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Chiu T, Li Y. Polygalacturonase-inhibiting proteins as an exogenously applied natural solution for prevention of postharvest fungal infections. Synth Syst Biotechnol 2024; 9:481-493. [PMID: 38651095 PMCID: PMC11035021 DOI: 10.1016/j.synbio.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Polygalacturonase inhibiting proteins (PGIPs) are plant proteins involved in the inhibition of polygalacturonases (PGs), cell-wall degrading enzymes often secreted by phytopathogenic fungi. Previously, we confirmed that PGIP2 from Phaseolus vulgaris (PvPGIP2) can inhibit the growth of Aspergillus niger and Botrytis cinerea on agar plate. In this study, we further validated the feasibility of using PGIP as an environmental and ecological friendly agent to prevent fungal infection post-harvest. We found that application of either purified PGIP (full length PvPGIP2 or truncated tPvPGIP2_5-8), or PGIP-secreting Saccharomyces cerevisiae strains can effectively inhibit fungal growth and necrotic lesions on tobacco leaf. We also examined the effective amount and thermostability of PGIP when applied on plants. A concentration of 0.75 mg/mL or higher can significantly reduce the area of B. cinerea lesions. The activity of full-length PvPGIPs is not affected after incubation at various temperatures ranging from -20 to 42 °C for 24 h, while truncated tPvPGIP2_5-8 lost some efficacy after incubation at 42 °C. Furthermore, we have also examined the efficacy of PGIP on tomato fruit. When the purified PvPGIP2 proteins were applied to tomato fruit inoculated with B. cinerea at a concentration of roughly 1.0 mg/mL, disease incidence and area of disease had reduced by more than half compared to the controls without PGIP treatment. This study explores the potential of PGIPs as exogenously applied, eco-friendly fungal control agents on fruit and vegetables post-harvest.
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Affiliation(s)
- Tiffany Chiu
- Graduate Program in Genetics, Genomics, and Bioinformatics, 1140 Batchelor Hall, University of California Riverside, California, 92521, USA
| | - Yanran Li
- Program of Chemical Engineering, Department of Nanoengineering, University of California, San Diego, CA, 92521, USA
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Li ZX, Chen M, Miao YX, Li Q, Ren Y, Zhang WL, Lan JB, Liu YQ. The role of AcPGIP in the kiwifruit (Actinidia chinensis) response to Botrytis cinerea. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1254-1263. [PMID: 34600600 DOI: 10.1071/fp21054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/05/2021] [Indexed: 05/23/2023]
Abstract
Kiwifruit (Actinidia chinensis) is rich in nutritional and medicinal value. However, the organism responsible for grey mould, Botrytis cinerea, causes great economic losses and food safety problems to the kiwifruit industry. Understanding the molecular mechanism underlying postharvest kiwifruit responses to B. cinerea is important for preventing grey mould decay and enhancing resistance breeding. Kiwifruit cv. 'Hongyang' was used as experimental material. The AcPGIP gene was cloned and virus-induced gene silencing (VIGS) was used to explore the function of the polygalacturonase inhibiting protein (PGIP) gene in kiwifruit resistance to B. cinerea. Virus-induced silencing of AcPGIP resulted in enhanced susceptibility of kiwifruit to B. cinerea. Antioxidant enzymes, secondary metabolites and endogenous hormones were analysed to investigate kiwifruit responses to B. cinerea infection. Kiwifruit effectively activated antioxidant enzymes and secondary metabolite production in response to B. cinerea, which significantly increased Indole-3-acetic acid (IAA), gibberellin 3 (GA3) and abscisic acid (ABA) content relative to those in uninfected fruit. Silencing of AcPGIP enabled kiwifruit to quickly activate hormone-signaling pathways through an alternative mechanism to trigger defence responses against B. cinerea infection. These results expand our understanding of the regulatory mechanism for disease resistance in kiwifruit; further, they provide gene-resource reserves for molecular breeding of kiwifruit for disease resistance.
