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Singh M, Singh H, Kaur K, Shubhankar S, Singh S, Kaur A, Singh P. Characterization and regulation of salt upregulated cyclophilin from a halotolerant strain of Penicillium oxalicum. Sci Rep 2023; 13:17433. [PMID: 37833355 PMCID: PMC10575979 DOI: 10.1038/s41598-023-44606-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023] Open
Abstract
Penicillium species are an industrially important group of fungi. Cyclophilins are ubiquitous proteins and several members of this family exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity. We had earlier demonstrated that the salt-induced PPIase activity in a halotolerant strain of P. oxalicum was associated with enhanced expression of a cyclophilin gene, PoxCYP18. Cloning and characterization of PoxCYP18 revealed that its cDNA consists of 522 bp encoding a protein of 173 amino acid residues, with predicted molecular mass and pI values of 18.91 kDa and 8.87, respectively. The recombinant PoxCYP18 can catalyze cis-trans isomerization of peptidyl-prolyl bond with a catalytic efficiency of 1.46 × 107 M-1 s-1 and is inhibited specifically only by cyclosporin A, with an inhibition constant of 5.04 ± 1.13 nM. PoxCYP18 consists of two cysteine residues at positions - 45 and - 170, and loses its activity under oxidizing conditions. Substitution of these residues alone or together by site-directed mutagenesis revealed that the PPIase activity of PoxCYP18 is regulated through a redox mechanism involving the formation of disulfide linkages. Heterologous expression of PoxCYP18 conferred enhanced tolerance to salt stress in transgenic E. coli cells, implying that this protein imparts protection to cellular processes against salt-induced damage.
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Affiliation(s)
- Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab, 144008, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Shubhankar Shubhankar
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Amarjeet Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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Tasnim A, Jahan I, Azim T, Karmoker D, Seraj ZI. Paired growth of cultivated and halophytic wild rice under salt stress induces bacterial endophytes and gene expression responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1244743. [PMID: 37746015 PMCID: PMC10516563 DOI: 10.3389/fpls.2023.1244743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023]
Abstract
Introduction Utilizing salt-affected marginal lands in coastal regions can help meet the growing demand for rice. We explored a nature-based solution involving wild halophytic rice (O. coarctata, Oc) and commercial rice BRRI Dhan 67 (O. sativa, Os) grown in close proximity to each other under salt stress. Methods This was to investigate whether a paired planting strategy could help complement rice growth and yield under stress. We also investigated the gene expression and endophytic bacterial profiles of both Os and Oc in unpaired and paired conditions without and with salt. Results Paired plants exhibited lower salt damage indicators such as smaller reduction in plant height, electrolyte leakage and chlorophyll loss, as well as higher K+/Na+ ratio under saline stress. Some of the 39 endophytic bacteria in the mutualism experiment were unique to Oc and transferred to Os when paired. Differentially expressed genes in leaves of paired Os versus unpaired Os were 1097 (994 up-regulated, 101 down-regulated) without salt and 893 (763 up-regulated, 130 down-regulated) under salt stress. The presence of Oc plants under salt stress influenced major biological processes in Os, including oxidative stress; chitinase activity; phenylalanine catabolic process and response to ABA. Protein binding and serine/threonine kinase activity were primarily affected in molecular function. The downregulated WRKY transcription factor 22 in paired conditions under salt stress played a role in the MAPK signaling pathway, reducing respiratory cell death. The upregulated auxin-responsive protein IAA18 gene, involved in hormone signaling and cell enlargement, was present only in paired plants. Discussion Our findings therefore, offer insights into developing more effective cultivation strategies for sustainable rice production.
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Yadav C, Bahuguna RN, Dhankher OP, Singla-Pareek SL, Pareek A. Physiological and molecular signatures reveal differential response of rice genotypes to drought and drought combination with heat and salinity stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:899-910. [PMID: 35592483 PMCID: PMC9110620 DOI: 10.1007/s12298-022-01162-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 05/26/2023]
Abstract
UNLABELLED Rice is the staple food for more than 3.5 billion people worldwide. The sensitivity of rice to heat, drought, and salinity is well documented. However, rice response to combinations of these stresses is not well understood. A contrasting set of rice genotypes for heat (N22, Gharib), drought (Moroberekan, Pusa 1121) and salinity (Pokkali, IR64) were selected to characterize their response under drought, and combination of drought with heat and salinity at the sensitive seedling stage. Sensitive genotypes (IR64, Pusa 1121, Gharib) recorded higher reactive oxygen species accumulation (20-40%), membrane damage (8-65%) and reduction in photosynthetic efficiency (10-23%) across the stress and stress combinations as compared to stress tolerant checks. On the contrary, N22 and Pokkali performed best under drought + heat, and drought + salinity combination, respectively. Moreover, gene expression pattern revealed the highest expression of catalase (CAT), ascorbate peroxidase (APX) and GATA28a in N22 under heat + drought, whereas the highest expression of CAT, APX, superoxide dismutase (SOD), DEHYDRIN, GATA28a and GATA28b in Pokkali under drought + salinity. Interestingly, the phenotypic variation and expression level of genes highlighted the role of different set of physiological traits and genes under drought and drought combination with heat and salinity stress. This study reveals that rice response to stress combinations was unique with rapid readjustment at physiological and molecular levels. Moreover, phenotypic changes under stress combinations showed substantial adaptive plasticity in rice, which warrant further investigations at molecular level. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01162-y.
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Affiliation(s)
- Chhaya Yadav
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Rajeev Nayan Bahuguna
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003 USA
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
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Roy S, Mishra M, Kaur G, Singh S, Rawat N, Singh P, Singla-Pareek SL, Pareek A. OsCyp2-P, an auxin-responsive cyclophilin, regulates Ca 2+ calmodulin interaction for an ion-mediated stress response in rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13631. [PMID: 35049071 DOI: 10.1111/ppl.13631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/23/2021] [Accepted: 01/14/2022] [Indexed: 05/24/2023]
Abstract
OsCYP2-P is an active cyclophilin (having peptidyl-prolyl cis/trans-isomerase activity, PPIase) isolated from the wild rice Pokkali having a natural capacity to grow and yield seeds in coastal saline regions of India. Transcript abundance analysis in rice seedlings showed the gene is inducible by multiple stresses, including salinity, drought, high temperature, and heavy metals. To dissect the role of OsCYP2-P gene in stress response, we raised overexpression (OE) and knockdown (KD) transgenic rice plants with >2-3 folds higher and approximately 2-fold lower PPIase activity, respectively. Plants overexpressing this gene had more favorable physiological and biochemical parameters (K+ /Na+ ratio, electrolytic leakage, membrane damage, antioxidant enzymes) than wild type, and the reverse was observed in plants that were knocked down for this gene. We propose that OsCYP2-P contributes to stress tolerance via maintenance of ion homeostasis and thus prevents toxic cellular ion buildup and membrane damage. OE plants were found to have a higher harvest index and higher number of filled grains under salinity and drought stress than wild type. OsCYP2-P interacts with calmodulin, indicating it functions via the Ca-CaM pathway. Compared to the WT, the germinating OE seeds exhibited a substantially higher auxin level, and this hormone was below the detection limits in the WT and KD lines. These observations strongly indicate that OsCyp2-P affects the signaling and transport of auxin in rice.
