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Gulzar RMA, Ren CX, Fang X, Xu YP, Saand MA, Cai XZ. Glutamate Receptor-like (GLR) Family in Brassica napus: Genome-Wide Identification and Functional Analysis in Resistance to Sclerotinia sclerotiorum. Int J Mol Sci 2024; 25:5670. [PMID: 38891858 PMCID: PMC11172227 DOI: 10.3390/ijms25115670] [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: 04/19/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Plant glutamate receptor-like channels (GLRs) are homologs of animal ionotropic glutamate receptors. GLRs are critical in various plant biological functions, yet their genomic features and functions in disease resistance remain largely unknown in many crop species. Here, we report the results on a thorough genome-wide study of the GLR family in oilseed rape (Brassica napus) and their role in resistance to the fungal pathogen Sclerotinia sclerotiorum. A total of 61 GLRs were identified in oilseed rape. They comprised three groups, as in Arabidopsis thaliana. Detailed computational analyses, including prediction of domain and motifs, cellular localization, cis-acting elements, PTM sites, and amino acid ligands and their binding pockets in BnGLR proteins, unveiled a set of group-specific characteristics of the BnGLR family, which included chromosomal distribution, motif composition, intron number and size, and methylation sites. Functional dissection employing virus-induced gene silencing of BnGLRs in oilseed rape and Arabidopsis mutants of BnGLR homologs demonstrated that BnGLR35/AtGLR2.5 positively, while BnGLR12/AtGLR1.2 and BnGLR53/AtGLR3.2 negatively, regulated plant resistance to S. sclerotiorum, indicating that GLR genes were differentially involved in this resistance. Our findings reveal the complex involvement of GLRs in B. napus resistance to S. sclerotiorum and provide clues for further functional characterization of BnGLRs.
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Affiliation(s)
- Rana Muhammad Amir Gulzar
- Key Laboratory of Biology and Ecological Control of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chun-Xiu Ren
- Key Laboratory of Biology and Ecological Control of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi Fang
- Key Laboratory of Biology and Ecological Control of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - Mumtaz Ali Saand
- Department of Botany, Shah Abdul Latif University, Khairpur 66020, Sindh, Pakistan
| | - Xin-Zhong Cai
- Key Laboratory of Biology and Ecological Control of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
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2
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Chai L, Li H, Zhao X, Cui C, Zheng B, Zhang K, Jiang J, Zhang J, Jiang L. Analysis of Altered Flowering Related Genes in a Multi-Silique Rapeseed ( Brassica napus L.) Line zws-ms Based on Combination of Genome, Transcriptome and Proteome Data. PLANTS (BASEL, SWITZERLAND) 2023; 12:2429. [PMID: 37446989 DOI: 10.3390/plants12132429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
Based on previous researches, we further investigated the multi-silique trait in rapeseed (Brassica napus L.) line zws-ms. In this study, we used a relatively comprehensive list of flowering related genes in rapeseed and compared them between zws-ms and its near-isogenic line (NIL) zws-217. Genes were studied on genome, transcriptome and proteome levels and then we focused on genes with non-synonymous single nucleotide polymorphism (SNP) or frame-shift insertion-deletion (InDel), finding some genes on the list which changes their sequences. Then, combined with their annotation and the information of their orthologs, certain genes such as BnaA09g05900D, ortholog of AGAMOUS-LIKE 42 (AGL42), which encodes an MADS-box protein, were assumed as probably responsible for the multi-silique trait. Also, we analyzed the Differentially Accumulated Proteins (DAPs) between zws-ms and zws-217, revealing some genes involved in homologous recombination and mismatch repair pathways. Since the development of flowers/siliques is crucial to crops and it influences the yield of rapeseed, this study paved a way to deeply understand the mechanism of the multi-pistil flower formation, which may facilitate researches on rapeseed production in future.
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Affiliation(s)
- Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Xiaoguang Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, China
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Ka Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jinfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
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Yadav BG, Aakanksha, Kumar R, Yadava SK, Kumar A, Ramchiary N. Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops. J Proteome Res 2023; 22:660-680. [PMID: 36786770 DOI: 10.1021/acs.jproteome.2c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.
