flavonoid biosynthetic pathway using a dihydroflavonol 4-reductase (DFR) mutant (tt3) and quantitative RT-PCR (qRT-PCR) analysis, and found that the tt3 mutant was deprived of transcriptional up-regulation of three genes related to anthocyanin biosynthesis, modification and transport under Pi deficiency. These results showed that Pi deficiency probably enhances the anthocyanin accumulation by promoting the flavonoid biosynthesis. The exact functions of these proteins remain to be examined. Nevertheless, our study increases the understanding of the mechanisms implicated in the anthocyanin accumulation induced by Pi deficiency and adaptive responses of plants to Pi starvation.
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Büttner D. Behind the lines-actions of bacterial type III effector proteins in plant cells. FEMS Microbiol Rev 2018; 40:894-937. [PMID: 28201715 PMCID: PMC5091034 DOI: 10.1093/femsre/fuw026] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 07/03/2016] [Indexed: 01/30/2023] Open
Abstract
Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed.
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Affiliation(s)
- Daniela Büttner
- Genetics Department, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Min CW, Lee SH, Cheon YE, Han WY, Ko JM, Kang HW, Kim YC, Agrawal GK, Rakwal R, Gupta R, Kim ST. In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism. J Proteomics 2017; 169:125-135. [PMID: 28669816 DOI: 10.1016/j.jprot.2017.06.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 01/23/2023]
Abstract
Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins. Of these identified proteins, 146 showed significant changes in protein abundance, where 5 and 141 had increased and decreased abundances, respectively while 352 proteins were completely degraded during CDT. Gene ontology and KEGG analyses suggested the association of differential proteins with primary metabolism, ROS detoxification, translation elongation and initiation, protein folding, and proteolysis, where most, if not all, had decreased abundance during CDT. Western blotting confirmed reduced level of antioxidant enzymes (DHAR, APx1, MDAR, and SOD) upon CDT. This in-depth integrated study reveals a major downshift in seed metabolism upon CDT. Reported data here serve as a resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality. BIOLOGICAL SIGNIFICANCE Controlled deterioration treatment (CDT) is one of the major events that negatively affects the quality and nutrient composition of agricultural seeds. However, the molecular mechanism of CDT is largely unknown. A combination of gel-based and gel-free proteomic approach was utilized to investigate the effects of CDT in soybean seeds. Moreover, we utilized protamine sulfate precipitation method for enrichment of low-abundance proteins, which are generally masked due to the presence of high-abundance seed storage proteins. Reported data here serve as resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Seo Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Ye Eun Cheon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Won Young Han
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Jong Min Ko
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Hang Won Kang
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Yong Chul Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea; National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1Tennodai, Tsukuba 305-8574, Ibaraki, Japan
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea.
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea.
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Min CW, Lee SH, Cheon YE, Han WY, Ko JM, Kang HW, Kim YC, Agrawal GK, Rakwal R, Gupta R, Kim ST. In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.022 pmid: 28669816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Discovery of MicroRNAs and Their Target Genes Related to Drought in Paulownia "Yuza 1" by High-Throughput Sequencing. Int J Genomics 2017; 2017:3674682. [PMID: 28695124 PMCID: PMC5485484 DOI: 10.1155/2017/3674682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/04/2017] [Accepted: 03/09/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia "yuza 1." Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia "yuza 1" and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia "yuza 1" may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.
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Hanhart P, Thieß M, Amari K, Bajdzienko K, Giavalisco P, Heinlein M, Kehr J. Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. Sci Rep 2017; 7:1514. [PMID: 28473712 PMCID: PMC5431436 DOI: 10.1038/s41598-017-01596-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.
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Affiliation(s)
- Patrizia Hanhart
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Khalid Amari
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Krzysztof Bajdzienko
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Julia Kehr
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany.