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Affiliation(s)
- Zhe-Xin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Min Chen
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | | | - Qiang Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Yun Ren
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Wen-Lin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Jian-Bin Lan
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
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Chiu T, Behari A, Chartron JW, Putman A, Li Y. Exploring the potential of engineering polygalacturonase-inhibiting protein as an ecological, friendly, and nontoxic pest control agent. Biotechnol Bioeng 2021; 118:3200-3214. [PMID: 34050940 PMCID: PMC8486366 DOI: 10.1002/bit.27845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/03/2021] [Accepted: 05/22/2021] [Indexed: 11/11/2022]
Abstract
In plants, polygalacturonase-inhibiting proteins (PGIPs) play critical roles for resistance to fungal disease by inhibiting the pectin-depolymerizing activity of endopolygalacturonases (PGs), one type of enzyme secreted by pathogens that compromises plant cell walls and leaves the plant susceptible to disease. Here, the interactions between PGIPs from Phaseolus vulgaris (PvPGIP1 and PvPGIP2) and PGs from Aspergillus niger (AnPG2), Botrytis cinerea (BcPG1 and BcPG2), and Fusarium moniliforme (FmPG3) were reconstituted through a yeast two hybrid (Y2H) system to investigate the inhibition efficiency of various PvPGIP1 and 2 truncations and mutants. We found that tPvPGIP2_5-8, which contains LRR5 to LRR8 and is only one-third the size of the full length peptide, exhibits the same level of interactions with AnPG and BcPGs as the full length PvPGIP2 via Y2H. The inhibitory activities of tPvPGIP2_5-8 on the growth of A. niger and B. cinerea were then examined and confirmed on pectin agar. On pectin assays, application of both full length PvPGIP2 and tPvPGIP2_5-8 clearly slows down the growth of A. niger and B. cinerea. Investigation on the sequence-function relationships of PGIP utilizing a combination of site directed mutagenesis and a variety of peptide truncations suggests that LRR5 could have the most essential structural feature for the inhibitory activities, and may be a possible target for the future engineering of PGIP with enhanced activity. This study highlights the potential of plant-derived PGIPs as a candidate for future in planta evaluation as a pest control agent.
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Affiliation(s)
- Tiffany Chiu
- Department of Chemical and Environmental Engineering, 900 University Avenue, Bourns Hall, Suite A220, Riverside, California 92521, USA
| | - Anita Behari
- Department of Microbiology and Plant Pathology, 900 University Avenue, Boyce Hall, Room 1415, Riverside, California 92521, USA
| | - Justin W. Chartron
- Department of Bioengineering, 900 University Avenue, MSE 205, Riverside, California 92521, USA
| | - Alexander Putman
- Department of Microbiology and Plant Pathology, 900 University Avenue, Boyce Hall, Room 1415, Riverside, California 92521, USA
| | - Yanran Li
- Department of Chemical and Environmental Engineering, 900 University Avenue, Bourns Hall, Suite A220, Riverside, California 92521, USA
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Tsvetkov VO, Yarullina LG. Structural and Functional Characteristics of Hydrolytic Enzymes of Phytophagon Insects and Plant Protein Inhibitors (Review). APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819050156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chen X, Chen Y, Zhang L, He Z, Huang B, Chen C, Zhang Q, Zuo S. Amino acid substitutions in a polygalacturonase inhibiting protein (OsPGIP2) increases sheath blight resistance in rice. RICE (NEW YORK, N.Y.) 2019; 12:56. [PMID: 31359264 PMCID: PMC6663954 DOI: 10.1186/s12284-019-0318-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/18/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND An economic strategy to control plant disease is to improve plant defense to pathogens by deploying resistance genes. Plant polygalacturonase inhibiting proteins (PGIPs) have a vital role in plant defense against phytopathogenic fungi by inhibiting fungal polygalacturonase (PG) activity. We previously reported that rice PGIP1 (OsPGIP1) inhibits PG activity in Rhizoctonia solani, the causal agent of rice sheath blight (SB), and is involved in regulating resistance to SB. RESULT Here, we report that OsPGIP2, the protein ortholog of OsPGIP1, does not possess PGIP activity; however, a few amino acid substitutions in a derivative of OsPGIP2, of which we provide support for L233F being the causative mutation, appear to impart OsPGIP2 with PG inhibition capability. Furthermore, the overexpression of mutated OsPGIP2L233F in rice significantly increased the resistance of transgenic lines and decreased SB disease rating scores. OsPGIP2L233F transgenic lines displayed an increased ability to reduce the tissue degradation caused by R. solani PGs as compared to control plants. Rice plants overexpressing OsPGIP2L233F showed no difference in agronomic traits and grain yield as compared to controls, thus demonstrating its potential use in rice breeding programs. CONCLUSIONS In summary, our results provide a new target gene for breeding SB resistance through genome-editing or natural allele mining.
