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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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2
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Qiao ZW, Wang DR, Wang X, You CX, Wang XF. Genome-wide identification and stress response analysis of cyclophilin gene family in apple (Malus × domestica). BMC Genomics 2022; 23:806. [PMID: 36474166 PMCID: PMC9727951 DOI: 10.1186/s12864-022-08976-w] [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: 03/21/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cyclophilin (CYP) belongs to the immunophilin family and has peptidyl-prolyl cis-trans isomerase (PPIase) activity, which catalyzes the cis-trans isomerization process of proline residues. CYPs widely exist in eukaryotes and prokaryotes, and contain a conserved cyclophilin-like domain (CLD). Plant cyclophilins are widely involved in a range of biological processes including stress response, metabolic regulation, and growth and development. RESULT In this study, 30 cyclophilin genes on 15 chromosomes were identified from the 'Golden Delicious' apple (M. domestica) genome. Phylogenetic analysis showed that the cyclophilin family genes can be divided into three clades in Malus. Collinear analysis showed that ten gene pairs were the result of segmental duplication. Analysis of gene and protein structure further supported the phylogenetic tree and collinearity analysis. The expression of MdCYPs in different organs was higher in leaves, flowers, and fruits. Ten and eight CYPs responded to drought and salt stress, respectively. MdCYP16, a nuclear-localized MD CYP, was screened from the intersection of the two expression profiling datasets and was highly sensitive to drought and salt stress. GUS staining of transgenic Arabidopsis indicated that MdCYP16 may be involved in the regulation of abiotic stress. CONCLUSION This study systematically analyzed members of the apple cyclophilin family and confirmed the involvement of MdCYP16 as a nuclear-localized MD cyclophilin that acts in response to salt and drought stress in apple. Our work identifies members of the apple cyclophilin gene family, and provides an important theoretical basis for in-depth study of cyclophilin function. Additionally, the analysis provides candidate genes that may be involved in stress response in apple.
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Affiliation(s)
- Zhi-Wen Qiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Da-Ru Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xun Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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3
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Jo SH, Park HJ, Lee A, Jung H, Park JM, Kwon SY, Kim HS, Lee HJ, Kim YS, Jung C, Cho HS. The Arabidopsis cyclophilin CYP18-1 facilitates PRP18 dephosphorylation and the splicing of introns retained under heat stress. THE PLANT CELL 2022; 34:2383-2403. [PMID: 35262729 PMCID: PMC9134067 DOI: 10.1093/plcell/koac084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/05/2022] [Indexed: 05/13/2023]
Abstract
In plants, heat stress induces changes in alternative splicing, including intron retention; these events can rapidly alter proteins or downregulate protein activity, producing nonfunctional isoforms or inducing nonsense-mediated decay of messenger RNA (mRNA). Nuclear cyclophilins (CYPs) are accessory proteins in the spliceosome complexes of multicellular eukaryotes. However, whether plant CYPs are involved in pre-mRNA splicing remain unknown. Here, we found that Arabidopsis thaliana CYP18-1 is necessary for the efficient removal of introns that are retained in response to heat stress during germination. CYP18-1 interacts with Step II splicing factors (PRP18a, PRP22, and SWELLMAP1) and associates with the U2 and U5 small nuclear RNAs in response to heat stress. CYP18-1 binds to phospho-PRP18a, and increasing concentrations of CYP18-1 are associated with increasing dephosphorylation of PRP18a. Furthermore, interaction and protoplast transfection assays revealed that CYP18-1 and the PP2A-type phosphatase PP2A B'η co-regulate PRP18a dephosphorylation. RNA-seq and RT-qPCR analysis confirmed that CYP18-1 is essential for splicing introns that are retained under heat stress. Overall, we reveal the mechanism of action by which CYP18-1 activates the dephosphorylation of PRP18 and show that CYP18-1 is crucial for the efficient splicing of retained introns and rapid responses to heat stress in plants.
