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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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Shumilak A, El-Shetehy M, Soliman A, Tambong JT, Daayf F. Goss's Wilt Resistance in Corn Is Mediated via Salicylic Acid and Programmed Cell Death but Not Jasmonic Acid Pathways. PLANTS (BASEL, SWITZERLAND) 2023; 12:1475. [PMID: 37050101 PMCID: PMC10097360 DOI: 10.3390/plants12071475] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
A highly aggressive strain (CMN14-5-1) of Clavibacter nebraskensis bacteria, which causes Goss's wilt in corn, induced severe symptoms in a susceptible corn line (CO447), resulting in water-soaked lesions followed by necrosis within a few days. A tolerant line (CO450) inoculated with the same strain exhibited only mild symptoms such as chlorosis, freckling, and necrosis that did not progress after the first six days following infection. Both lesion length and disease severity were measured using the area under the disease progression curve (AUDPC), and significant differences were found between treatments. We analyzed the expression of key genes related to plant defense in both corn lines challenged with the CMN14-5-1 strain. Allene oxide synthase (ZmAOS), a gene responsible for the production of jasmonic acid (JA), was induced in the CO447 line in response to CMN14-5-1. Following inoculation with CMN14-5-1, the CO450 line demonstrated a higher expression of salicylic acid (SA)-related genes, ZmPAL and ZmPR-1, compared to the CO447 line. In the CO450 line, four genes related to programmed cell death (PCD) were upregulated: respiratory burst oxidase homolog protein D (ZmrbohD), polyphenol oxidase (ZmPPO1), ras-related protein 7 (ZmRab7), and peptidyl-prolyl cis-trans isomerase (ZmPPI). The differential gene expression in response to CMN14-5-1 between the two corn lines provided an indication that SA and PCD are involved in the regulation of corn defense responses against Goss's wilt disease, whereas JA may be contributing to disease susceptibility.
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Affiliation(s)
- Alexander Shumilak
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Mohamed El-Shetehy
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Atta Soliman
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Genetics, Faculty of Agriculture, University of Tanta, Tanta 31527, Egypt
| | - James T Tambong
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Fouad Daayf
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Rose T, Wilkinson M, Lowe C, Xu J, Hughes D, Hassall KL, Hassani‐Pak K, Amberkar S, Noleto‐Dias C, Ward J, Heuer S. Novel molecules and target genes for vegetative heat tolerance in wheat. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2022; 3:264-289. [PMID: 37284432 PMCID: PMC10168084 DOI: 10.1002/pei3.10096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 06/08/2023]
Abstract
To prevent yield losses caused by climate change, it is important to identify naturally tolerant genotypes with traits and related pathways that can be targeted for crop improvement. Here we report on the characterization of contrasting vegetative heat tolerance in two UK bread wheat varieties. Under chronic heat stress, the heat-tolerant cultivar Cadenza produced an excessive number of tillers which translated into more spikes and higher grain yield compared to heat-sensitive Paragon. RNAseq and metabolomics analyses revealed that over 5000 genotype-specific genes were differentially expressed, including photosynthesis-related genes, which might explain the observed ability of Cadenza to maintain photosynthetic rate under heat stress. Around 400 genes showed a similar heat-response in both genotypes. Only 71 genes showed a genotype × temperature interaction. As well as known heat-responsive genes such as heat shock proteins (HSPs), several genes that have not been previously linked to the heat response, particularly in wheat, have been identified, including dehydrins, ankyrin-repeat protein-encoding genes, and lipases. Contrary to primary metabolites, secondary metabolites showed a highly differentiated heat response and genotypic differences. These included benzoxazinoid (DIBOA, DIMBOA), and phenylpropanoids and flavonoids with known radical scavenging capacity, which was assessed via the DPPH assay. The most highly heat-induced metabolite was (glycosylated) propanediol, which is widely used in industry as an anti-freeze. To our knowledge, this is the first report on its response to stress in plants. The identified metabolites and candidate genes provide novel targets for the development of heat-tolerant wheat.