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Affiliation(s)
- Xijun Chen
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
| | - Yuwen Chen
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Lina Zhang
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Zhen He
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Benli Huang
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Chen Chen
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Qingxia Zhang
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Shimin Zuo
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
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Chen X, Chen Y, Zhang L, He Z, Huang B, Chen C, Zhang Q, Zuo S. Amino acid substitutions in a polygalacturonase inhibiting protein (OsPGIP2) increases sheath blight resistance in rice. RICE (NEW YORK, N.Y.) 2019; 12:56. [PMID: 31359264 DOI: 10.1186/s12284-019-0318-316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/18/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND An economic strategy to control plant disease is to improve plant defense to pathogens by deploying resistance genes. Plant polygalacturonase inhibiting proteins (PGIPs) have a vital role in plant defense against phytopathogenic fungi by inhibiting fungal polygalacturonase (PG) activity. We previously reported that rice PGIP1 (OsPGIP1) inhibits PG activity in Rhizoctonia solani, the causal agent of rice sheath blight (SB), and is involved in regulating resistance to SB. RESULT Here, we report that OsPGIP2, the protein ortholog of OsPGIP1, does not possess PGIP activity; however, a few amino acid substitutions in a derivative of OsPGIP2, of which we provide support for L233F being the causative mutation, appear to impart OsPGIP2 with PG inhibition capability. Furthermore, the overexpression of mutated OsPGIP2L233F in rice significantly increased the resistance of transgenic lines and decreased SB disease rating scores. OsPGIP2L233F transgenic lines displayed an increased ability to reduce the tissue degradation caused by R. solani PGs as compared to control plants. Rice plants overexpressing OsPGIP2L233F showed no difference in agronomic traits and grain yield as compared to controls, thus demonstrating its potential use in rice breeding programs. CONCLUSIONS In summary, our results provide a new target gene for breeding SB resistance through genome-editing or natural allele mining.
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Affiliation(s)
- Xijun Chen
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
| | - Yuwen Chen
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Lina Zhang
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Zhen He
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Benli Huang
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Chen Chen
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Qingxia Zhang
- Horticulture and Plant Protection College, Yangzhou University, Yangzhou, 225009, China
| | - Shimin Zuo
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
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Liu N, Sun Y, Wang P, Duan H, Ge X, Li X, Pei Y, Li F, Hou Y. Mutation of key amino acids in the polygalacturonase-inhibiting proteins CkPGIP1 and GhPGIP1 improves resistance to Verticillium wilt in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:546-561. [PMID: 30053316 DOI: 10.1111/tpj.14048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
Verticillium wilt, one of the most devastating diseases of cotton (Gossypium hirsutum), causes severe yield and quality losses. Given the effectiveness of plant polygalacturonase-inhibiting proteins (PGIPs) in reducing fungal polygalacturonase (PG) activity, it is necessary to uncover the key functional amino acids to enhance cotton resistance to Verticillium dahliae. To identify novel antifungal proteins, the selectivity of key amino acids was investigated by screening against a panel of relevant PG-binding residues. Based on the obtained results, homologous models of the mutants were established. The docking models showed that hydrogen bonds and structural changes in the convex face in the conserved portion of leucine-rich repeats (LRRs) may be essential for enhanced recognition of PG. Additionally, we successfully constructed Cynanchum komarovii PGIP1 (CkPGIP1) mutants Asp176Val, Pro249Gln, and Asp176Val/Pro249Gln and G. hirsutum PGIP1 (GhPGIP1) mutants Glu169Val, Phe242Gln, and Glu169Val/Phe242Gln with site-directed mutagenesis. The proteins of interest can effectively inhibit VdPG1 activity and V. dahliae mycelial growth in a dose-dependent manner. Importantly, mutants that overproduced PGIP in Arabidopsis and cotton showed enhanced resistance to V. dahliae, with reduced Verticillium-associated chlorosis and wilting. Furthermore, the lignin content was measured in mutant-overexpressing plants, and the results showed enhanced lignification of the xylem, which blocked the spread of V. dahliae. Thus, using site-directed mutagenesis assays, we showed that mutations in CkPGIP1 and GhPGIP1 give rise to PGIP versatility, which allows evolving recognition specificities for PG and is required to promote Verticillium resistance in cotton by restricting the growth of invasive fungal pathogens.