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Affiliation(s)
- Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University
of Science and Technology, Daejeon 34113, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo
Bio, Anseong 17558, Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology
Institute/Green Bio Science and Technology, Seoul National University,
Pyeongchang 25354, Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major
in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National
University, Seoul 08826, Korea
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4
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Mo C, Xie C, Wang G, Tian T, Liu J, Zhu C, Xiao X, Xiao Y. Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi. Nucleic Acids Res 2021; 49:12358-12376. [PMID: 34792171 PMCID: PMC8643696 DOI: 10.1093/nar/gkab1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/14/2022] Open
Abstract
The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.
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Affiliation(s)
- Chenmi Mo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chong Xie
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Gaofeng Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Tian Tian
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Juan Liu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chunxiao Zhu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yannong Xiao
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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5
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Cyclophilins and Their Functions in Abiotic Stress and Plant-Microbe Interactions. Biomolecules 2021; 11:biom11091390. [PMID: 34572603 PMCID: PMC8464771 DOI: 10.3390/biom11091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 01/12/2023] Open
Abstract
Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.
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6
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Singh M, Kaur K, Sharma A, Kaur R, Joshi D, Chatterjee M, Dandapath I, Kaur A, Singh H, Singh P. Genome-wide characterization of peptidyl-prolyl cis-trans isomerases in Penicillium and their regulation by salt stress in a halotolerant P. oxalicum. Sci Rep 2021; 11:12292. [PMID: 34112860 PMCID: PMC8192932 DOI: 10.1038/s41598-021-91602-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Peptidyl-prolyl cis-trans isomerases (PPIases) are the only class of enzymes capable of cis-trans isomerization of the prolyl peptide bond. The PPIases, comprising of different families viz., cyclophilins, FK506-binding proteins (FKBPs), parvulins and protein phosphatase 2A phosphatase activators (PTPAs), play essential roles in different cellular processes. Though PPIase gene families have been characterized in different organisms, information regarding these proteins is lacking in Penicillium species, which are commercially an important fungi group. In this study, we carried out genome-wide analysis of PPIases in different Penicillium spp. and investigated their regulation by salt stress in a halotolerant strain of Penicillium oxalicum. These analyses revealed that the number of genes encoding cyclophilins, FKBPs, parvulins and PTPAs in Penicillium spp. varies between 7-11, 2-5, 1-2, and 1-2, respectively. The halotolerant P. oxalicum depicted significant enhancement in the mycelial PPIase activity in the presence of 15% NaCl, thus, highlighting the role of these enzymes in salt stress adaptation. The stress-induced increase in PPIase activity at 4 and 10 DAI in P. oxalicum was associated with higher expression of PoxCYP18. Characterization of PPIases in Penicillium spp. will provide an important database for understanding their cellular functions and might facilitate their applications in industrial processes through biotechnological interventions.
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Affiliation(s)
- Mangaljeet Singh
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Kirandeep Kaur
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Avinash Sharma
- grid.411894.10000 0001 0726 8286Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Rajvir Kaur
- grid.411894.10000 0001 0726 8286Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Dimple Joshi
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Megha Chatterjee
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Iman Dandapath
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Amarjeet Kaur
- grid.411894.10000 0001 0726 8286Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Harpreet Singh
- grid.506003.00000 0004 1778 5641Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab 144008 India
| | - Prabhjeet Singh
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
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7
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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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Yang J, Wang G, Ke H, Zhang Y, Ji L, Huang L, Zhang C, Wang X, Ma Z. Genome-wide identification of cyclophilin genes in Gossypium hirsutum and functional characterization of a CYP with antifungal activity against Verticillium dahliae. BMC PLANT BIOLOGY 2019; 19:272. [PMID: 31226952 PMCID: PMC6588949 DOI: 10.1186/s12870-019-1848-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/24/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cyclophilins (CYPs), belonging to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily, play important roles during plant responses to biotic and abiotic stresses. RESULTS Here, a total of 79 CYPs were identified in the genome of Gossypium hirsutum. Of which, 65 GhCYPs only contained one cyclophilin type PPIase domain, others 14 GhCYPs contain additional domains. A number of cis-acting elements related to phytohormone signaling were predicated in the upstream of GhCYPs ORF. The expression analysis revealed that GhCYPs were induced in response to cold, hot, salt, PEG and Verticillium dahliae infection. In addition, the functional importance of GhCYP-3 in Verticillium wilt resistance was also presented in this study. GhCYP-3 showed both cytoplasmic and nuclear localization. Overexpression of GhCYP-3 in Arabidopsis significantly improved Verticillium wilt resistance of the plants. Recombinant GhCYP-3 displayed PPIase activity and evident inhibitory effects on V. dahliae in vitro. Moreover, the extracts from GhCYP-3 transgenic Arabidopsis displayed significantly inhibit activity to conidia germinating and hyphal growth of V. dahliae. CONCLUSIONS Our study identified the family members of cotton CYP genes using bioinformatics tools. Differential expression patterns of GhCYPs under various abiotic stress and V. dahliae infection conditions provide a comprehensive understanding of the biological functions of candidate genes. Moreover, GhCYP-3 involved in the resistance of cotton to V. dahliae infection presumably through antifungal activity.