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Dong J, Piñeros MA, Li X, Yang H, Liu Y, Murphy AS, Kochian LV, Liu D. An Arabidopsis ABC Transporter Mediates Phosphate Deficiency-Induced Remodeling of Root Architecture by Modulating Iron Homeostasis in Roots. MOLECULAR PLANT 2017; 10:244-259. [PMID: 27847325 DOI: 10.1016/j.molp.2016.11.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/24/2016] [Accepted: 11/05/2016] [Indexed: 05/21/2023]
Abstract
The remodeling of root architecture is a major developmental response of plants to phosphate (Pi) deficiency and is thought to enhance a plant's ability to forage for the available Pi in topsoil. The underlying mechanism controlling this response, however, is poorly understood. In this study, we identified an Arabidopsis mutant, hps10 (hypersensitive to Pi starvation 10), which is morphologically normal under Pi sufficient condition but shows increased inhibition of primary root growth and enhanced production of lateral roots under Pi deficiency. hps10 is a previously identified allele (als3-3) of the ALUMINUM SENSITIVE3 (ALS3) gene, which is involved in plant tolerance to aluminum toxicity. Our results show that ALS3 and its interacting protein AtSTAR1 form an ABC transporter complex in the tonoplast. This protein complex mediates a highly electrogenic transport in Xenopus oocytes. Under Pi deficiency, als3 accumulates higher levels of Fe3+ in its roots than the wild type does. In Arabidopsis, LPR1 (LOW PHOSPHATE ROOT1) and LPR2 encode ferroxidases, which when mutated, reduce Fe3+ accumulation in roots and cause root growth to be insensitive to Pi deficiency. Here, we provide compelling evidence showing that ALS3 cooperates with LPR1/2 to regulate Pi deficiency-induced remodeling of root architecture by modulating Fe homeostasis in roots.
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Affiliation(s)
- Jinsong Dong
- Ministry of Education Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Miguel A Piñeros
- USDA-ARS, Robert Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14580, USA
| | - Xiaoxuan Li
- Ministry of Education Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haibing Yang
- Department of Horticulture, Purdue University, West Lafayette, IN 47907-2010, USA
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Angus S Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon S7N 4J8, Canada
| | - Dong Liu
- Ministry of Education Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Characterization of 4 TaGAST genes during spike development and seed germination and their response to exogenous phytohormones in common wheat. Mol Biol Rep 2016; 43:1435-1449. [PMID: 27649990 DOI: 10.1007/s11033-016-4077-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
Gibberellic acid (GA) is involved in the regulation of plant growth and development. We defined GA-stimulated transcript (GAST) gene family and characterized its four members (TaGAST1, 2, 3, and 4) in wheat spikes. Triticum aestivum whole spikes were collected at ten developmental stages and dehulled spikelets were obtained at various days after flowering. Expression of TaGAST1, 2, 3, and 4 was analyzed using RT-PCR at inflorescence development stages, in different tissues, and after phytohormones application. To identify proteins interacting with TaGAST1, yeast two-hybridization was performed and BiFC analysis was used for verification. TaGAST1 was expressed at the inflorescence stage and only expressed in seedlings under abscisic acid (ABA) treatment after phytohormone treatment. TaGAST2 and TaGAST3 showed moderate expression in the spike, vigorous transcript accumulation in the seedling, and up-regulation by exogenous GA in early germination stages. TaGAST4 was predominantly expressed in the seedling. Wheat cyclophilin A-1 (TaCypA1), identified as a TaGAST1-interacting protein, showed opposite expression pattern in the developing spike to TaGAST1. TaCypA1 transcript was slightly up-regulated by GA, slightly down-regulated by paclobutrazol, and was maintained after ABA treatment. The interaction of TaGAST1 with TaCypA1 is targeted to the plasma membrane. TaGAST1 was specifically expressed in the wheat spike and was stimulated by exogenous GA treatment. TaGAST2 and TaGAST3 expression in germinating seeds and seedlings was higher than that in the spike stage. TaGAST4 was not expressed in all developmental stages. TaGAST1 and TaCypA1 might be expressed antagonistically during wheat spike development.
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Takáč T, Vadovič P, Pechan T, Luptovčiak I, Šamajová O, Šamaj J. Comparative proteomic study of Arabidopsis mutants mpk4 and mpk6. Sci Rep 2016; 6:28306. [PMID: 27324189 PMCID: PMC4915016 DOI: 10.1038/srep28306] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/02/2016] [Indexed: 01/24/2023] Open
Abstract
Arabidopsis MPK4 and MPK6 are implicated in different signalling pathways responding to diverse external stimuli. This was recently correlated with transcriptomic profiles of Arabidopsis mpk4 and mpk6 mutants, and thus it should be reflected also on the level of constitutive proteomes. Therefore, we performed a shot gun comparative proteomic analysis of Arabidopsis mpk4 and mpk6 mutant roots. We have used bioinformatic tools and propose several new proteins as putative MPK4 and MPK6 phosphorylation targets. Among these proteins in the mpk6 mutant were important modulators of development such as CDC48A and phospholipase D alpha 1. In the case of the mpk4 mutant transcriptional reprogramming might be mediated by phosphorylation and change in the abundance of mRNA decapping complex VCS. Further comparison of mpk4 and mpk6 root differential proteomes showed differences in the composition and regulation of defense related proteins. The mpk4 mutant showed altered abundances of antioxidant proteins. The examination of catalase activity in response to oxidative stress revealed that this enzyme might be preferentially regulated by MPK4. Finally, we proposed developmentally important proteins as either directly or indirectly regulated by MPK4 and MPK6. These proteins contribute to known phenotypic defects in the mpk4 and mpk6 mutants.