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Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yun Sun
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Ping Wang
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Hongxia Duan
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiancai Li
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yakun Pei
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuxia Hou
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
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Liu N, Zhang X, Sun Y, Wang P, Li X, Pei Y, Li F, Hou Y. Molecular evidence for the involvement of a polygalacturonase-inhibiting protein, GhPGIP1, in enhanced resistance to Verticillium and Fusarium wilts in cotton. Sci Rep 2017; 7:39840. [PMID: 28079053 PMCID: PMC5228132 DOI: 10.1038/srep39840] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/29/2016] [Indexed: 01/29/2023] Open
Abstract
Polygalacturonase-inhibiting protein (PGIP), belonging to a group of plant defence proteins, specifically inhibits endopolygalacturonases secreted by pathogens. Herein, we showed that purified GhPGIP1 is a functional inhibitor of Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum, the two fungal pathogens causing cotton wilt. Transcription of GhPGIP1 was increased in cotton upon infection, wounding, and treatment with defence hormone and H2O2. Resistance by GhPGIP1 was examined by its virus-induced gene silencing in cotton and overexpression in Arabidopsis. GhPGIP1-silenced cotton was highly susceptible to the infections. GhPGIP1 overexpression in transgenic Arabidopsis conferred resistance to the infection, accompanied by enhanced expression of pathogenesis-related proteins (PRs), isochorismate synthase 1 (ICS1), enhanced disease susceptibility 1 (EDS1), and phytoalexin-deficient 4 (PAD4) genes. Transmission electron microscopy revealed cell wall alteration and cell disintegration in plants inoculated with polygalacturonase (PGs), implying its role in damaging the cell wall. Docking studies showed that GhPGIP1 interacted strongly with C-terminal of V. dahliae PG1 (VdPG1) beyond the active site but weakly interacted with C-terminal of F. oxysporum f. sp. vasinfectum (FovPG1). These findings will contribute towards the understanding of the roles of PGIPs and in screening potential combat proteins with novel recognition specificities against evolving pathogenic factors for countering pathogen invasion.
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Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, People’s Republic of China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, People’s Republic of China
| | - Yun Sun
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, People’s Republic of China
| | - Ping Wang
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, People’s Republic of China
| | - Xiancai Li
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, People’s Republic of China
| | - Yakun Pei
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, People’s Republic of China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, People’s Republic of China
| | - Yuxia Hou
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, People’s Republic of China
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Identification of Biomarkers for Resistance to Fusarium oxysporum f. sp. cubense Infection and in Silico Studies in Musa paradisiaca Cultivar Puttabale through Proteomic Approach. Proteomes 2016; 4:proteomes4010009. [PMID: 28248219 PMCID: PMC5217371 DOI: 10.3390/proteomes4010009] [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: 12/23/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 01/10/2023] Open
Abstract
Panama wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the major disease constraints of banana production. Previously, we reported the disease resistance Musa paradisiaca cv. puttabale clones developed from Ethylmethanesulfonate and Foc culture filtrate against Foc inoculation. Here, the same resistant clones and susceptible clones were used for the study of protein accumulation against Foc inoculation by two-dimensional gel electrophoresis (2-DE), their expression pattern and an in silico approach. The present investigation revealed mass-spectrometry identified 16 proteins that were over accumulated and 5 proteins that were under accumulated as compared to the control. The polyphosphoinositide binding protein ssh2p (PBPssh2p) and Indoleacetic acid-induced-like (IAA) protein showed significant up-regulation and down-regulation. The docking of the pathogenesis-related protein (PR) with the fungal protein endopolygalacturonase (PG) exemplify the three ionic interactions and seven hydrophobic residues that tends to good interaction at the active site of PG with free energy of assembly dissociation (1.5 kcal/mol). The protein-ligand docking of the Peptide methionine sulfoxide reductase chloroplastic-like protein (PMSRc) with the ligand β-1,3 glucan showed minimum binding energy (−6.48 kcal/mol) and docking energy (−8.2 kcal/mol) with an interaction of nine amino-acid residues. These explorations accelerate the research in designing the host pathogen interaction studies for the better management of diseases.