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Affiliation(s)
- Jun Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Guoning Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Huifeng Ke
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Yan Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Lianlian Ji
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Lizhi Huang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Chunying Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Xingfen Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Zhiying Ma
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
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Chen Q, Chen QJ, Sun GQ, Zheng K, Yao ZP, Han YH, Wang LP, Duan YJ, Yu DQ, Qu YY. Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense. Int J Mol Sci 2019; 20:E349. [PMID: 30654456 PMCID: PMC6359516 DOI: 10.3390/ijms20020349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 11/17/2022] Open
Abstract
Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.
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Affiliation(s)
- Qin Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Quan-Jia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Guo-Qing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Zheng-Pei Yao
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Yu-Hui Han
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Li-Ping Wang
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Ya-Jie Duan
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Dao-Qian Yu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yan-Ying Qu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
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10
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Barbosa Dos Santos I, Park SW. Versatility of Cyclophilins in Plant Growth and Survival: A Case Study in Arabidopsis. Biomolecules 2019; 9:biom9010020. [PMID: 30634678 PMCID: PMC6358970 DOI: 10.3390/biom9010020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signaling pathways, stress adaptation and defense responses. These important but diverse activities of CYPs must be reflected by their versatility as cellular and molecular modulators. However, our current knowledge regarding their mode of actions is still far from complete. This review will briefly revisit recent progresses on the roles and mechanisms of CYPs in Arabidopsis studies, and information gaps within, which help understanding the phenotypic and environmental plasticity of plants.
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Affiliation(s)
| | - Sang-Wook Park
- Department of Entomology and Plant Pathology Auburn University, Auburn, AL 36849, USA.
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11
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The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly. Cell Rep 2018. [PMID: 28636937 DOI: 10.1016/j.celrep.2017.05.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNAi factors and their catalytic activities are essential for heterochromatin assembly in S. pombe. This has led to the idea that siRNAs can promote H3K9 methylation by recruiting the cryptic loci regulator complex (CLRC), also known as recombination in K complex (RIKC), to the nucleation site. The conserved RNA-binding protein Rct1 (AtCyp59/SIG-7) interacts with splicing factors and RNA polymerase II. Here we show that Rct1 promotes processing of pericentromeric transcripts into siRNAs via the RNA recognition motif. Surprisingly, loss of siRNA in rct1 mutants has no effect on H3K9 di- or tri-methylation, resembling other splicing mutants, suggesting that post-transcriptional gene silencing per se is not required to maintain heterochromatin. Splicing of the Argonaute gene is also defective in rct1 mutants and contributes to loss of silencing but not to loss of siRNA. Our results suggest that Rct1 guides transcripts to the RNAi machinery by promoting splicing of elongating non-coding transcripts.