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Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Pavol Vadovič
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Tibor Pechan
- Institute for Genomics, Biocomputing &Biotechnology, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, MS 39759, USA
| | - Ivan Luptovčiak
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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14
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Lee SS, Park HJ, Yoon DH, Kim BG, Ahn JC, Luan S, Cho HS. Rice cyclophilin OsCYP18-2 is translocated to the nucleus by an interaction with SKIP and enhances drought tolerance in rice and Arabidopsis. PLANT, CELL & ENVIRONMENT 2015; 38:2071-87. [PMID: 25847193 DOI: 10.1111/pce.12531] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 05/19/2023]
Abstract
Cyclophilin 18-2 (CYP18-2) genes, homologues of human peptidyl-prolyl isomerase-like 1 (PPiL1), are conserved across multicellular organisms and Schizosaccharomyces pombe. Although PPiL1 is known to interact with ski-interacting protein (SKIP), a transcriptional co-regulator and spliceosomal component, there have been no functional analyses of PPiL1 homologues in plants. Rice cyclophilin 18-2 (OsCYP18-2) bound directly to amino acids 56-95 of OsSKIP and its binding was independent of cyclosporin A, a cyclophilin-binding drug. Moreover, OsCYP18-2 exhibited PPIase activity regardless of its interaction with OsSKIP. Therefore, the binding site for OsCYP18-2's interaction with SKIP was distinct from the PPIase active site. OsCYP18-2's interaction with SKIP full-length protein enabled OsCYP18-2's translocation from the cytoplasm into the nucleus and AtSKIP interacted in planta with both AtCYP18-2 and OsCYP18-2. Drought and salt stress induced similar expression of OsCYP18-2 and OsSKIP. Overexpression of OsCYP18-2 in transgenic rice and Arabidopsis thaliana plants enhanced drought tolerance and altered expression and pre-mRNA splicing patterns of stress-related genes in Arabidopsis under drought conditions. Furthermore, OsCYP18-2 caused transcriptional activation with/without OsSKIP in the GAL4 system of yeast; thus the OsSKIP-OsCYP18-2 interaction has an important role in the transcriptional and post-transcriptional regulation of stress-related genes and increases tolerance to drought stress.
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Affiliation(s)
- Sang Sook Lee
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | - Hyun Ji Park
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | - Dae Hwa Yoon
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
- Department of Pharmacology, College of Medicine, Seonam University, Namwon, 590-170, Korea
| | - Beom-Gi Kim
- Divisions of Bio-Crops Development, National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Korea
| | - Jun Cheul Ahn
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
- Department of Pharmacology, College of Medicine, Seonam University, Namwon, 590-170, Korea
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, 73072, USA
| | - Hye Sun Cho
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
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15
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Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signalling. Nat Commun 2015; 6:7395. [PMID: 26096057 DOI: 10.1038/ncomms8395] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 05/05/2015] [Indexed: 12/11/2022] Open
Abstract
In plants, auxin signalling is initiated by the auxin-promoted interaction between the auxin receptor TIR1, an E3 ubiquitin ligase, and the Aux/IAA transcriptional repressors, which are subsequently degraded by the proteasome. Gain-of-function mutations in the highly conserved domain II of Aux/IAAs abolish the TIR1-Aux/IAA interaction and thus cause an auxin-resistant phenotype. Here we show that peptidyl-prolyl isomerization of rice OsIAA11 catalysed by LATERAL ROOTLESS2 (LRT2), a cyclophilin-type peptidyl-prolyl cis/trans isomerase, directly regulates the stability of OsIAA11. NMR spectroscopy reveals that LRT2 efficiently catalyses the cis/trans isomerization of OsIAA11. The lrt2 mutation reduces OsTIR1-OsIAA11 interaction and consequently causes the accumulation of a higher level of OsIAA11 protein. Moreover, knockdown of the OsIAA11 expression partially rescues the lrt2 mutant phenotype in lateral root development. Together, these results illustrate cyclophilin-catalysed peptidyl-prolyl isomerization promotes Aux/IAA degradation, as a mechanism regulating auxin signalling.