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Liu N, Ma X, Zhou S, Wang P, Sun Y, Li X, Hou Y. Molecular and Functional Characterization of a Polygalacturonase-Inhibiting Protein from Cynanchum komarovii That Confers Fungal Resistance in Arabidopsis. PLoS One 2016; 11:e0146959. [PMID: 26752638 PMCID: PMC4709088 DOI: 10.1371/journal.pone.0146959] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/23/2015] [Indexed: 02/03/2023] Open
Abstract
Compliance with ethical standards: This study did not involve human participants and animals, and the plant of interest is not an endangered species. Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat proteins that plants produce against polygalacturonase, a key virulence agent in pathogens. In this paper, we cloned and purified CkPGIP1, a gene product from Cynanchum komarovii that effectively inhibits polygalacturonases from Botrytis cinerea and Rhizoctonia solani. We found the expression of CkPGIP1 to be induced in response to salicylic acid, wounding, and infection with B. cinerea and R. solani. In addition, transgenic overexpression in Arabidopsis enhanced resistance against B. cinerea. Furthermore, CkPGIP1 obtained from transgenic Arabidopsis inhibited the activity of B. cinerea and R. solani polygalacturonases by 62.7-66.4% and 56.5-60.2%, respectively. Docking studies indicated that the protein interacts strongly with the B1-sheet at the N-terminus of the B. cinerea polygalacturonase, and with the C-terminus of the polygalacturonase from R. solani. This study highlights the significance of CkPGIP1 in plant disease resistance, and its possible application to manage fungal pathogens.
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Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Xiaowen Ma
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Sihong Zhou
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Ping Wang
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Yun Sun
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Xiancai Li
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Yuxia Hou
- College of Science, China Agricultural University, Beijing, 100193, China
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Liu N, Ma X, Zhou S, Wang P, Sun Y, Li X, Hou Y. Molecular and Functional Characterization of a Polygalacturonase-Inhibiting Protein from Cynanchum komarovii That Confers Fungal Resistance in Arabidopsis. PLoS One 2016. [PMID: 26752638 DOI: 10.1371/journal.pone.014695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Compliance with ethical standards: This study did not involve human participants and animals, and the plant of interest is not an endangered species. Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat proteins that plants produce against polygalacturonase, a key virulence agent in pathogens. In this paper, we cloned and purified CkPGIP1, a gene product from Cynanchum komarovii that effectively inhibits polygalacturonases from Botrytis cinerea and Rhizoctonia solani. We found the expression of CkPGIP1 to be induced in response to salicylic acid, wounding, and infection with B. cinerea and R. solani. In addition, transgenic overexpression in Arabidopsis enhanced resistance against B. cinerea. Furthermore, CkPGIP1 obtained from transgenic Arabidopsis inhibited the activity of B. cinerea and R. solani polygalacturonases by 62.7-66.4% and 56.5-60.2%, respectively. Docking studies indicated that the protein interacts strongly with the B1-sheet at the N-terminus of the B. cinerea polygalacturonase, and with the C-terminus of the polygalacturonase from R. solani. This study highlights the significance of CkPGIP1 in plant disease resistance, and its possible application to manage fungal pathogens.
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Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Xiaowen Ma
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Sihong Zhou
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Ping Wang
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Yun Sun
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Xiancai Li
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Yuxia Hou
- College of Science, China Agricultural University, Beijing, 100193, China
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Kalunke RM, Tundo S, Benedetti M, Cervone F, De Lorenzo G, D'Ovidio R. An update on polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein that protects crop plants against pathogens. FRONTIERS IN PLANT SCIENCE 2015; 6:146. [PMID: 25852708 PMCID: PMC4367531 DOI: 10.3389/fpls.2015.00146] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/23/2015] [Indexed: 05/20/2023]
Abstract
Polygalacturonase inhibiting proteins (PGIPs) are cell wall proteins that inhibit the pectin-depolymerizing activity of polygalacturonases secreted by microbial pathogens and insects. These ubiquitous inhibitors have a leucine-rich repeat structure that is strongly conserved in monocot and dicot plants. Previous reviews have summarized the importance of PGIP in plant defense and the structural basis of PG-PGIP interaction; here we update the current knowledge about PGIPs with the recent findings on the composition and evolution of pgip gene families, with a special emphasis on legume and cereal crops. We also update the information about the inhibition properties of single pgip gene products against microbial PGs and the results, including field tests, showing the capacity of PGIP to protect crop plants against fungal, oomycetes and bacterial pathogens.