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Dilworth D, Upadhyay SK, Bonnafous P, Edoo AB, Bourbigot S, Pesek-Jardim F, Gudavicius G, Serpa JJ, Petrotchenko EV, Borchers CH, Nelson CJ, Mackereth CD. The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module. Nucleic Acids Res 2017; 45:11989-12004. [PMID: 29036638 PMCID: PMC5714180 DOI: 10.1093/nar/gkx852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/13/2017] [Indexed: 11/14/2022] Open
Abstract
Prolyl isomerases are defined by a catalytic domain that facilitates the cis–trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets.
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Affiliation(s)
- David Dilworth
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Santosh K Upadhyay
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France.,CSIR-Institute of Genomics and Integrative Biology, New Delhi 110020, India
| | - Pierre Bonnafous
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Amiirah Bibi Edoo
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Sarah Bourbigot
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Francy Pesek-Jardim
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Geoff Gudavicius
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Jason J Serpa
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada
| | - Evgeniy V Petrotchenko
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada
| | - Christopher J Nelson
- Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Cameron D Mackereth
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.,Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
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Köster T, Marondedze C, Meyer K, Staiger D. RNA-Binding Proteins Revisited - The Emerging Arabidopsis mRNA Interactome. TRENDS IN PLANT SCIENCE 2017; 22:512-526. [PMID: 28412036 DOI: 10.1016/j.tplants.2017.03.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/10/2017] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
RNA-protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture - where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.
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Affiliation(s)
- Tino Köster
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudius Marondedze
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Cambridge, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katja Meyer
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
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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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15
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Reichel M, Liao Y, Rettel M, Ragan C, Evers M, Alleaume AM, Horos R, Hentze MW, Preiss T, Millar AA. In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings. THE PLANT CELL 2016; 28:2435-2452. [PMID: 27729395 PMCID: PMC5134986 DOI: 10.1105/tpc.16.00562] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/15/2016] [Accepted: 10/11/2016] [Indexed: 05/17/2023]
Abstract
RNA binding proteins (RBPs) control the fate and expression of a transcriptome. Despite this fundamental importance, our understanding of plant RBPs is rudimentary, being mainly derived via bioinformatic extrapolation from other kingdoms. Here, we adapted the mRNA-protein interactome capture method to investigate the RNA binding proteome in planta. From Arabidopsis thaliana etiolated seedlings, we captured more than 700 proteins, including 300 with high confidence that we have defined as the At-RBP set. Approximately 75% of these At-RBPs are bioinformatically linked with RNA biology, containing a diversity of canonical RNA binding domains (RBDs). As no prior experimental RNA binding evidence exists for the majority of these proteins, their capture now authenticates them as RBPs. Moreover, we identified protein families harboring emerging and potentially novel RBDs, including WHIRLY, LIM, ALBA, DUF1296, and YTH domain-containing proteins, the latter being homologous to animal RNA methylation readers. Other At-RBP set proteins include major signaling proteins, cytoskeleton-associated proteins, membrane transporters, and enzymes, suggesting the scope and function of RNA-protein interactions within a plant cell is much broader than previously appreciated. Therefore, our foundation data set has provided an unbiased insight into the RNA binding proteome of plants, on which future investigations into plant RBPs can be based.
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Affiliation(s)
- Marlene Reichel
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Yalin Liao
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 2601, Australia
| | - Mandy Rettel
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Chikako Ragan
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 2601, Australia
| | - Maurits Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 2601, Australia
| | | | - Rastislav Horos
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 2601, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
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16
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Ahn JH, Rechsteiner A, Strome S, Kelly WG. A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans. PLoS Genet 2016; 12:e1006227. [PMID: 27541139 PMCID: PMC4991786 DOI: 10.1371/journal.pgen.1006227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023] Open
Abstract
The elongation phase of transcription by RNA Polymerase II (Pol II) involves numerous events that are tightly coordinated, including RNA processing, histone modification, and chromatin remodeling. RNA splicing factors are associated with elongating Pol II, and the interdependent coupling of splicing and elongation has been documented in several systems. Here we identify a conserved, multi-domain cyclophilin family member, SIG-7, as an essential factor for both normal transcription elongation and co-transcriptional splicing. In embryos depleted for SIG-7, RNA levels for over a thousand zygotically expressed genes are substantially reduced, Pol II becomes significantly reduced at the 3' end of genes, marks of transcription elongation are reduced, and unspliced mRNAs accumulate. Our findings suggest that SIG-7 plays a central role in both Pol II elongation and co-transcriptional splicing and may provide an important link for their coordination and regulation.