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16
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Lee SS, Park HJ, Jung WY, Lee A, Yoon DH, You YN, Kim HS, Kim BG, Ahn JC, Cho HS. OsCYP21-4, a novel Golgi-resident cyclophilin, increases oxidative stress tolerance in rice. FRONTIERS IN PLANT SCIENCE 2015; 6:797. [PMID: 26483814 PMCID: PMC4589654 DOI: 10.3389/fpls.2015.00797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/13/2015] [Indexed: 05/20/2023]
Abstract
OsCYP21-4 is a rice cyclophilin protein that binds to cyclosporine A, an immunosuppressant drug. CYP21-4s in Arabidopsis and rice were previously shown to function as mitochondrial cyclophilins, as determined by TargetP analysis. In the current study, we found that OsCYP21-4-GFP localized to the Golgi, rather than mitochondria, in Nicotiana benthamiana leaves, which was confirmed based on its co-localization with cis Golgi α-ManI-mCherry protein. OsCYP21-4 transcript levels increased in response to treatments with various abiotic stresses and the phytohormone abscisic acid, revealing its stress-responsiveness. CYP21-4 homologs do not possess key peptidyl prolyl cis/trans isomerase (PPIase) activity/cyclosporine A (CsA) binding residues, and recombinant OsCYP21-4 protein did not convert the synthetic substrate Suc-AAPF-pNA via cis- trans- isomerization in vitro. In addition, transgenic plants overexpressing OsCYP21-4 exhibited increased tolerance to salinity and hydrogen peroxide treatment, along with increased peroxidase activity. These results demonstrate that OsCYP21-4 is a novel Golgi-localized cyclophilin that plays a role in oxidative stress tolerance, possibly by regulating peroxidase activity.
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Affiliation(s)
- Sang S. Lee
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Hyun J. Park
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Won Y. Jung
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Areum Lee
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Dae H. Yoon
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Young N. You
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Hyun-Soon Kim
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, Rural Development of AgricultureJeonju, South Korea
| | - Jun C. Ahn
- Department of Pharmacology, College of Medicine, Seonam UniversityNamwon, South Korea
| | - Hye S. Cho
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
- *Correspondence: Hye S. Cho, Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, South Korea
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17
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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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18
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Mainali HR, Chapman P, Dhaubhadel S. Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max). BMC PLANT BIOLOGY 2014; 14:282. [PMID: 25348509 PMCID: PMC4220052 DOI: 10.1186/s12870-014-0282-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the importance of many PPIases in plant biology, but no genome-wide analysis of the CYP gene family has been conducted for a legume species. RESULTS Here we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5' and 3' untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns. CONCLUSIONS Overall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications.
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Affiliation(s)
| | - Patrick Chapman
- />Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON Canada
| | - Sangeeta Dhaubhadel
- />Department of Biology, University of Western Ontario, London, ON Canada
- />Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON Canada
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19
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Li M, Ma X, Chiang YH, Yadeta KA, Ding P, Dong L, Zhao Y, Li X, Yu Y, Zhang L, Shen QH, Xia B, Coaker G, Liu D, Zhou JM. Proline isomerization of the immune receptor-interacting protein RIN4 by a cyclophilin inhibits effector-triggered immunity in Arabidopsis. Cell Host Microbe 2014; 16:473-83. [PMID: 25299333 PMCID: PMC4768788 DOI: 10.1016/j.chom.2014.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/24/2014] [Accepted: 08/25/2014] [Indexed: 11/15/2022]
Abstract
In the absence of pathogen infection, plant effector-triggered immune (ETI) receptors are maintained in a preactivation state by intermolecular interactions with other host proteins. Pathogen effector-induced alterations activate the receptor. In Arabidopsis, the ETI receptor RPM1 is activated via bacterial effector AvrB-induced phosphorylation of the RPM1-interacting protein RIN4 at Threonine 166. We find that RIN4 also interacts with the prolyl-peptidyl isomerase (PPIase) ROC1, which is reduced upon RIN4 Thr166 phosphorylation. ROC1 suppresses RPM1 immunity in a PPIase-dependent manner. Consistent with this, RIN4 Pro149 undergoes cis/trans isomerization in the presence of ROC1. While the RIN4(P149V) mutation abolishes RPM1 resistance, the deletion of Pro149 leads to RPM1 activation in the absence of RIN4 phosphorylation. These results support a model in which RPM1 directly senses conformational changes in RIN4 surrounding Pro149 that is controlled by ROC1. RIN4 Thr166 phosphorylation indirectly regulates RPM1 resistance by modulating the ROC1-mediated RIN4 isomerization.