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Affiliation(s)
- Suchismita Roy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manjari Mishra
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Nishtha Rawat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
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Tiwari S, Nutan KK, Deshmukh R, Sarsu F, Gupta KJ, Singh AK, Singla-Pareek SL, Pareek A. Seedling-stage salinity tolerance in rice: Decoding the role of transcription factors. PHYSIOLOGIA PLANTARUM 2022; 174:e13685. [PMID: 35419814 DOI: 10.1111/ppl.13685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/10/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Rice is an important staple food crop that feeds over half of the human population, particularly in developing countries. Increasing salinity is a major challenge for continuing rice production. Though rice is affected by salinity at all the developmental stages, it is most sensitive at the early seedling stage. The yield thus depends on how many seedlings can withstand saline water at the stage of transplantation, especially in coastal farms. The rapid development of "omics" approaches has assisted researchers in identifying biological molecules that are responsive to salt stress. Several salinity-responsive quantitative trait loci (QTL) contributing to salinity tolerance have been identified and validated, making it essential to narrow down the search for the key genes within QTLs. Owing to the impressive progress of molecular tools, it is now clear that the response of plants toward salinity is highly complex, involving multiple genes, with a specific role assigned to the repertoire of transcription factors (TF). Targeting the TFs for improving salinity tolerance can have an inbuilt advantage of influencing multiple downstream genes, which in turn can contribute toward tolerance to multiple stresses. This is the first comparative study for TF-driven salinity tolerance in contrasting rice cultivars at the seedling stage that shows how tolerant genotypes behave differently than sensitive ones in terms of stress tolerance. Understanding the complexity of salt-responsive TF networks at the seedling stage will be helpful to alleviate crop resilience and prevent crop damage at an early growth stage in rice.
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Affiliation(s)
- Shalini Tiwari
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Kamlesh Kant Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
| | - Fatma Sarsu
- General Directorate of Agricultural Research and Policies, Ministry of Agriculture and Forestry, Ankara, Turkey
| | | | - Anil K Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
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Multiple Abiotic Stresses Applied Simultaneously Elicit Distinct Responses in Two Contrasting Rice Cultivars. Int J Mol Sci 2022; 23:ijms23031739. [PMID: 35163659 PMCID: PMC8836074 DOI: 10.3390/ijms23031739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes—Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly. Abscisic acid (ABA) levels increased at least five-fold but did not differ significantly between the genotypes. Tandem Mass Tag isotopic labelling quantitative proteomics revealed 6215 reproducibly identified proteins in mature leaves across the two genotypes and three time points (0, 2 and 4 days of stress). Of these, 987 were differentially expressed due to stress (cf. control plants), including 41 proteins that changed significantly in abundance in all stressed plants. Heat shock proteins, late embryogenesis abundant proteins and photosynthesis-related proteins were consistently responsive to stress in both Nipponbare and IAC1131. Remarkably, even after 2 days of stress there were almost six times fewer proteins differentially expressed in IAC1131 than Nipponbare. This contrast in the translational response to multiple stresses is consistent with the known tolerance of IAC1131 to dryland conditions.
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Anwar K, Joshi R, Morales A, Das G, Yin X, Anten NPR, Raghuvanshi S, Bahuguna RN, Singh MP, Singh RK, Zanten M, Sasidharan R, Singla‐Pareek SL, Pareek A. Genetic diversity reveals synergistic interaction between yield components could improve the sink size and yield in rice. Food Energy Secur 2022. [DOI: 10.1002/fes3.334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- Division of Biotechnology CSIR‐Institute of Himalayan Bioresource Technology Palampur India
| | - Alejandro Morales
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
- Molecular Plant Physiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
- Plant Ecophysiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Gourab Das
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Xinyou Yin
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
| | - Niels P. R. Anten
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology University of Delhi South Campus New Delhi India
| | - Rajeev N. Bahuguna
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- Center for Advance Studies on Climate Change Dr. Rajendra Prasad Central Agricultural University, Pusa Samastipur India
| | - Madan Pal Singh
- Division of Plant Physiology Indian Agricultural Research Institute PUSA New Delhi India
| | - Rakesh K. Singh
- Crop Diversification and Genetics International Center for Biosaline Agriculture Academic City Dubai United Arab Emirates
| | - Martijn Zanten
- Molecular Plant Physiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Rashmi Sasidharan
- Plant Ecophysiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Sneh L. Singla‐Pareek
- Plant Stress Biology International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- National Agri‐Food Biotechnology Institute Mohali India
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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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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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Nutan KK, Singla-Pareek SL, Pareek A. The Saltol QTL-localized transcription factor OsGATA8 plays an important role in stress tolerance and seed development in Arabidopsis and rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:684-698. [PMID: 31613368 DOI: 10.1093/jxb/erz368] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/06/2019] [Indexed: 05/23/2023]
Abstract
GATA represents a highly conserved family of transcription factors reported in organisms ranging from fungi to angiosperms. A member of this family, OsGATA8, localized within the Saltol QTL in rice, has been reported to be induced by salinity, drought, and ABA. However, its precise role in stress tolerance has not yet been elucidated. Using genetic, molecular, and physiological analyses, in this study we show that OsGATA8 increases seed size and tolerance to abiotic stresses in both Arabidopsis and rice. Transgenic lines of rice were generated with 3-fold overexpression of OsGATA8 compared to the wild-type together with knockdown lines with 2-fold lower expression. The overexpressing lines showed higher biomass accumulation and higher photosynthetic efficiency in seedlings compared to the wild-type and knockdown lines under both normal and salinity-stress conditions. OsGATA8 appeared to be an integrator of diverse cellular processes, including K+/Na+ content, photosynthetic efficiency, relative water content, Fv/Fm ratio, and the stability to sub-cellular organelles. It also contributed to maintaining yield under stress, which was ~46% higher in overexpression plants compared with the wild-type. OsGATA8 produced these effects by regulating the expression of critical genes involved in stress tolerance, scavenging of reactive oxygen species, and chlorophyll biosynthesis.
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Affiliation(s)
- Kamlesh K Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Genome-Wide Identification and Characterization of the Cyclophilin Gene Family in the Nematophagous Fungus Purpureocillium lilacinum. Int J Mol Sci 2019; 20:ijms20122978. [PMID: 31216716 PMCID: PMC6627767 DOI: 10.3390/ijms20122978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 11/17/2022] Open
Abstract
Purpureocillium lilacinum has been widely used as a commercial biocontrol agent for the control of plant parasitic nematodes. Whole genome analysis promotes the identification of functional genes and the exploration of their molecular mechanisms. The Cyclophilin (CYP) gene family belongs to the immunophillin superfamily, and has a conserved cyclophilin-like domain (CLD). CYPs are widely identified in prokaryotes and eukaryotes, and can be divided into single- and multi-domain proteins. In the present study, 10 CYP genes possessing the CLD, named PlCYP1-P10, were identified from the genome of P. lilacinum strain 36-1. Those 10 PlCYPs were predicted to have different cellular localizations in P. lilacinum. Phylogenetic and gene structure analysis revealed the evolutionary differentiation of CYPs between Ascomycotina and Saccharomycotina fungi, but conservation within the Ascomycotina fungi. Motif and gene structure distributions further support the result of phylogenetic analysis. Each PlCYP gene had a specific expression pattern in different development stages of P. lilacinum and its parasitism stage on eggs of Meloidogyne incognita. In addition, the 10 PlCYP genes exhibited different expression abundances in response to abiotic stresses, among which PlCYP4 was highly expressed at a high temperature (35 °C), while PlCYP6 was up-regulated under 5 mM of H2O2 stress. Furthermore, the heterologous expression of PlCYP4 and PlCYP6 in Escherichia coli enhanced the cellular tolerance against a high temperature and H2O2. In summary, our study indicates the potential functions of PlCYPs in virulence and the stress response, and also provides a frame for further analysis of the CYP gene family in Ascomycotina fungi.