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Affiliation(s)
| | | | | | | | | | | | | | - Sandeep Amberkar
- Rothamsted ResearchHarpendenUK
- Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | | | | | - Sigrid Heuer
- Rothamsted ResearchHarpendenUK
- National Institute of Agricultural Botany (NIAB)CambridgeUK
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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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Fan M, Zhang Y, Li X, Wu S, Yang M, Yin H, Liu W, Fan Z, Li J. Multi-Approach Analysis Reveals Pathways of Cold Tolerance Divergence in Camellia japonica. FRONTIERS IN PLANT SCIENCE 2022; 13:811791. [PMID: 35283896 PMCID: PMC8914472 DOI: 10.3389/fpls.2022.811791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Understanding the molecular mechanism of the cold response is critical to improve horticultural plant cold tolerance. Here, we documented the physiological, transcriptome, proteome, and hormonal dynamics to cold stress in temperate genotype (Tg) and subtropical genotype (Sg) populations of Camellia japonica. Tg C. japonica suffered minimal osmotic and oxidative damage compared to Sg C. japonica under the same cold treatment. Transcriptional and translational differences increased under the cold treatment, indicating that Tg C. japonica was affected by the environment and displayed both conserved and divergent mechanisms. About 60% of the genes responding to cold had similar dynamics in the two populations, but 1,896 transcripts and 455 proteins differentially accumulated in response to the cold between Tg and Sg C. japonica. Co-expression analysis showed that the ribosomal protein and genes related to photosynthesis were upregulated in Tg C. japonica, and tryptophan, phenylpropanoid, and flavonoid metabolism were regulated differently between the two populations under cold stress. The divergence of these genes reflected a difference in cold responsiveness. In addition, the decrease in the abscisic acid (ABA)/gibberellic acid (GA) ratio regulated by biosynthetic signal transduction pathway enhanced cold resistance in Tg C. japonica, suggesting that hormones may regulate the difference in cold responsiveness. These results provide a new understanding of the molecular mechanism of cold stress and will improve cold tolerance in horticultural plants.
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Affiliation(s)
| | | | - XinLei Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Bashyal BM, Parmar P, Zaidi NW, Aggarwal R. Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice ( Oryza sativa L.). Front Microbiol 2021; 12:655165. [PMID: 33927706 PMCID: PMC8076752 DOI: 10.3389/fmicb.2021.655165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host-T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.
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Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
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Moenga SM, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM, Cook DR. Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1195-1214. [PMID: 32920943 DOI: 10.1111/tpj.14988] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.
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Affiliation(s)
- Susan M Moenga
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Yunpeng Gai
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Laura M Perilla-Henao
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Douglas R Cook
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
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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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Comparative expression profiling reveals the role of the hot pepper apoplast under drought conditions. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00579-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sircar G, Bhowmik M, Sarkar RK, Najafi N, Dasgupta A, Focke-Tejkl M, Flicker S, Mittermann I, Valenta R, Bhattacharya K, Gupta Bhattacharya S. Molecular characterization of a fungal cyclophilin allergen Rhi o 2 and elucidation of antigenic determinants responsible for IgE-cross-reactivity. J Biol Chem 2019; 295:2736-2748. [PMID: 31882546 DOI: 10.1074/jbc.ra119.011659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/16/2019] [Indexed: 01/12/2023] Open
Abstract
Cyclophilins are structurally conserved pan-allergens showing extensive cross-reactivity. So far, no precise information on cross-reactive IgE-epitopes of cyclophilins is available. Here, an 18-kDa IgE-reactive cyclophilin (Rhi o 2) was purified from Rhizopus oryzae, an indoor mold causing allergic sensitization. Based on LC-MS/MS-derived sequences of natural Rhi o 2, the full-length cDNA was cloned, and expressed as recombinant (r) allergen. Purified rRhi o 2 displayed IgE-reactivity and basophil degranulation with sera from all cyclophilin-positive patients. The melting curve of properly folded rRhi o 2 showed partial refolding after heat denaturation. The allergen displayed monomeric functional peptidyl-prolyl cis-trans isomerase (PPIase) activity. In IgE-inhibition assays, rRhi o 2 exhibited extensive cross-reactivity with various other cyclophilins reported as allergens from diverse sources including its homologous human autoantigen. By generating a series of deletion mutants, a conserved 69-residue (Asn81-Asn149) fragment at C terminus of Rhi o 2 was identified as crucial for IgE-recognition and cross-reactivity. Grafting of the Asn81-Asn149 fragment within the primary structure of yeast cyclophilin CPR1 by replacing its homologous sequence resulted in a hybrid molecule with structural folds similar to Rhi o 2. The IgE-reactivity and allergenic activity of the hybrid cyclophilin were greater than that of CPR1. Therefore, the Asn81-Asn149 fragment can be considered as the site of IgE recognition of Rhi o 2. Hence, Rhi o 2 serves as a candidate antigen for the molecular diagnosis of mold allergy, and determination of a major cross-reactive IgE-epitope has clinical potential for the design of next-generation immunotherapeutics against cyclophilin-induced allergies.