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Affiliation(s)
- Raviraj M. Kalunke
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università della TusciaViterbo, Italy
| | - Silvio Tundo
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università della TusciaViterbo, Italy
| | - Manuel Benedetti
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di RomaRoma, Italy
| | - Felice Cervone
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di RomaRoma, Italy
| | - Giulia De Lorenzo
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di RomaRoma, Italy
- Giulia De Lorenzo, Dipartimento di Biologia e Biotecnologie “Charles Darwin,” Sapienza Università di Roma, Roma, Italy
| | - Renato D'Ovidio
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università della TusciaViterbo, Italy
- *Correspondence: Renato D'Ovidio, Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università Degli Studi Della Tuscia, 01100 Viterbo, Italy
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Prabhu SA, Singh R, Kolkenbrock S, Sujeeth N, El Gueddari NE, Moerschbacher BM, Kini RK, Wagenknecht M. Experimental and bioinformatic characterization of a recombinant polygalacturonase-inhibitor protein from pearl millet and its interaction with fungal polygalacturonases. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5033-47. [PMID: 24980909 PMCID: PMC4144779 DOI: 10.1093/jxb/eru266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Polygalacturonases (PGs) are hydrolytic enzymes employed by several phytopathogens to weaken the plant cell wall by degrading homopolygalacturonan, a major constituent of pectin. Plants fight back by employing polygalacturonase-inhibitor proteins (PGIPs). The present study compared the inhibition potential of pearl millet PGIP (Pennisetum glaucum; PglPGIP1) with the known inhibition of Phaseolus vulgaris PGIP (PvPGIP2) against two PGs, the PG-II isoform from Aspergillus niger (AnPGII) and the PG-III isoform from Fusarium moniliforme (FmPGIII). The key rationale was to elucidate the relationship between the extent of sequence similarity of the PGIPs and the corresponding PG inhibition potential. First, a pearl millet pgip gene (Pglpgip1) was isolated and phylogenetically placed among monocot PGIPs alongside foxtail millet (Setaria italica). Upstream sequence analysis of Pglpgip1 identified important cis-elements responsive to light, plant stress hormones, and anoxic stress. PglPGIP1, heterologously produced in Escherichia coli, partially inhibited AnPGII non-competitively with a pH optimum between 4.0 and 4.5, and showed no inhibition against FmPGIII. Docking analysis showed that the concave surface of PglPGIP1 interacted strongly with the N-terminal region of AnPGII away from the active site, whereas it weakly interacted with the C-terminus of FmPGIII. Interestingly, PglPGIP1 and PvPGIP2 employed similar motif regions with few identical amino acids for interaction with AnPGII at non-substrate-binding sites; however, they engaged different regions of AnPGII. Computational mutagenesis predicted D126 (PglPGIP1)-K39 (AnPGII) to be the most significant binding contact in the PglPGIP1-AnPGII complex. Such protein-protein interaction studies are crucial in the future generation of designer host proteins for improved resistance against ever-evolving pathogen virulence factors.
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Affiliation(s)
- S Ashok Prabhu
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore-570 006, Karnataka, India Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Ratna Singh
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Stephan Kolkenbrock
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Neerakkal Sujeeth
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nour Eddine El Gueddari
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Bruno M Moerschbacher
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Ramachandra K Kini
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore-570 006, Karnataka, India
| | - Martin Wagenknecht
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
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Yang L, Wu K, Gao P, Liu X, Li G, Wu Z. GsLRPK, a novel cold-activated leucine-rich repeat receptor-like protein kinase from Glycine soja, is a positive regulator to cold stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 215-216:19-28. [PMID: 24388511 DOI: 10.1016/j.plantsci.2013.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/12/2013] [Accepted: 10/17/2013] [Indexed: 05/11/2023]
Abstract
Plant LRR-RLKs serve as protein interaction platforms, and as regulatory modules of protein activation. Here, we report the isolation of a novel plant-specific LRR-RLK from Glycine soja (termed GsLRPK) by differential screening. GsLRPK expression was cold-inducible and shows Ser/Thr protein kinase activity. Subcellular localization studies using GFP fusion protein indicated that GsLRPK is localized in the plasma membrane. Real-time PCR analysis indicated that temperature, salt, drought, and ABA treatment can alter GsLRPK gene transcription in G. soja. However, just protein induced by cold stress not by salinity and ABA treatment in tobacco was found to possess kinase activity. Furthermore, we found that overexpression of GsLRPK in yeast and Arabidopsis can enhance resistance to cold stress and increase the expression of a number of cold responsive gene markers.