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Razzaque S, Elias SM, Haque T, Biswas S, Jewel GMNA, Rahman S, Weng X, Ismail AM, Walia H, Juenger TE, Seraj ZI. Gene Expression analysis associated with salt stress in a reciprocally crossed rice population. Sci Rep 2019; 9:8249. [PMID: 31160691 PMCID: PMC6546764 DOI: 10.1038/s41598-019-44757-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/21/2019] [Indexed: 11/27/2022] Open
Abstract
The rice landrace Horkuch, endemic to the southern saline coast of Bangladesh, is known to have salt tolerance traits and can therefore contribute to a high yielding recipient for breeding purposes. In this study, we reciprocally crossed Horkuch with high yielding but salt sensitive IR29 to detect the complement of genes that were responsible for conferring salt tolerance versus sensitivity at the seedling developmental stage. We looked at tolerant and sensitive F3 families from individual F2 segregating plants and analyzed them for differential gene expressions using RNAseq. In general, we observed higher numbers of genes differentially expressed in leaves compared to root tissues. This included both upregulation and downregulation of gene expression across our experimental factors. Gene expression decreased in sensitive leaf after stress exposure where tolerant plants showed the opposite trend. In root, tolerant plants expression decreased at higher time points of stress exposure. We also observed a strong maternal cytoplasmic effect on gene expression and this was most evident in roots where there was upregulation in functional enrichments related to phosphorylation, electron carriers, transporter and cation transmembrane activities. Stress groups (tolerant and sensitive) response in F3 families were distinctive in both cytoplasmic backgrounds and involved uniquely upregulated genes in tolerant progenies including membrane sensor proteins, enzymes involved with signaling pathways, such as those producing trehalose and G-protein coupled receptor proteins, photosynthesis-related enzymes and golgi body recycling as well as prolamin precursor proteins involved in refolding of proteins. On the other hand, sensitivity was found to be associated with differential upregulation of only a few redox proteins and higher number of apoptosis related genes compared to the tolerant response. Overall, our highly replicated experimental design was powerful and allowed the detection of relatively subtle differential expression. Our future goal is to correlate these expression differences with QTLs in this population, which would help identify the relative importance of specific genetic loci and provide a direct avenue for combining higher levels of salt tolerance with better agronomic traits in rice.
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Affiliation(s)
- Samsad Razzaque
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Sabrina M Elias
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, 68583, USA
| | - Taslima Haque
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Sudip Biswas
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - G M Nurnabi Azad Jewel
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sazzadur Rahman
- Plant Physiology Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | | | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, 68583, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Zeba I Seraj
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
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13
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Wang J, Mao X, Wang R, Li A, Zhao G, Zhao J, Jing R. Identification of wheat stress-responding genes and TaPR-1-1 function by screening a cDNA yeast library prepared following abiotic stress. Sci Rep 2019; 9:141. [PMID: 30644420 PMCID: PMC6333785 DOI: 10.1038/s41598-018-37859-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/06/2018] [Indexed: 11/29/2022] Open
Abstract
Abiotic stress significantly impacts growth and yield of crop plants. It is imperative for crop improvement to discover and utilize stress-tolerant functional genes. In this study, genes responding to abiotic stresses, such as freezing, salt and osmotic stress, were screened from a cDNA yeast library that was constructed from the drought- and heat-tolerant wheat variety Hanxuan 10. After screening for surviving clones we isolated 7,249, 4,313 and 4,469 raw sequences, corresponding to 4,695, 2,641 and 2,771 genes following each treatment. Venn diagrams revealed 377 overlapping genes. GO analysis suggested that these genes were mainly involved in the metabolic and stress signal pathways. KEGG pathway enrichment analysis indicated that the isolated genes predominantly belonged to pathways concerning energy and metabolism. Overlapping gene TaPR-1-1 within the pathogenesis-related (PR) protein family was selected for detailed characterization. Although previous studies had shown that PR genes function during pathogen attack, our results demonstrated that TaPR-1-1 expression was also induced by freezing, salinity, and osmotic stresses. Overexpression in yeast and Arabidopsis showed that TaPR-1-1 conferred tolerance to these stresses. We concluded that screening cDNA yeast libraries following abiotic stress is an efficient way to identify stress-tolerance genes.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangyao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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14
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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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15
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Acevedo LA, Nicholson LK. 1H, 13C and 15N NMR assignments of cyclophilin LRT2 (OsCYP2) from rice. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:171-174. [PMID: 29353448 PMCID: PMC5944331 DOI: 10.1007/s12104-018-9803-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/10/2018] [Indexed: 05/06/2023]
Abstract
Cyclophilins are enzymes that catalyze the isomerization of a prolyl-peptide bond and are found in both prokaryotes and eukaryotes. LRT2 (also known as OsCYP2) is a cyclophilin in rice (Oryza sativa), that has importance in lateral root development and stress tolerance. LRT2 is 172 amino acids long and has a molecular weight of 18.3 kDa. Here, we report the backbone and sidechain resonance assignments of 1H, 13C, 15N in the LRT2 protein using several 2D and 3D heteronuclear NMR experiments at pH 6.7 and 298 K. Our chemical shift data analysis predicts a secondary structure like the cytosolic wheat cyclophilin TaCypA-1 with 87.7% sequence identity. These assignments will be useful for further analysis in the NMR studies for function and structure of this enzyme.
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Affiliation(s)
- Lucila Andrea Acevedo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Linda K Nicholson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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16
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Zhang H, Wang J, Li S, Wang S, Liu M, Wang W, Zhao Y. Molecular cloning, expression, purification and functional characterization of an antifungal cyclophilin protein from Panax ginseng. Biomed Rep 2017; 7:527-531. [PMID: 29188056 PMCID: PMC5702963 DOI: 10.3892/br.2017.998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/02/2017] [Indexed: 12/28/2022] Open
Abstract
Cyclophilins (CyPs), a member of peptidyl-prolyl cis-trans isomerases (PPIases), are ubiquitously distributed in organisms such as bacteria, yeast, plants and animals. CyPs have diverse biological functions, with some exhibiting antifungal and antiviral activities. In this study, Panax ginseng cyclophilin (pgCyP), a novel gene encoding an antifungal protein from Panax ginseng, was cloned, and its protein product was expressed in Escherichia coli, and then fractionated by affinity chromatography. The open reading frame of the pgCyP full-length coding sequence was found to encode a single-domain CyP-like protein of 174 amino residues with a calculated molecular weight of 18.7 kDa. The pGEX system was used to express pgCyP fused to glutathione S-transferase. After affinity purification, the protein showed a strong fungal resistance effect on Phytophthora cactorum. In addition, pgCyP showed high PPIase activity. To the best of our knowledge, the present study is the first successful effort to clone and characterize a CyP-like protein gene from Panax ginseng.