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Affiliation(s)
- Jeong H. Ahn
- Biology Department, Emory University, Atlanta, Georgia, United States of America
- Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, United States of America
| | - Andreas Rechsteiner
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - William G. Kelly
- Biology Department, Emory University, Atlanta, Georgia, United States of America
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17
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Blackburn EA, Wear MA, Landré V, Narayan V, Ning J, Erman B, Ball KL, Walkinshaw MD. Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90. Biosci Rep 2015; 35:e00258. [PMID: 26330616 PMCID: PMC4721547 DOI: 10.1042/bsr20150124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 02/06/2023] Open
Abstract
Cyclophilin 40 (Cyp40) comprises an N-terminal cyclophilin domain with peptidyl-prolyl isomerase (PPIase) activity and a C-terminal tetratricopeptide repeat (TPR) domain that binds to the C-terminal-EEVD sequence common to both heat shock protein 70 (Hsp70) and Hsp90. We show in the present study that binding of peptides containing the MEEVD motif reduces the PPIase activity by ∼30%. CD and fluorescence assays show that the TPR domain is less stable than the cyclophilin domain and is stabilized by peptide binding. Isothermal titration calorimetry (ITC) shows that the affinity for the-MEEVD peptide is temperature sensitive in the physiological temperature range. Results from these biophysical studies fit with the MD simulations of the apo and holo (peptide-bound) structures which show a significant reduction in root mean square (RMS) fluctuation in both TPR and cyclophilin domains when-MEEVD is bound. The MD simulations of the apo-protein also highlight strong anti-correlated motions between residues around the PPIase-active site and a band of residues running across four of the seven helices in the TPR domain. Peptide binding leads to a distortion in the shape of the active site and a significant reduction in these strongly anti-correlated motions, providing an explanation for the allosteric effect of ligand binding and loss of PPIase activity. Together the experimental and MD results suggest that on heat shock, dissociation of Cyp40 from complexes mediated by the TPR domain leads to an increased pool of free Cyp40 capable of acting as an isomerase/chaperone in conditions of cellular stress.
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Affiliation(s)
- Elizabeth A Blackburn
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Vivian Landré
- IGMM-Edinburgh Cancer Research Centre, University of Edinburgh, Crewe Road South, EH4 2XR, U.K
| | - Vikram Narayan
- IGMM-Edinburgh Cancer Research Centre, University of Edinburgh, Crewe Road South, EH4 2XR, U.K
| | - Jia Ning
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Burak Erman
- Chemical and Biological Engineering Department, Koc University, Istanbul 34415, Turkey
| | - Kathryn L Ball
- IGMM-Edinburgh Cancer Research Centre, University of Edinburgh, Crewe Road South, EH4 2XR, U.K
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K.