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Affiliation(s)
- Gaurab Sircar
- Department of Botany, Visva-Bharati, Santiniketan 731235, India; Division of Plant Biology (Main campus), Bose Institute, 93/1 Acharya Prafulla Chandra Rd., Kolkata 700009, India.
| | - Moumita Bhowmik
- Division of Plant Biology (Main campus), Bose Institute, 93/1 Acharya Prafulla Chandra Rd., Kolkata 700009, India
| | | | - Nazanin Najafi
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Währinger Gürtel 18-20, A-1090 Vienna, Austria
| | - Angira Dasgupta
- Department of Chest Medicine, B. R. Singh Hospital and Center for Medical Education and Research, Kolkata 700014, India
| | - Margarete Focke-Tejkl
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Währinger Gürtel 18-20, A-1090 Vienna, Austria
| | - Sabine Flicker
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Währinger Gürtel 18-20, A-1090 Vienna, Austria
| | - Irene Mittermann
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Währinger Gürtel 18-20, A-1090 Vienna, Austria
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Währinger Gürtel 18-20, A-1090 Vienna, Austria; NRC Institute of Immunology FMBA of Russia, 115478 Moscow, Russia; Department of Clinical Immunology and Allergy, Sechenov First Moscow State Medical University, 119146 Moscow, Russian Federation
| | | | - Swati Gupta Bhattacharya
- Division of Plant Biology (Main campus), Bose Institute, 93/1 Acharya Prafulla Chandra Rd., Kolkata 700009, India.
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Liu S, Zenda T, Dong A, Yang Y, Liu X, Wang Y, Li J, Tao Y, Duan H. Comparative Proteomic and Morpho-Physiological Analyses of Maize Wild-Type Vp16 and Mutant vp16 Germinating Seed Responses to PEG-Induced Drought Stress. Int J Mol Sci 2019; 20:E5586. [PMID: 31717328 PMCID: PMC6888951 DOI: 10.3390/ijms20225586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 01/21/2023] Open
Abstract
Drought stress is a major abiotic factor compromising plant cell physiological and molecular events, consequently limiting crop growth and productivity. Maize (Zea mays L.) is among the most drought-susceptible food crops. Therefore, understanding the mechanisms underlying drought-stress responses remains critical for crop improvement. To decipher the molecular mechanisms underpinning maize drought tolerance, here, we used a comparative morpho-physiological and proteomics analysis approach to monitor the changes in germinating seeds of two incongruent (drought-sensitive wild-type Vp16 and drought-tolerant mutant vp16) lines exposed to polyethylene-glycol-induced drought stress for seven days. Our physiological analysis showed that the tolerant line mutant vp16 exhibited better osmotic stress endurance owing to its improved reactive oxygen species scavenging competency and robust osmotic adjustment as a result of greater cell water retention and enhanced cell membrane stability. Proteomics analysis identified a total of 1200 proteins to be differentially accumulated under drought stress. These identified proteins were mainly involved in carbohydrate and energy metabolism, histone H2A-mediated epigenetic regulation, protein synthesis, signal transduction, redox homeostasis and stress-response processes; with carbon metabolism, pentose phosphate and glutathione metabolism pathways being prominent under stress conditions. Interestingly, significant congruence (R2 = 81.5%) between protein and transcript levels was observed by qRT-PCR validation experiments. Finally, we propose a hypothetical model for maize germinating-seed drought tolerance based on our key findings identified herein. Overall, our study offers insights into the overall mechanisms underpinning drought-stress tolerance and provides essential leads into further functional validation of the identified drought-responsive proteins in maize.
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Affiliation(s)
- Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Xinyue Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yafei Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Jiao Li
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yongsheng Tao
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
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13
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Enzyme activity and structural features of three single-domain phloem cyclophilins from Brassica napus. Sci Rep 2019; 9:9368. [PMID: 31249367 PMCID: PMC6597583 DOI: 10.1038/s41598-019-45856-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/14/2019] [Indexed: 01/05/2023] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous prolyl cis/trans isomerases (PPIases). It was shown that plants possess the most diverse CYP families and that these are abundant in the phloem long-distance translocation stream. Since phloem exudate showed PPIase activity, three single-domain CYPs that occur in phloem samples from Brassica napus were characterised on functional and structural levels. It could be shown that they exhibit isomerase activity and that this activity is controlled by a redox regulation mechanism, which has been postulated for divergent CYPs. The structure determination by small-angle X-ray scattering experiments revealed a conserved globular shape. In addition, the high-resolution crystal structure of BnCYP19-1 was resolved and refined to 2.0 Å resolution, and the active sites of related CYPs as well as substrate binding were modelled. The obtained data and results support the hypothesis that single domain phloem CYPs are active phloem PPIases that may function as chaperones.