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Affiliation(s)
- Hui Zhang
- Traditional Chinese Medicine and Biotechnology Research and Development Center, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Jiawen Wang
- Traditional Chinese Medicine and Biotechnology Research and Development Center, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Shuaijun Li
- Traditional Chinese Medicine and Biotechnology Research and Development Center, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Siming Wang
- Traditional Chinese Medicine and Biotechnology Research and Development Center, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Meichen Liu
- Traditional Chinese Medicine and Biotechnology Research and Development Center, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Weinan Wang
- School of Pharmaceutical Sciences, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Yu Zhao
- Traditional Chinese Medicine and Biotechnology Research and Development Center, Changchun University of Traditional Chinese Medicine, Changchun, Jilin 130117, P.R. China
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17
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Cui P, Liu H, Ruan S, Ali B, Gill RA, Ma H, Zheng Z, Zhou W. A zinc finger protein, interacted with cyclophilin, affects root development via IAA pathway in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:496-505. [PMID: 28267270 DOI: 10.1111/jipb.12531] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/28/2017] [Indexed: 05/23/2023]
Abstract
The plant hormone auxin plays a crucial role in lateral root development. To better understand the molecular mechanisms underlying lateral root formation, an auxin-responsive gene OsCYP2 (Os02g0121300) was characterized from rice. Compared to the wild type, OsCYP2-RNAi (RNA interference) lines exhibited distinctive defects in lateral root development. Yeast two-hybrid and glutathione S-transferase pull-down results confirmed that OsCYP2 interacted with a C2HC-type zinc finger protein (OsZFP, Os01g0252900) which is located in the rice nucleus. T2 OsZFP-RNAi lines had significantly fewer lateral roots than did wild-type plants, which suggests a role for OsCYP2 and OsZFP in regulating lateral root development. Quantitative real-time polymerase chain reaction showed that the expression of certain Aux/IAA (auxin/indole-3-acetic acid) genes was altered in OsCYP2- and OsZFP-RNAi lines in response to IAA. These findings imply that OsCYP2 and OsZFP participate in IAA signal pathways controlling lateral root development. More importantly, OsIAA11 showed functional redundancy not only in OsCYP2-RNAi lines but also in OsZFP-RNAi lines, which provides important clues for the elucidation of mechanisms controlling lateral root development in response to auxin.
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Affiliation(s)
- Peng Cui
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an 311300, China
| | - Hongbo Liu
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an 311300, China
| | - Songlin Ruan
- Plant Molecular Biology and Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Basharat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Rafaqat Ali Gill
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Huasheng Ma
- Plant Molecular Biology and Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Zhifu Zheng
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an 311300, China
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
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18
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Nongpiur RC, Singla-Pareek SL, Pareek A. Genomics Approaches For Improving Salinity Stress Tolerance in Crop Plants. Curr Genomics 2016; 17:343-57. [PMID: 27499683 PMCID: PMC4955028 DOI: 10.2174/1389202917666160331202517] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 08/04/2015] [Indexed: 11/22/2022] Open
Abstract
Salinity is one of the major factors which reduces crop production worldwide. Plant responses to salinity are highly complex and involve a plethora of genes. Due to its multigenicity, it has been difficult to attain a complete understanding of how plants respond to salinity. Genomics has progressed tremendously over the past decade and has played a crucial role towards providing necessary knowledge for crop improvement. Through genomics, we have been able to identify and characterize the genes involved in salinity stress response, map out signaling pathways and ultimately utilize this information for improving the salinity tolerance of existing crops. The use of new tools, such as gene pyramiding, in genetic engineering and marker assisted breeding has tremendously enhanced our ability to generate stress tolerant crops. Genome editing technologies such as Zinc finger nucleases, TALENs and CRISPR/Cas9 also provide newer and faster avenues for plant biologists to generate precisely engineered crops.
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Affiliation(s)
- Ramsong Chantre Nongpiur
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067,India
| | - Sneh Lata Singla-Pareek
- Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi 110067,India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067,India
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19
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The peptidyl-prolyl cis-trans isomerase activity of the wheat cyclophilin, TaCypA-1, is essential for inducing thermotolerance in Escherichia coli. BIOCHIMIE OPEN 2015; 2:9-15. [PMID: 29632833 PMCID: PMC5889472 DOI: 10.1016/j.biopen.2015.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/19/2015] [Indexed: 11/22/2022]
Abstract
Growth at high temperatures is one of the desired features for industrial applications of microbes, as it results in decrease in contamination and enhanced solubility of certain substrates. In this study, it is demonstrated that heterologous expression of a wheat cyclophilin, TaCypA-1, confers thermotolerance to Escherichia coli. The TaCypA-1 possesses peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyses cis to trans isomerization of the peptidyl prolyl bonds, a rate limiting step in protein folding. Expression of deleted mutants of TaCypA-1, that lacked PPIase activity, resulted in abrogation of thermotolerance, providing the first evidence that this activity plays a key role in stress tolerance of cells and can be exploited for industrial applications. Further, we also demonstrate that TaCypA-1 interacts with calmodulin (CaM), and the CaM-binding domain is localized to amino acid residues 51-71 in the N-terminus region.
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20
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Ponmani T, Guo R, Ki JS. A novel cyclophilin gene from the dinoflagellate Prorocentrum minimum and its possible role in the environmental stress response. CHEMOSPHERE 2015; 139:260-7. [PMID: 26150195 DOI: 10.1016/j.chemosphere.2015.06.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 06/18/2015] [Accepted: 06/21/2015] [Indexed: 05/20/2023]
Abstract
Cyclophilins (CYPs) are a family of proteins that bind to cyclosporine and are thought to be involved in the stress response. In dinoflagellate algae, CYPs may function as a survival strategy in cells exposed to environmental stressors. Here, we identified a novel cyclophilin gene (referred to as PmCYP, comprising a 516-bp open reading frame, encoding a 171-aa protein with a molecular mass of 17.5kDa) from the dinoflagellate Prorocentrum minimum, and evaluated the role of dinoflagellate CYP in cells exposed to environmental pollutants copper and polychlorinated biphenyl. In addition, we assessed the cytoprotective role of nitric oxide in relation to the expression of PmCYP. These stressors strongly affected the physiology of the cells, as judged by cell counting, reactive oxygen species (ROS) imaging, and photosynthetic parameters (Fv/Fm and PIABS). PmCYP expression was significantly (P<0.05) induced upon exposure of the cells to all the test pollutants used in this study. These clearly indicate that PmCYP plays a vital role in the oxidative stress response in dinoflagellate survival, although the gene was initially known only for its housekeeping function.
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Affiliation(s)
- Thangaraj Ponmani
- Institute of Natural Sciences, Sangmyung University, Seoul 110-743, South Korea
| | - Ruoyu Guo
- Department of Life Science, Sangmyung University, Seoul 110-743, South Korea
| | - Jang-Seu Ki
- Institute of Natural Sciences, Sangmyung University, Seoul 110-743, South Korea; Department of Life Science, Sangmyung University, Seoul 110-743, South Korea.