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Singh K, Zouhar M, Mazakova J, Rysanek P. Genome wide identification of the immunophilin gene family in Leptosphaeria maculans: a causal agent of Blackleg disease in Oilseed Rape (Brassica napus). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:645-57. [PMID: 25259854 DOI: 10.1089/omi.2014.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract Phoma stem canker (blackleg) is a disease of world-wide importance on oilseed rape (Brassica napus) and can cause serious losses for crops globally. The disease is caused by dothideomycetous fungus, Leptosphaeria maculans, which is highly virulent/aggressive. Cyclophilins (CYPs) and FK506-binding proteins (FKBPs) are ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) family. They are collectively referred to as immunophilins (IMMs). In the present study, IMM genes, CYP and FKBP in haploid strain v23.1.3 of L. maculans genome, were identified and classified. Twelve CYPs and five FKBPs were determined in total. Domain architecture analysis revealed the presence of a conserved cyclophilin-like domain (CLD) in the case of CYPs and FKBP_C in the case of FKBPs. Interestingly, IMMs in L. maculans also subgrouped into single domain (SD) and multidomain (MD) proteins. They were primarily found to be localized in cytoplasm, nuclei, and mitochondria. Homologous and orthologous gene pairs were also determined by comparison with the model organism Saccharomyces cerevisiae. Remarkably, IMMs of L. maculans contain shorter introns in comparison to exons. Moreover, CYPs, in contrast with FKBPs, contain few exons. However, two CYPs were determined as being intronless. The expression profile of IMMs in both mycelium and infected primary leaves of B. napus demonstrated their potential role during infection. Secondary structure analysis revealed the presence of atypical eight β strands and two α helices fold architecture. Gene ontology analysis of IMMs predicted their significant role in protein folding and PPIase activity. Taken together, our findings for the first time present new prospects of this highly conserved gene family in phytopathogenic fungus.
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Affiliation(s)
- Khushwant Singh
- Department of Plant Protection, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Czech Republic
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Abstract
Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs are often able to bind a large number of different RNAs. The currently available knowledge is already drawing an intricate network of interactions, whose deregulation is frequently associated to pathological states. Several different techniques were developed in the past years to obtain protein–RNA binding data in a high-throughput fashion. In parallel, in silico inference methods were developed for the accurate computational prediction of the interaction of RBP–lncRNA pairs. The field is growing rapidly, and it is foreseeable that in the near future, the protein–lncRNA interaction network will rise, offering essential clues for a better understanding of lncRNA cellular mechanisms and their disease-associated perturbations.
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Roles of Prolyl Isomerases in RNA-Mediated Gene Expression. Biomolecules 2015; 5:974-99. [PMID: 25992900 PMCID: PMC4496705 DOI: 10.3390/biom5020974] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/01/2015] [Accepted: 05/07/2015] [Indexed: 12/16/2022] Open
Abstract
The peptidyl-prolyl cis-trans isomerases (PPIases) that include immunophilins (cyclophilins and FKBPs) and parvulins (Pin1, Par14, Par17) participate in cell signaling, transcription, pre-mRNA processing and mRNA decay. The human genome encodes 19 cyclophilins, 18 FKBPs and three parvulins. Immunophilins are receptors for the immunosuppressive drugs cyclosporin A, FK506, and rapamycin that are used in organ transplantation. Pin1 has also been targeted in the treatment of Alzheimer’s disease, asthma, and a number of cancers. While these PPIases are characterized as molecular chaperones, they also act in a nonchaperone manner to promote protein-protein interactions using surfaces outside their active sites. The immunosuppressive drugs act by a gain-of-function mechanism by promoting protein-protein interactions in vivo. Several immunophilins have been identified as components of the spliceosome and are essential for alternative splicing. Pin1 plays roles in transcription and RNA processing by catalyzing conformational changes in the RNA Pol II C-terminal domain. Pin1 also binds several RNA binding proteins such as AUF1, KSRP, HuR, and SLBP that regulate mRNA decay by remodeling mRNP complexes. The functions of ribonucleoprotein associated PPIases are largely unknown. This review highlights PPIases that play roles in RNA-mediated gene expression, providing insight into their structures, functions and mechanisms of action in mRNP remodeling in vivo.