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Affiliation(s)
- Liang Yang
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, Fujian, China
| | - Kangcheng Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, Fujian, China
| | - Peng Gao
- College of Horticulture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Xiaojuan Liu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, Fujian, China
| | - Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, Fujian, China.
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Maulik A, Basu S. Study of Q224K, V152G double mutation in bean PGIP2, an LRR protein for plant defense--an in silico approach. Proteins 2012; 81:852-62. [PMID: 23255146 DOI: 10.1002/prot.24243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 11/22/2012] [Accepted: 11/29/2012] [Indexed: 11/11/2022]
Abstract
Polygalacturonase inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins from plants that are organized into multigene families. They act as specific inhibitors against Polygalacturonases (PGs) from phytopathogens and share high sequence identity within species. We performed in silico mutation (Q224K and V152G) in PGIP2 from Phaseolus vulgaris to corresponding residues of another member, PGIP1. This mutation is known to cause 100% loss of inhibition against the PG of fungus Fusarium phyllophilum (Fp). A comparative analysis between PGIP2 and the double mutant, using 50 ns molecular dynamics simulations explored structural difference affecting PG binding properties. Simulations revealed that the mutation at 224, strains this residue which acts as a lock for the PGIP-PG complex through main chain H-bond. Changes in secondary structural elements and strain in the bend region along the convex face of the solenoidal protein affected the flexibility of the mutant protein. At the concave interacting face of the mutant, subtle changes in the sidechain behavior of the PG-binding residues occurred in a concerted manner revealing flipping of aromatic rings to be crucial to avoid steric clash with FpPG in PGIP2. Docking PGIP2 and the mutant protein individually to FpPG illustrated the inability of the latter to inhibit FpPG leaving its active site free. Our study demonstrates that the effect of mutation affects the flexibility of the protein along the convex face, while binding specificity is altered through the concave face imparting minimal change in the typical structure supported by the LRRs.
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Affiliation(s)
- Aditi Maulik
- Department of Biotechnology, School of Biotechnology and Biological Sciences, West Bengal University of Technology, Salt Lake, Kolkata, India
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Maulik A, Sarkar AI, Devi S, Basu S. Polygalacturonase-inhibiting proteins--leucine-rich repeat proteins in plant defence. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14 Suppl 1:22-30. [PMID: 22039764 DOI: 10.1111/j.1438-8677.2011.00501.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Plant polygalacturonase-inhibiting proteins (PGIPs) belong to the leucine-rich repeat (LRR) family and are known to prevent pathogen invasion by inhibiting the plant cell wall degrading enzyme, polygalacturonase. Our study reveals that these multigene-encoded defence proteins found in flowering plants only exhibit identical domain architecture with 10 tandemly-arranged LRRs. This implies that variations of PGIP inhibitory properties are not associated with the number of the repeats but with subtle changes in the sequence content of the repeats. The first and eighth repeat contain more mutations compared to the strict conservation of the plant-specific LRRs or any repeat at other positions. Each of these repeats forms a separate cluster in the phylogenetic tree, both within and across plant families, thus suggesting uniqueness with respect to their position. A study of the genes encoding PGIPs, shows the existence of two categories (i) single exon and hence no intron; and (ii) two exons with an intron in between. Analyses of the intron phase and correlation of the exon-intron structure with the compact structural modules in PGIPs support insertion of introns in the pre-existing single exon genes and thus the intron late model. Lack of conservation of phase across families and formation of individual clusters for each family in the phylogenetic tree drawn with the intron sequences illustrate the event of insertion that took place separately in each of these families.