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21
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Kaur G, Singh S, Singh H, Chawla M, Dutta T, Kaur H, Bender K, Snedden WA, Kapoor S, Pareek A, Singh P. Characterization of Peptidyl-Prolyl Cis-Trans Isomerase- and Calmodulin-Binding Activity of a Cytosolic Arabidopsis thaliana Cyclophilin AtCyp19-3. PLoS One 2015; 10:e0136692. [PMID: 26317213 PMCID: PMC4552658 DOI: 10.1371/journal.pone.0136692] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/06/2015] [Indexed: 12/25/2022] Open
Abstract
Cyclophilins, which bind to immunosuppressant cyclosporin A (CsA), are ubiquitous proteins and constitute a multigene family in higher organisms. Several members of this family are reported to catalyze cis-trans isomerisation of the peptidyl-prolyl bond, which is a rate limiting step in protein folding. The physiological role of these proteins in plants, with few exceptions, is still a matter of speculation. Although Arabidopsis genome is predicted to contain 35 cyclophilin genes, biochemical characterization, imperative for understanding their cellular function(s), has been carried only for few of the members. The present study reports the biochemical characterization of an Arabidopsis cyclophilin, AtCyp19-3, which demonstrated that this protein is enzymatically active and possesses peptidyl-prolyl cis-trans isomerase (PPIase) activity that is specifically inhibited by CsA with an inhibition constant (Ki) of 18.75 nM. The PPIase activity of AtCyp19-3 was also sensitive to Cu(2+), which covalently reacts with the sulfhydryl groups, implying redox regulation. Further, using calmodulin (CaM) gel overlay assays it was demonstrated that in vitro interaction of AtCyp19-3 with CaM is Ca(2+)-dependent, and CaM-binding domain is localized to 35-70 amino acid residues in the N-terminus. Bimolecular fluorescence complementation assays showed that AtCyp19-3 interacts with CaM in vivo also, thus, validating the in vitro observations. However, the PPIase activity of the Arabidopsis cyclophilin was not affected by CaM. The implications of these findings are discussed in the context of Ca(2+) signaling and cyclophilin activity in Arabidopsis.
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Affiliation(s)
- Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidayalaya, Jalandhar, Punjab, India
| | - Mrinalini Chawla
- Interdiscipinary Center for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Tanima Dutta
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Harsimran Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Kyle Bender
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | - W. A. Snedden
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | - Sanjay Kapoor
- Interdiscipinary Center for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal, Nehru University, New Delhi, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
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22
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Kumari S, Joshi R, Singh K, Roy S, Tripathi AK, Singh P, Singla-Pareek SL, Pareek A. Expression of a cyclophilin OsCyp2-P isolated from a salt-tolerant landrace of rice in tobacco alleviates stress via ion homeostasis and limiting ROS accumulation. Funct Integr Genomics 2015; 15:395-412. [PMID: 25523384 DOI: 10.1007/s10142-014-0429-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/23/2014] [Accepted: 11/30/2014] [Indexed: 10/24/2022]
Abstract
Cyclophilins are a set of ubiquitous proteins present in all subcellular compartments, involved in a wide variety of cellular processes. Comparative bioinformatics analysis of the rice and Arabidopsis genomes led us to identify novel putative cyclophilin gene family members in both the genomes not reported previously. We grouped cyclophilin members with similar molecular weight and subtypes together in the phylogenetic tree which indicated their co-evolution in rice and Arabidopsis. We also characterized a rice cyclophilin gene, OsCyp2-P (Os02g0121300), isolated from a salinity-tolerant landrace, Pokkali. Publicly available massively parallel signature sequencing (MPSS) and microarray data, besides our quantitative real time PCR (qRT-PCR) data suggest that transcript abundance of OsCyp2-P is regulated under different stress conditions in a developmental and organ specific manner. Ectopic expression of OsCyp2-P imparted multiple abiotic stress tolerance to transgenic tobacco plants as evidenced by higher root length, shoot length, chlorophyll content, and K(+)/Na(+) ratio under stress conditions. Transgenic plants also showed reduced lipid peroxidase content, electrolyte leakage, and superoxide content under stress conditions suggesting better ion homeostasis than WT plants. Localization studies confirmed that OsCyp2-P is localized in both cytosol and nucleus, indicating its possible interaction with several other proteins. The overall results suggest the explicit role of OsCyp2-P in bestowing multiple abiotic stress tolerance at the whole plant level. OsCyp2-P operates via reactive oxygen species (ROS) scavenging and ion homeostasis and thus is a promising candidate gene for enhancing multiple abiotic stress tolerance in crop plants.
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Affiliation(s)
- Sumita Kumari
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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23
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Huerta-Ocampo JA, Barrera-Pacheco A, Mendoza-Hernández CS, Espitia-Rangel E, Mock HP, Barba de la Rosa AP. Salt stress-induced alterations in the root proteome of Amaranthus cruentus L. J Proteome Res 2014; 13:3607-27. [PMID: 24942474 DOI: 10.1021/pr500153m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Salt stress is one of the major factors limiting crop productivity worldwide. Amaranth is a highly nutritious pseudocereal with remarkable nutraceutical properties; it is also a stress-tolerant plant, making it an alternative crop for sustainable food production in semiarid conditions. A two-dimensional electrophoresis gel coupled with a liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) approach was applied in order to analyze the changes in amaranth root protein accumulation in plants subjected to salt stress under hydroponic conditions during the osmotic phase (1 h), after recovery (24 h), and during the ionic phase of salt stress (168 h). A total of 101 protein spots were differentially accumulated in response to stress, in which 77 were successfully identified by LC-MS/MS and a database search against public and amaranth transcriptome databases. The resulting proteins were grouped into different categories of biological processes according to Gene Ontology. The identification of several protein isoforms with a change in pI and/or molecular weight reveals the importance of the salt-stress-induced posttranslational modifications in stress tolerance. Interestingly stress-responsive proteins unique to amaranth, for example, Ah24, were identified. Amaranth is a stress-tolerant alternative crop for sustainable food production, and the understanding of amaranth's stress tolerance mechanisms will provide valuable input to improve stress tolerance of other crop plants.
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Affiliation(s)
- José A Huerta-Ocampo
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. , Camino a la Presa San José No. 2055, Lomas 4a Sección, 78216 San Luis Potosí, S.L.P., México
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24
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Trivedi DK, Ansari MW, Dutta T, Singh P, Tuteja N. Molecular characterization of cyclophilin A-like protein from Piriformospora indica for its potential role to abiotic stress tolerance in E. coli. BMC Res Notes 2013; 6:555. [PMID: 24365575 PMCID: PMC3878271 DOI: 10.1186/1756-0500-6-555] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/19/2013] [Indexed: 11/16/2022] Open
Abstract
Background Cyclophilins (CyP), conserved in all genera, are known to have regulatory responses of various cellular processes including stress tolerance. Interestingly, CyP has a crucial role as peptidyl-prolyl cis–trans isomerases (PPIases). Our earlier in silico based approach resulted into the identification of cyclophilin family from rice, Arabidopsis and yeast. In our recent report, we discovered a new OsCYP-25 from rice. Here, we identified a novel cyclophylin A-like protein (PiCyP) from Piriformospora indica which is responsible for abiotic stress tolerance in E. coli. Results Cyclophylin A-like protein (CyPA) (accession number GQ214003) was selected from cDNA library. The genomic organization CyPA revealed a 1304 bp of CyPA in P. indica genome, showing 10 exons and 9 introns. Further, CyPA was evident in PCR with gDNA and cDNA and Southern blot analysis. The phylogenetic examination of CyPA of P. indica showed that it is closed to human cyclophilin. The uniqueness of PiCyPA protein was apparent in western blot study. Kinetics of purified PiCyPA protein for its PPIas activity was determined via first order rate constant (0.104 s-1) in the presence of 1 μg of PiCyPA, with increasing PiCyPA concentration, in the presence of cyclosporin A (CsA) and the inhibition constant (4.435 nM) of CsA for inhibition of PiCyPA. The differential response of E. coli harbouring pET28a-PiCypA was observed for their different degree of tolerance to different abiotic stresses as compared to empty pET28a vector. Conclusions Overexpression of PiCyPA protein E. coli cells confer enhanced tolerance to wide range of abiotic stresses. Thus, this study provides the significance of PiCypA as a molecular chaperone which advanced cellular stress responses of E. coli cells under adverse conditions, and it, furthermore, confirms the mounting the sustainability of E. coli for exploitation in recombinant proteins production. Additionally, the PiCyPA gene cooperates substantial functions in cellular network of stress tolerance mechanism, essentially required for various developmental stages, and might be a potential paramount candidate for crop improvement and its sustainable production under adverse conditions.