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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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Schiene-Fischer C. Multidomain Peptidyl Prolyl cis/trans Isomerases. Biochim Biophys Acta Gen Subj 2014; 1850:2005-16. [PMID: 25445709 DOI: 10.1016/j.bbagen.2014.11.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Peptidyl prolyl cis/trans isomerases (PPIases) assist the folding and restructuring of client proteins by catalysis of the slow rotational motion of peptide bonds preceding a proline residue. Catalysis is performed by relatively small, distinct protein domains of 10 to 18kDa for all PPIase families. PPIases are involved in a wide variety of physiological and pathophysiological processes like signal transduction, cell differentiation, apoptosis as well as viral, bacterial and parasitic infection. SCOPE OF REVIEW There are multidomain PPIases consisting of one to up to four catalytic domains of the respective PPIase family supplemented by N- or C-terminal extensions. This review examines the biochemical and functional properties of the members of the PPIase class of enzymes which contain additional protein domains with defined biochemical functions. MAJOR CONCLUSIONS The versatile domain architecture of multidomain PPIases is important for the control of enzyme specificity and organelle-specific targeting, the establishment of molecular connections and hence the coordination of PPIase functions across the cellular network. GENERAL SIGNIFICANCE Accessory domains covalently linked to a PPIase domain supply an additional layer of control to the catalysis of prolyl isomerization in specific client proteins. Understanding these control mechanisms will provide new insights into the physiological mode of action of the multidomain PPIases and their ability to form therapeutic targets. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany.
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Hanes SD. Prolyl isomerases in gene transcription. Biochim Biophys Acta Gen Subj 2014; 1850:2017-34. [PMID: 25450176 DOI: 10.1016/j.bbagen.2014.10.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Peptidyl-prolyl isomerases (PPIases) are enzymes that assist in the folding of newly-synthesized proteins and regulate the stability, localization, and activity of mature proteins. They do so by catalyzing reversible (cis-trans) rotation about the peptide bond that precedes proline, inducing conformational changes in target proteins. SCOPE OF REVIEW This review will discuss how PPIases regulate gene transcription by controlling the activity of (1) DNA-binding transcription regulatory proteins, (2) RNA polymerase II, and (3) chromatin and histone modifying enzymes. MAJOR CONCLUSIONS Members of each family of PPIase (cyclophilins, FKBPs, and parvulins) regulate gene transcription at multiple levels. In all but a few cases, the exact mechanisms remain elusive. Structure studies, development of specific inhibitors, and new methodologies for studying cis/trans isomerization in vivo represent some of the challenges in this new frontier that merges two important fields. GENERAL SIGNIFICANCE Prolyl isomerases have been found to play key regulatory roles in all phases of the transcription process. Moreover, PPIases control upstream signaling pathways that regulate gene-specific transcription during development, hormone response and environmental stress. Although transcription is often rate-limiting in the production of enzymes and structural proteins, post-transcriptional modifications are also critical, and PPIases play key roles here as well (see other reviews in this issue). This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Steven D Hanes
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E Adams St., Syracuse, NY 13210 USA.
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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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Trivedi DK, Bhatt H, Pal RK, Tuteja R, Garg B, Johri AK, Bhavesh NS, Tuteja N. Structure of RNA-interacting cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants. Sci Rep 2013; 3:3001. [PMID: 24141523 PMCID: PMC3801112 DOI: 10.1038/srep03001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/03/2013] [Indexed: 11/09/2022] Open
Abstract
Soil salinity problems are widespread around the globe with increased risk of spreading over the years. The fungus Piriformospora indica, identified in Indian Thar desert, colonizes the roots of monocotyledon plants and provides resistance towards biotic as well as abiotic stress conditions. We have identified a cyclophilin A-like protein from P. indica (PiCypA), which shows higher expression levels during salinity stress. The transgenic tobacco plants overexpressing PiCypA develop osmotic tolerance and exhibit normal growth under osmotic stress conditions. The crystal structure and NMR spectroscopy of PiCypA show a canonical cyclophilin like fold exhibiting a novel RNA binding activity. The RNA binding activity of the protein and identification of the key residues involved in the RNA recognition is unique for this class of protein. Here, we demonstrate for the first time a direct evidence of countering osmotic stress tolerance in plant by genetic modification using a P. indica gene.
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Affiliation(s)
| | - Harshesh Bhatt
- Structural and Computational Biology group
- These authors contributed equally to this work
| | - Ravi Kant Pal
- National Institute of Immunology (NII), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Renu Tuteja
- Malaria group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067 India
| | | | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067 India
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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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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