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Affiliation(s)
- Meng Li
- College of Life Sciences, Peking University, No. 5 YiheYuan Road, Beijing 100871, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Xiqing Ma
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, Tsinghua Yuan 1, School of Life Sciences, Beijing 100084, China
| | - Yi-Hsuan Chiang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Koste A Yadeta
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Pengfei Ding
- College of Life Sciences, Peking University, No. 5 YiheYuan Road, Beijing 100871, China
| | - Liansai Dong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Xiuming Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Yufei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Ling Zhang
- Center for Molecular Agrobiology and State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Qian-Hua Shen
- Center for Molecular Agrobiology and State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Bin Xia
- College of Life Sciences, Peking University, No. 5 YiheYuan Road, Beijing 100871, China
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Dong Liu
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, Tsinghua Yuan 1, School of Life Sciences, Beijing 100084, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China.
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20
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Galland M, Huguet R, Arc E, Cueff G, Job D, Rajjou L. Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination. Mol Cell Proteomics 2014; 13:252-68. [PMID: 24198433 PMCID: PMC3879618 DOI: 10.1074/mcp.m113.032227] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/23/2013] [Indexed: 01/02/2023] Open
Abstract
During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.
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Affiliation(s)
- Marc Galland
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Romain Huguet
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Erwann Arc
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Gwendal Cueff
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Dominique Job
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Loïc Rajjou
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
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Campos BM, Sforça ML, Ambrosio ALB, Domingues MN, Brasil de Souza TDAC, Barbosa JARG, Leme AFP, Perez CA, Whittaker SBM, Murakami MT, Zeri ACDM, Benedetti CE. A redox 2-Cys mechanism regulates the catalytic activity of divergent cyclophilins. PLANT PHYSIOLOGY 2013; 162:1311-23. [PMID: 23709667 PMCID: PMC3707534 DOI: 10.1104/pp.113.218339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/23/2013] [Indexed: 05/20/2023]
Abstract
The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.
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Affiliation(s)
- Bruna Medéia Campos
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Mauricio Luis Sforça
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Andre Luis Berteli Ambrosio
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Mariane Noronha Domingues
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | | | | | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Carlos Alberto Perez
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Sara Britt-Marie Whittaker
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Mario Tyago Murakami
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Ana Carolina de Matos Zeri
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
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O'Rourke JA, Iniguez LP, Bucciarelli B, Roessler J, Schmutz J, McClean PE, Jackson SA, Hernandez G, Graham MA, Stupar RM, Vance CP. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar. FRONTIERS IN PLANT SCIENCE 2013; 4:210. [PMID: 23805147 PMCID: PMC3691542 DOI: 10.3389/fpls.2013.00210] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/03/2013] [Indexed: 05/22/2023]
Abstract
A small fast neutron (FN) mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five P. vulgaris cv. Red Hawk FN mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation (SV); between cultivar variation, natural variation within the FN mutant population, and FN induced mutagenesis. Our analyses focused on the latter two classes. We identified 23 large deletions (>40 bp) common to multiple individuals, illustrating residual heterogeneity and regions of SV within the common bean cv. Red Hawk. An additional 18 large deletions were identified in individual mutant plants. These deletions, ranging in size from 40 bp to 43,000 bp, are potentially the result of FN mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype.
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Affiliation(s)
- Jamie A. O'Rourke
- Plant Science Research Unit, USDA-Agricultural Research ServiceSt. Paul, MN, USA
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
- *Correspondence: Jamie A. O'Rourke, Plant Science Research Unit, USDA-Agricultural Research Service, 495 Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, St. Paul, MN 55108, USA e-mail:
| | - Luis P. Iniguez
- Centro de Ciencias Genomicas-Universidad Nacional Autonoma de MexicoCuernavaca, Mexico
| | - Bruna Bucciarelli
- Plant Science Research Unit, USDA-Agricultural Research ServiceSt. Paul, MN, USA
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
| | - Jeffrey Roessler
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
| | - Jeremy Schmutz
- Hudson Alpha Institute for BiotechnologyHuntsville, AL, USA
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Scott A. Jackson
- Department of Crop and Soil Sciences, University of GeorgiaAthens, GA, USA
| | - Georgina Hernandez
- Centro de Ciencias Genomicas-Universidad Nacional Autonoma de MexicoCuernavaca, Mexico
| | - Michelle A. Graham
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research ServiceAmes, IA, USA
| | - Robert M. Stupar
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
| | - Carroll P. Vance
- Plant Science Research Unit, USDA-Agricultural Research ServiceSt. Paul, MN, USA
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
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