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Affiliation(s)
| | | | | | | | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067, India.
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Sekhon SS, Kaur H, Dutta T, Singh K, Kumari S, Kang S, Park SG, Park BC, Jeong DG, Pareek A, Woo EJ, Singh P, Yoon TS. Structural and biochemical characterization of the cytosolic wheat cyclophilin TaCypA-1. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:555-63. [PMID: 23519664 DOI: 10.1107/s0907444912051529] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/20/2012] [Indexed: 11/10/2022]
Abstract
Cyclophilins belong to a family of proteins that bind to the immunosuppressive drug cyclosporin A (CsA). Several members of this protein family catalyze the cis-trans isomerization of peptide bonds preceding prolyl residues. The present study describes the biochemical and structural characteristics of a cytosolic cyclophilin (TaCypA-1) cloned from wheat (Triticum aestivum L.). Purified TaCypA-1 expressed in Escherichia coli showed peptidyl-prolyl cis-trans isomerase activity, which was inhibited by CsA with an inhibition constant of 78.3 nM. The specific activity and catalytic efficiency (kcat/Km) of the purified TaCypA-1 were 99.06 ± 0.13 nmol s(-1) mg(-1) and 2.32 × 10(5) M(-1) s(-1), respectively. The structures of apo TaCypA-1 and the TaCypA-1-CsA complex were determined at 1.25 and 1.20 Å resolution, respectively, using X-ray diffraction. Binding of CsA to the active site of TaCypA-1 did not result in any significant conformational change in the apo TaCypA-1 structure. This is consistent with the crystal structure of the human cyclophilin D-CsA complex reported at 0.96 Å resolution. The TaCypA-1 structure revealed the presence of a divergent loop of seven amino acids (48)KSGKPLH(54) which is a characteristic feature of plant cyclophilins. This study is the first to elucidate the structure of an enzymatically active plant cyclophilin which shows peptidyl-prolyl cis-trans isomerase activity and the presence of a divergent loop.
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Affiliation(s)
- Simranjeet Singh Sekhon
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
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26
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Ma X, Song L, Yang Y, Liu D. A gain-of-function mutation in the ROC1 gene alters plant architecture in Arabidopsis. THE NEW PHYTOLOGIST 2013; 197:751-762. [PMID: 23206262 DOI: 10.1111/nph.12056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 10/21/2012] [Indexed: 05/20/2023]
Abstract
Plant architecture is an important agronomic trait and is useful for identification of plant species. The molecular basis of plant architecture, however, is largely unknown. Forward genetics was used to identify an Arabidopsis mutant with altered plant architecture. Using genetic and molecular approaches, we analyzed the roles of a mutated cyclophilin in the control of plant architecture. The Arabidopsis mutant roc1 has reduced stem elongation and increased shoot branching, and the mutant phenotypes are strongly affected by temperature and photoperiod. Map-based cloning and transgenic experiments demonstrated that the roc1 mutant phenotypes are caused by a gain-of-function mutation in a cyclophilin gene, ROC1. Besides, application of the plant hormone gibberellic acid (GA) further suppresses stem elongation in the mutant. GA treatment enhances the accumulation of mutated but not of wildtype (WT) ROC1 proteins. The roc1 mutation does not seem to interfere with GA biosynthesis or signaling. GA signaling, however, antagonizes the effect of the roc1 mutation on stem elongation. The altered plant architecture may result from the activation of an R gene by the roc1 protein. We also present a working model for the interaction between the roc1 mutation and GA signaling in regulating stem elongation.
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Affiliation(s)
- Xiqing Ma
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Li Song
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yaxuan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dong Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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27
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Kumari S, Roy S, Singh P, Singla-Pareek SL, Pareek A. Cyclophilins: proteins in search of function. PLANT SIGNALING & BEHAVIOR 2013; 8:e22734. [PMID: 23123451 PMCID: PMC3745578 DOI: 10.4161/psb.22734] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 05/19/2023]
Abstract
Cyclophilins constitute a subgroup of large family of proteins called immunophilins, which also include FKBPs and Parvulins. They are remarkably conserved in all genera, highlighting their pivotal role in important cellular processes. Most cyclophilins display PPIase enzymatic activity, multiplicity, diverse cellular locations and active role in protein folding which render them to be included in the class of diverse set of proteins called molecular chaperones. Due to their distinct PPIase function, besides protein disulfide isomerases and protein foldases, cyclophilins have been deemed necessary for in vivo chaperoning activity. Unlike other cellular chaperones, these proteins are specific in their respective targets. Not all cyclophilin proteins possess PPIase activity, indicating a loss of their PPIase activity during the course of evolution and gain of function independent of their PPIase activity. The PPIase function of cyclophilins is also compensated by their functional homologs, like FKBPs. Multiple cyclophilin members in plants like Arabidopsis and rice have been reported to be associated with diverse functions and regulatory pathways through their foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins were reported or suggested, the physiological relevance and molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. However, their wide distribution and ubiquitous nature signifies their fundamental importance in plant survival. Several of these members have also been directly linked to multiple stresses. This review attempts to deal with plant cyclophilins with respect to their role in stress response.