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Affiliation(s)
- A Maulik
- Department of Biotechnology, School of Biotechnology and Biological Sciences, West Bengal University of Technology, Salt Lake, Kolkata, India
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Lara-Márquez A, Zavala-Páramo MG, López-Romero E, Calderón-Cortés N, López-Gómez R, Conejo-Saucedo U, Cano-Camacho H. Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianum and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms. BMC Microbiol 2011; 11:260. [PMID: 22151976 PMCID: PMC3271051 DOI: 10.1186/1471-2180-11-260] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 12/09/2011] [Indexed: 11/10/2022] Open
Abstract
Background Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera Aspergillus and Penicillium and from some pathogens such as Colletotrichum gloeosporioides. The organism used in the present study, Colletotrichum lindemuthianum, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, Phaseolus vulgaris. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively. Results Here we report the isolation and sequence analysis of the Clpnl2 gene, which encodes the pectin lyase 2 of C. lindemuthianum, and its expression in pathogenic and non-pathogenic races of C. lindemuthianum grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from C. gloeosporioides. Conclusions The Clpnl2 gene of C. lindemuthianum shares the characteristic elements of genes coding for pectin lyases. A time-course analysis revealed significant differences between the two fungal races in terms of the expression of Clpnl2 encoding for pectin lyase 2. According to the results, pectin lyases from bacteria and fungi separated early during evolution. Likewise, the enzymes from fungi and oomycetes diverged in accordance with their differing lifestyles. It is possible that the diversity and nature of the assimilatory carbon substrates processed by these organisms played a determinant role in this phenomenon.
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Affiliation(s)
- Alicia Lara-Márquez
- Centro Multidisciplinario de Estudios en Biotecnología, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, Tarímbaro, C.P. 58000, Michoacán, México
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Clemente-Casares P, López-Jiménez AJ, Bellón-Echeverría I, Encinar JA, Martínez-Alfaro E, Pérez-Flores R, Mas A. De novo polymerase activity and oligomerization of hepatitis C virus RNA-dependent RNA-polymerases from genotypes 1 to 5. PLoS One 2011; 6:e18515. [PMID: 21490973 PMCID: PMC3072391 DOI: 10.1371/journal.pone.0018515] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/04/2011] [Indexed: 01/20/2023] Open
Abstract
Hepatitis C virus (HCV) shows a great geographical diversity reflected in the high number of circulating genotypes and subtypes. The response to HCV treatment is genotype specific, with the predominant genotype 1 showing the lowest rate of sustained virological response. Virally encoded enzymes are candidate targets for intervention. In particular, promising antiviral molecules are being developed to target the viral NS3/4A protease and NS5B polymerase. Most of the studies with the NS5B polymerase have been done with genotypes 1b and 2a, whilst information about other genotypes is scarce. Here, we have characterized the de novo activity of NS5B from genotypes 1 to 5, with emphasis on conditions for optimum activity and kinetic constants. Polymerase cooperativity was determined by calculating the Hill coefficient and oligomerization through a new FRET-based method. The Vmax/Km ratios were statistically different between genotype 1 and the other genotypes (p<0.001), mainly due to differences in Vmax values, but differences in the Hill coefficient and NS5B oligomerization were noted. Analysis of sequence changes among the studied polymerases and crystal structures show the αF helix as a structural component probably involved in NS5B-NS5B interactions. The viability of the interaction of αF and αT helixes was confirmed by docking studies and calculation of electrostatic surface potentials for genotype 1 and point mutants corresponding to mutations from different genotypes. Results presented in this study reveal the existence of genotypic differences in NS5B de novo activity and oligomerization. Furthermore, these results allow us to define two regions, one consisting of residues Glu128, Asp129, and Glu248, and the other consisting of residues of αT helix possibly involved in NS5B-NS5B interactions.
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Affiliation(s)
- Pilar Clemente-Casares
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
| | - Alberto J. López-Jiménez
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
- Infectious Disease Unit, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Itxaso Bellón-Echeverría
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
| | - José Antonio Encinar
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Elisa Martínez-Alfaro
- Infectious Disease Unit, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Ricardo Pérez-Flores
- Digestive Department, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Antonio Mas
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
- * E-mail:
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Ranganathan S, Eisenhaber F, Tong JC, Tan TW. Extending Asia Pacific bioinformatics into new realms in the "-omics" era. BMC Genomics 2009; 10 Suppl 3:S1. [PMID: 19958472 PMCID: PMC2788361 DOI: 10.1186/1471-2164-10-s3-s1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.
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