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14
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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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15
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Functional Analysis of Peptidyl-prolyl cis-trans Isomerase from Aspergillus flavus. Int J Mol Sci 2019; 20:ijms20092206. [PMID: 31060313 PMCID: PMC6539592 DOI: 10.3390/ijms20092206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
Aspergillus flavus, a ubiquitous filamentous fungus found in soil, plants and other substrates has been reported not only as a pathogen for plants, but also a carcinogen producing fungus for human. Peptidyl-Prolyl Isomerase (PPIases) plays an important role in cell process such as protein secretion cell cycle control and RNA processing. However, the function of PPIase has not yet been identified in A. flavus. In this study, the PPIases gene from A. flavus named ppci1 was cloned into expression vector and the protein was expressed in prokaryotic expression system. Activity of recombinant ppci1 protein was particularly inhibited by FK506, CsA and rapamycin. 3D-Homology model of ppci1 has been constructed with the template, based on 59.7% amino acid similarity. The homologous recombination method was used to construct the single ppci1 gene deletion strain Δppci1. We found that, the ppci1 gene plays important roles in A. flavus growth, conidiation, and sclerotia formation, all of which showed reduction in Δppci1 and increased in conidiation compared with the wild-type and complementary strains in A. flavus. Furthermore, aflatoxin and peanut seeds infection assays indicated that ppci1 contributes to virulence of A. flavus. Furthermore, we evaluated the effect of PPIase inhibitors on A. flavus growth, whereby these were used to treat wild-type strains. We found that the growths were inhibited under every inhibitor. All, these results may provide valuable information for designing inhibitors in the controlling infections of A. flavus.
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16
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Braga CB, Silva WGDP, Rittner R. Conformational preferences of N-acetyl-N′-methylprolineamide in different media: a 1H NMR and theoretical investigation. NEW J CHEM 2019. [DOI: 10.1039/c8nj05035j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational preferences and role of non-covalent interactions on the geometries of Ac–Pro–NHMe were elucidated in isolated phase and solution.
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Affiliation(s)
- Carolyne B. Braga
- Institute of Chemistry
- University of Campinas
- Campinas
- São Paulo 13083-970
- Brazil
| | | | - Roberto Rittner
- Institute of Chemistry
- University of Campinas
- Campinas
- São Paulo 13083-970
- Brazil
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17
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Štefanić PP, Cvjetko P, Biba R, Domijan AM, Letofsky-Papst I, Tkalec M, Šikić S, Cindrić M, Balen B. Physiological, ultrastructural and proteomic responses of tobacco seedlings exposed to silver nanoparticles and silver nitrate. CHEMOSPHERE 2018; 209:640-653. [PMID: 29958162 DOI: 10.1016/j.chemosphere.2018.06.128] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
Since silver nanoparticles (AgNPs) are a dominant nanomaterial in consumer products, there is growing concern about their impact on the environment. Although numerous studies on the effects of AgNPs on living organisms have been conducted, the interaction of AgNPs with plants has not been fully clarified. To reveal the plant mechanisms activated after exposure to AgNPs and to differentiate between effects specific to nanoparticles and ionic silver, we investigated the physiological, ultrastructural and proteomic changes in seedlings of tobacco (Nicotiana tabacum) exposed to commercial AgNPs and ionic silver (AgNO3) from the seed stage. A higher Ag content was measured in seedlings exposed to AgNPs than in those exposed to the same concentration of AgNO3. However, the results on oxidative stress parameters obtained revealed that, in general, higher toxicity was recorded in AgNO3-treated seedlings than in those exposed to nanosilver. Ultrastructural analysis of root cells confirmed the presence of silver in the form of nanoparticles, which may explain the lower toxicity of AgNPs. However, the ultrastructural changes of chloroplasts as well as proteomic study showed that both AgNPs and AgNO3 can affect photosynthesis. Moreover, the majority of the proteins involved in the primary metabolism were up-regulated after both types of treatments, indicating that enhanced energy production, which can be used to reinforce defensive mechanisms, enables plants to cope with silver-induced toxicity.