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Affiliation(s)
- Sumita Kumari
- Sher-e-Kashmir University of Agricultural Sciences and Technology; Jammu, India
| | - Suchismita Roy
- Stress Physiology and Molecular Biology Laboratory; School of Life Sciences; Jawaharlal Nehru University; New Delhi, India
| | - Prabhjeet Singh
- Department of Biotechnology; Guru Nanak Dev University; Amritsar, India
| | - Sneh L. Singla-Pareek
- Plant Molecular Biology; International Centre for Genetic Engineering and Biotechnology; New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory; School of Life Sciences; Jawaharlal Nehru University; New Delhi, India
- Correspondence to: Ashwani Pareek,
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Basak S, Jiang R. Enhancing E. coli tolerance towards oxidative stress via engineering its global regulator cAMP receptor protein (CRP). PLoS One 2012; 7:e51179. [PMID: 23251448 PMCID: PMC3522674 DOI: 10.1371/journal.pone.0051179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/30/2012] [Indexed: 12/11/2022] Open
Abstract
Oxidative damage to microbial hosts often occurs under stressful conditions during bioprocessing. Classical strain engineering approaches are usually both time-consuming and labor intensive. Here, we aim to improve E. coli performance under oxidative stress via engineering its global regulator cAMP receptor protein (CRP), which can directly or indirectly regulate redox-sensing regulators SoxR and OxyR, and other ~400 genes in E. coli. Error-prone PCR technique was employed to introduce modifications to CRP, and three mutants (OM1~OM3) were identified with improved tolerance via H(2)O(2) enrichment selection. The best mutant OM3 could grow in 12 mM H(2)O(2) with the growth rate of 0.6 h(-1), whereas the growth of wild type was completely inhibited at this H(2)O(2) concentration. OM3 also elicited enhanced thermotolerance at 48°C as well as resistance against cumene hydroperoxide. The investigation about intracellular reactive oxygen species (ROS), which determines cell viability, indicated that the accumulation of ROS in OM3 was always lower than in WT with or without H(2)O(2) treatment. Genome-wide DNA microarray analysis has shown not only CRP-regulated genes have demonstrated great transcriptional level changes (up to 8.9-fold), but also RpoS- and OxyR-regulated genes (up to 7.7-fold). qRT-PCR data and enzyme activity assay suggested that catalase (katE) could be a major antioxidant enzyme in OM3 instead of alkyl hydroperoxide reductase or superoxide dismutase. To our knowledge, this is the first work on improving E. coli oxidative stress resistance by reframing its transcription machinery through its native global regulator. The positive outcome of this approach may suggest that engineering CRP can be successfully implemented as an efficient strain engineering alternative for E. coli.
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Affiliation(s)
- Souvik Basak
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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Kumar R, Mustafiz A, Sahoo KK, Sharma V, Samanta S, Sopory SK, Pareek A, Singla-Pareek SL. Functional screening of cDNA library from a salt tolerant rice genotype Pokkali identifies mannose-1-phosphate guanyl transferase gene (OsMPG1) as a key member of salinity stress response. PLANT MOLECULAR BIOLOGY 2012; 79:555-68. [PMID: 22644442 DOI: 10.1007/s11103-012-9928-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 05/13/2012] [Indexed: 05/19/2023]
Abstract
Salinity, one of the most deleterious stresses, affects growth and overall yield of crop plants. To identify new "candidate genes" having potential role in salinity tolerance, we have carried out 'functional screening' of a cDNA library (made from a salt tolerant rice-Pokkali). Based on this screening, we identified a cDNA clone that was allowing yeast cells to grow in the presence of 1.2 M NaCl. Sequencing and BLAST search identified it as mannose-1-phosphate guanyl transferase (OsMPG1) gene from rice. Analysis of rice genome sequence database indicated the presence of 3 additional genes for MPG. Out of four, three MPG genes viz. OsMPG1, 3 and 4 were able to functionally complement yeast MPG mutant -YDL055C. We have carried out detailed transcript profiling of all members of MPG family by qRT-PCR using two contrasting rice genotypes (IR64 and Pokkali) under different abiotic stresses (salinity, drought, oxidative stress, heat stress, cold or UV light). These MPG genes showed differential expression under various abiotic stresses with two genes (OsMPG1 and 3) showing high induction in response to multiple stresses. Analysis of rice microarray data indicated higher expression levels for OsMPG1 in specific tissues such as roots, leaves, shoot apical meristem and different stages of panicle and seed development, thereby indicating its developmental regulation. Functional validation of OsMPG1 carried out by overexpression in the transgenic tobacco revealed its involvement in enhancing salinity stress tolerance.
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Affiliation(s)
- Ritesh Kumar
- Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Zhu C, Wang Y, Li Y, Bhatti KH, Tian Y, Wu J. Overexpression of a cotton cyclophilin gene (GhCyp1) in transgenic tobacco plants confers dual tolerance to salt stress and Pseudomonas syringae pv. tabaci infection. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:1264-71. [PMID: 22000049 DOI: 10.1016/j.plaphy.2011.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 09/01/2011] [Indexed: 05/20/2023]
Abstract
The full-length cDNA of a cyclophilin-like gene was cloned from Gossypium hirsutum using rapid amplification of cDNA ends and was designated as GhCyp1, a member of the immunophilin protein family. GhCyp1 expression level was higher in roots and stems than in other tissues of cotton, as determined by real-time reverse transcription polymerase chain reaction (RT-PCR). To characterize the GhCyp1 gene, tobacco (Nicotiana tabacum) was transformed via Agrobacterium tumefaciens with a vector to express the gene under the control of a strong constitutive promoter, CaMV35S (Cauliflower Mosaic Virus). Based on analyses of tolerance to salinity stress and Pseudomonas syringae pv. tabaci (Pst) infection, the overexpression of GhCyp1 in transgenic plants conferred higher tolerance to salt stress and Pst infection compared with control plants. Therefore, we suggest that GhCyp1 may be a suitable candidate gene to produce transgenic plants with tolerance to abiotic and biotic stresses.
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Affiliation(s)
- Chuanfeng Zhu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, PR China
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Gammulla CG, Pascovici D, Atwell BJ, Haynes PA. Differential proteomic response of rice (Oryza sativa) leaves exposed to high- and low-temperature stress. Proteomics 2011; 11:2839-50. [PMID: 21695689 DOI: 10.1002/pmic.201100068] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/05/2011] [Accepted: 04/26/2011] [Indexed: 11/07/2022]
Abstract
Global mean surface temperature has been predicted to increase by 1.8-4°C within this century, accompanied by an increase in the magnitude and frequency of extreme temperature events. Developing rice cultivars better adapted to non-optimal temperatures is essential to increase rice yield in the future and, hence, understanding the molecular response of rice to temperature stress is necessary. In this study, we investigated the proteomic responses of leaves of 24-day-old rice seedlings to sudden temperature changes. Rice seedlings grown at 28/20°C (day/night) were subjected to 3-day exposure to 12/5°C or 20/12°C (day/night) for low-temperature stress, and 36/28°C or 44/36°C (day/night) for high-temperature stress, followed by quantitative label-free shotgun proteomic analysis on biological triplicates of each treatment. Out of over 1100 proteins identified in one or more temperature treatments, more than 400 were found to be responsive to temperature stress. Of these, 43, 126 and 47 proteins were exclusively found at 12/5, 20/12 and 44/36°C (day/night), respectively. Our results showed that a greater change occurs in the rice leaf proteome at 20/12°C (day/night) in comparison to other non-optimal temperature regimes. In addition, our study identified more than 20 novel stress-response proteins.
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Affiliation(s)
- C Gayani Gammulla
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Chen MM, Jiang M, Shang J, Lan X, Yang F, Huang J, Nuss DL, Chen B. CYP1, a hypovirus-regulated cyclophilin, is required for virulence in the chestnut blight fungus. MOLECULAR PLANT PATHOLOGY 2011; 12:239-46. [PMID: 21355996 PMCID: PMC3313458 DOI: 10.1111/j.1364-3703.2010.00665.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cyclophilins are peptidyl-prolyl cis-trans isomerases that are highly conserved throughout eukaryotes and are the cellular target of the immunosuppressive drug cyclosporin A (CsA). We cloned cyp1, a cyclophilin A-encoding gene in the phytopathogenic fungus Cryphonectria parasitica, and showed that this gene was downregulated following infection by a virulence-attenuating hypovirus. The function of cyp1 was further investigated by construction of a cyp1 deletion mutant. Although the wild-type C. parasitica strain EP155 was sensitive to CsA, the Δcyp1 strain was highly tolerant to CsA, indicating that CYP1 was the target of CsA. Deletion of cyp1 resulted in reduced virulence when inoculated to chestnut stems. Transcriptional analysis revealed that deletion of cyp1 also reduced transcript levels for genes encoding key components of the heterotrimeric guanosine triphosphate-binding protein signalling pathway that are essential for sensing environmental cues and are involved in C. parasitica development and virulence.
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Affiliation(s)
- Min-Mei Chen
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, The Key Laboratory of Ministry of Education of China for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
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Ruan SL, Ma HS, Wang SH, Fu YP, Xin Y, Liu WZ, Wang F, Tong JX, Wang SZ, Chen HZ. Proteomic identification of OsCYP2, a rice cyclophilin that confers salt tolerance in rice (Oryza sativa L.) seedlings when overexpressed. BMC PLANT BIOLOGY 2011; 11:34. [PMID: 21324151 PMCID: PMC3050798 DOI: 10.1186/1471-2229-11-34] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 02/16/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND High Salinity is a major environmental stress influencing growth and development of rice. Comparative proteomic analysis of hybrid rice shoot proteins from Shanyou 10 seedlings, a salt-tolerant hybrid variety, and Liangyoupeijiu seedlings, a salt-sensitive hybrid variety, was performed to identify new components involved in salt-stress signaling. RESULTS Phenotypic analysis of one protein that was upregulated during salt-induced stress, cyclophilin 2 (OsCYP2), indicated that OsCYP2 transgenic rice seedlings had better tolerance to salt stress than did wild-type seedlings. Interestingly, wild-type seedlings exhibited a marked reduction in maximal photochemical efficiency under salt stress, whereas no such change was observed for OsCYP2-transgenic seedlings. OsCYP2-transgenic seedlings had lower levels of lipid peroxidation products and higher activities of antioxidant enzymes than wild-type seedlings. Spatiotemporal expression analysis of OsCYP2 showed that it could be induced by salt stress in both Shanyou 10 and Liangyoupeijiu seedlings, but Shanyou 10 seedlings showed higher OsCYP2 expression levels. Moreover, circadian rhythm expression of OsCYP2 in Shanyou 10 seedlings occurred earlier than in Liangyoupeijiu seedlings. Treatment with PEG, heat, or ABA induced OsCYP2 expression in Shanyou 10 seedlings but inhibited its expression in Liangyoupeijiu seedlings. Cold stress inhibited OsCYP2 expression in Shanyou 10 and Liangyoupeijiu seedlings. In addition, OsCYP2 was strongly expressed in shoots but rarely in roots in two rice hybrid varieties. CONCLUSIONS Together, these data suggest that OsCYP2 may act as a key regulator that controls ROS level by modulating activities of antioxidant enzymes at translation level. OsCYP2 expression is not only induced by salt stress, but also regulated by circadian rhythm. Moreover, OsCYP2 is also likely to act as a key component that is involved in signal pathways of other types of stresses-PEG, heat, cold, or ABA.
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Affiliation(s)
- Song-Lin Ruan
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Hua-Sheng Ma
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
| | - Shi-Heng Wang
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
| | - Ya-Ping Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Ya Xin
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
| | - Wen-Zhen Liu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Fang Wang
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
| | - Jian-Xin Tong
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
| | - Shu-Zhen Wang
- Plant Molecular Biology & Proteomics Lab, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, PR China
| | - Hui-Zhe Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
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Sekhar K, Priyanka B, Reddy VD, Rao KV. Isolation and characterization of a pigeonpea cyclophilin (CcCYP) gene, and its over-expression in Arabidopsis confers multiple abiotic stress tolerance. PLANT, CELL & ENVIRONMENT 2010; 33:1324-38. [PMID: 20374537 DOI: 10.1111/j.1365-3040.2010.02151.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A full-length cDNA clone of pigeonpea (Cajanus cajan L.) encoding cyclophilin (CcCYP) has been isolated from the cDNA library of plants subjected to drought stress. Amino acid sequence of CcCYP disclosed similarity with that of single-domain cytosolic cyclophilins of various organisms. Expression profile of CcCYP in pigeonpea plants is strongly induced by different abiotic stresses, indicating its stress-responsive nature. Compared to the control plants, the transgenic Arabidopsis lines expressing CcCYP exhibited high-level tolerance against major abiotic stresses, viz., drought, salinity and extreme temperatures as evidenced by increased plant survival, biomass, chlorophyll content and profuse root growth. The CcCYP transgenics, compared to the controls, revealed enhanced peptidyl-propyl cis-trans isomerase (PPIase) activity under stressed conditions, owing to transcriptional activation of stress-related genes besides intrinsic chaperonic activity of the cyclophilin. The transgenic plants subjected to salt stress exhibited higher Na(+) ion accumulation in roots as compared to shoots, while a reverse trend was observed in the salt-stressed control plants, implicating the involvement of CcCYP in the maintenance of ion homeostasis. Expression pattern of CcCYP:GFP fusion protein confirmed the localization of CcCYP predominantly in the nucleus as revealed by intense green fluorescence. The overall results amply demonstrate the implicit role of CcCYP in conferring multiple abiotic stress tolerance at whole-plant level.
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Affiliation(s)
- Kambakam Sekhar
- Centre for Plant Molecular Biology, Osmania University, Hyderabad 500007, AP, India
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Karan R, Singla-Pareek SL, Pareek A. Histidine kinase and response regulator genes as they relate to salinity tolerance in rice. Funct Integr Genomics 2009; 9:411-7. [PMID: 19277738 DOI: 10.1007/s10142-009-0119-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 02/13/2009] [Accepted: 02/13/2009] [Indexed: 12/13/2022]
Abstract
We have previously shown that Oryza sativa L. Pokkali maintains higher levels of transcripts under non-saline conditions, which are otherwise induced under salinity in the sensitive genotype-IR64. We wanted to test this hypothesis of differential gene regulation further, within the members of a given stress responsive gene family, which share significant structural and functional similarities. For this purpose, we chose to work on the two-component system (TCS family) which plays an important role in stress perception and signal transduction under hormonal, abiotic stress, light and developmental regulation. We present data to show that all members of TCS family, including sensory histidine kinases, phosphotransfer proteins and response regulators, are having differential transcript abundance (under both non-stress and salinity stress conditions) in contrasting rice genotypes. Further, under non-stress conditions, transcript abundance for all TCS members (except RR21) was found to be higher in the salt-tolerant genotype-Pokkali. TCS transcripts are otherwise induced by salinity stress to a relatively higher level in the sensitive cultivar IR64. A few of these members were also found to be localised within important salinity-related quantitative trait loci identified earlier. Based on the above findings, we propose that the TCS members may have a significant role in salinity tolerance in rice and can serve as useful 'candidate genes' for raising salinity-tolerant crop plants.
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Affiliation(s)
- Ratna Karan
- Stress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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