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Affiliation(s)
- Petra Peharec Štefanić
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Petra Cvjetko
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Renata Biba
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ana-Marija Domijan
- Department of Pharmaceutical Botany, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000, Zagreb, Croatia
| | - Ilse Letofsky-Papst
- Institute of Electron Microscopy and Nanoanalysis (FELMI), Graz University of Technology, Graz Centre for Electron Microscopy (ZFE), Austrian Cooperative Research (ACR), Steyrergasse 17, 8010, Graz, Austria
| | - Mirta Tkalec
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Sandra Šikić
- Department of Ecology, Andrija Štampar Teaching Institute of Public Health, Mirogojska cesta 16, 10000, Zagreb, Croatia
| | - Mario Cindrić
- Ruđer Bošković Institute, POB 1016, 10 000, Zagreb, Croatia
| | - Biljana Balen
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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18
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Bulgakov VP, Vereshchagina YV, Bulgakov DV, Veremeichik GN, Shkryl YN. The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense. Sci Rep 2018; 8:2285. [PMID: 29396465 PMCID: PMC5797197 DOI: 10.1038/s41598-018-20694-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/23/2018] [Indexed: 01/11/2023] Open
Abstract
The rolB plant oncogene of Agrobacterium rhizogenes perturbs many biochemical processes in transformed plant cells, thereby causing their neoplastic reprogramming. The oncogene renders the cells more tolerant to environmental stresses and herbicides and inhibits ROS elevation and programmed cell death. In the present work, we performed a proteomic analysis of Arabidopsis thaliana rolB-expressing callus line AtB-2, which represents a line with moderate expression of the oncogene. Our results show that under these conditions rolB greatly perturbs the expression of some chaperone-type proteins such as heat-shock proteins and cyclophilins. Heat-shock proteins of the DnaK subfamily were overexpressed in rolB-transformed calli, whereas the abundance of cyclophilins, members of the closely related single-domain cyclophilin family was decreased. Real-time PCR analysis of corresponding genes confirmed the reliability of proteomics data because gene expression correlated well with the expression of proteins. Bioinformatics analysis indicates that rolB can potentially affect several levels of signaling protein modules, including effector-triggered immunity (via the RPM1-RPS2 signaling module), the miRNA processing machinery, auxin and cytokinin signaling, the calcium signaling system and secondary metabolism.
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Affiliation(s)
- Victor P Bulgakov
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia. .,Far Eastern Federal University, Vladivostok, 690950, Russia.
| | - Yulia V Vereshchagina
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia
| | - Dmitry V Bulgakov
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia
| | - Galina N Veremeichik
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia
| | - Yuri N Shkryl
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia
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19
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Min CW, Lee SH, Cheon YE, Han WY, Ko JM, Kang HW, Kim YC, Agrawal GK, Rakwal R, Gupta R, Kim ST. In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism. J Proteomics 2017; 169:125-135. [PMID: 28669816 DOI: 10.1016/j.jprot.2017.06.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 01/23/2023]
Abstract
Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins. Of these identified proteins, 146 showed significant changes in protein abundance, where 5 and 141 had increased and decreased abundances, respectively while 352 proteins were completely degraded during CDT. Gene ontology and KEGG analyses suggested the association of differential proteins with primary metabolism, ROS detoxification, translation elongation and initiation, protein folding, and proteolysis, where most, if not all, had decreased abundance during CDT. Western blotting confirmed reduced level of antioxidant enzymes (DHAR, APx1, MDAR, and SOD) upon CDT. This in-depth integrated study reveals a major downshift in seed metabolism upon CDT. Reported data here serve as a resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality. BIOLOGICAL SIGNIFICANCE Controlled deterioration treatment (CDT) is one of the major events that negatively affects the quality and nutrient composition of agricultural seeds. However, the molecular mechanism of CDT is largely unknown. A combination of gel-based and gel-free proteomic approach was utilized to investigate the effects of CDT in soybean seeds. Moreover, we utilized protamine sulfate precipitation method for enrichment of low-abundance proteins, which are generally masked due to the presence of high-abundance seed storage proteins. Reported data here serve as resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Seo Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Ye Eun Cheon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Won Young Han
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Jong Min Ko
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Hang Won Kang
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Yong Chul Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea; National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1Tennodai, Tsukuba 305-8574, Ibaraki, Japan
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea.
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea.
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20
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Min CW, Lee SH, Cheon YE, Han WY, Ko JM, Kang HW, Kim YC, Agrawal GK, Rakwal R, Gupta R, Kim ST. In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.022 pmid: 28669816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Zhang H, Zhou KX, Wang WQ, Liu SJ, Song SQ. Proteome analysis reveals an energy-dependent central process for Populus×canadensis seed germination. JOURNAL OF PLANT PHYSIOLOGY 2017; 213:134-147. [PMID: 28384531 DOI: 10.1016/j.jplph.2017.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
Poplar (Populus×canadensis) seeds rapidly germinated in darkness at 10, 15, and 20°C and reached 50% seed germination after about 22, 4.5, and 3.5h, respectively. Germination of poplar seeds was markedly inhibited by abscisic acid (ABA) at 50μM and cycloheximide (CHX) at 100μM, and these inhibitive roles were temperature-dependent. In the present study, mature poplar seeds were used to investigate the differentially changed proteome of seeds germinating in water, ABA, and CHX. A total of 130 protein spots showed a significant change (1.5-fold increase/decrease, P<0.05) in abundance, and 101 protein spots were successfully identified. Most of the proteins were associated with cell defense and rescue (21%), storage proteins (21%), protein synthesis and destination (20%), metabolism (16%), and energy (14%). The germination of poplar seeds is closely related with the increase in those proteins involved in amino acid and lipid metabolism, the tricarboxylic acid cycle and pentose phosphate pathway, protein synthesis and destination, cell defense and rescue, and degradation of storage proteins. ABA and CHX inhibit the germination of poplar seeds by decreasing the protein abundance associated with protein proteolysis, protein folding, and storage proteins. We conclude that poplar seed germination is an energy-dependent active process, and is accompanied by increasing amino acid activation, protein synthesis and destination, as well as cell defense and rescue, and degradation of storage proteins.
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Affiliation(s)
- Hong Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ke-Xin Zhou
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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22
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Hanhart P, Thieß M, Amari K, Bajdzienko K, Giavalisco P, Heinlein M, Kehr J. Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. Sci Rep 2017; 7:1514. [PMID: 28473712 PMCID: PMC5431436 DOI: 10.1038/s41598-017-01596-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.
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Affiliation(s)
- Patrizia Hanhart
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Khalid Amari
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Krzysztof Bajdzienko
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Julia Kehr
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany.
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Spiegelman Z, Omer S, Mansfeld BN, Wolf S. Function of Cyclophilin1 as a long-distance signal molecule in the phloem of tomato plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:953-964. [PMID: 28053189 PMCID: PMC5444435 DOI: 10.1093/jxb/erw487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tomato (Solanum lycopersicum) diageotropica (dgt) mutants, containing a single mutation in the Cyclophilin1 (SlCyp1) gene, are auxin-insensitive, exhibiting a pleiotropic phenotype including lack of geotropism, abnormal xylem structure, lack of lateral roots (LRs), and elevated shoot-to-root ratio. SlCyp1 is a putative peptidyl-prolyl isomerase that can traffic from shoot to root, where it induces changes in auxin response, LR formation, and xylem development, suggesting it has a role as a long-distance signaling molecule. Here, we explored the mechanism underlying SlCyp1 function in the phloem. Expression of SlCyp1 under a phloem-specific (AtSuc2) promoter in dgt plants partially restored the wild-type phenotype, including lateral root development, root branching, and xylem morphology. The observed developmental changes were associated with physiological alternations at the whole-plant level, including a reduction in shoot-to-root ratio, enhanced transpiration, and elevated photosynthetic rates. Conversely, phloem-specific expression of SlCyp1 active-site mutants did not restore the wild-type phenotype. Local inhibition of cyclophilin functioning in the target tissue reduced auxin sensitivity, suggesting that its enzymatic activity in the distant organ is required for its action as a long-distance signalling agent. The data presented suggest that SlCyp1 is a signal molecule trafficking from shoot to root where its activity is required for auxin-mediated lateral root development.
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Affiliation(s)
- Ziv Spiegelman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, The Robert H. Smith Faculty of Agriculture, Food and Environment, Rehovot 76100, Israel
| | - Sumita Omer
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, The Robert H. Smith Faculty of Agriculture, Food and Environment, Rehovot 76100, Israel
| | - Ben N Mansfeld
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, The Robert H. Smith Faculty of Agriculture, Food and Environment, Rehovot 76100, Israel
| | - Shmuel Wolf
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, The Robert H. Smith Faculty of Agriculture, Food and Environment, Rehovot 76100, Israel
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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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