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Affiliation(s)
- Bal Govind Yadav
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Aakanksha
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, Delhi, India
| | - Rahul Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi 110021, Delhi, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671316, Kerala, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
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Yu R, Zhang M, Ahmed T, Wu Z, Lv L, Zhou G, Li B. Metabolic and Proteomic Profiles Reveal the Response of the ASD-Associated Resistant Strain 6-1 of Lactobacillus plantarum to Propionic Acid. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:17020. [PMID: 36554909 PMCID: PMC9779356 DOI: 10.3390/ijerph192417020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/26/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Autism spectrum disorder (ASD) seriously affects children's health. In our previous study, we isolated and identified a bacterium (Lactobacillus plantarum strain 6-1) that is resistant to propionic acid (PA), which has been reported to play a significant role in the formation of ASD. In order to elucidate the mechanism of the resistance to PA, this study investigated the change in the metabolic and proteomic profile of L. plantarum strain 6-1 in the presence and absence of PA. The results show that 967 and 1078 proteins were specifically identified in the absence and the presence of PA, respectively, while 616 proteins were found under both conditions. Gene ontology enrichment analysis of 130 differentially expressed proteins accumulated in the presence and absence of PA indicated that most of the proteins belong to biological processes, cellular components, and molecular functions. Pathway enrichment analysis showed a great reduction in the metabolic pathway-related proteins when this resistant bacterium was exposed to PA compared to the control. Furthermore, there was an obvious difference in protein-protein interaction networks in the presence and the absence of propionic acid. In addition, there was a change in the metabolic profile of L. plantarum strain 6-1 when this bacterium was exposed to PA compared to the control, while six peaks at 696.46, 1543.022, 1905.241, 2004.277, 2037.374, and 2069.348 m/z disappeared. Overall, the results could help us to understand the mechanism of the resistance of gut bacteria to PA, which will provide a new insight for us to use PA-resistant bacteria to prevent the development of ASD in children.
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Affiliation(s)
- Rongrong Yu
- College of Education, Zhejiang University of Technology, Hangzhou 310032, China
| | - Muchen Zhang
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhifeng Wu
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luqiong Lv
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guoling Zhou
- Hangzhou Seventh People’s Hospital (HSPH), Hangzhou 310013, China
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Zhang X, Li X, Li H, Wang Z, Xia R, Hu J, Wang P, Zhou X, Wan L, Hong D, Yang G. Quantitative trait locus mapping and improved resistance to sclerotinia stem rot in a backbone parent of rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1056206. [PMID: 36438142 PMCID: PMC9684713 DOI: 10.3389/fpls.2022.1056206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
There are three main challenges to improving sclerotinia stem rot (SSR) resistance in rapeseed (Brassica napus L.). First, breeding materials such as the backbone parents have not been extensively investigated, making the findings of previous studies difficult to directly implement. Second, SSR resistance and flowering time (FT) loci are typically linked; thus, use of these loci requires sacrifice of the rapeseed growth period. Third, the SSR resistance loci in susceptible materials are often neglected, thereby reducing the richness of resistant resources. This study was conducted to investigate the stem resistance, disease index, and FT of a doubled haploid population consisting of 151 lines constructed from the backbone parent 19514A and conventional rapeseed cultivar ZY50 within multiple environments. Quantitative trait locus (QTL) mapping revealed 13 stem resistance QTLs, 9 disease index QTLs, and 20 FT QTLs. QTL meta-analysis showed that uqA04, uqC03.1, and uqC03.2 were repeatable SSR resistance QTLs derived from different parents but not affected by the FT. Based on these three QTLs, we proposed a strategy for improving the SSR resistance of 19514A and ZY50. This study improves the understanding of the resistance to rapeseed SSR and genetic basis of FT and demonstrates that SSR resistance QTLs can be mined from parents with a minimal resistance level difference, thereby supporting the application of backbone parents in related research and resistance improvement.
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Affiliation(s)
- Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Huining Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhuanrong Wang
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Rui Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jin Hu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xianming Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
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6
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He YH, Zhang ZR, Xu YP, Chen SY, Cai XZ. Genome-Wide Identification of Rapid Alkalinization Factor Family in Brassica napus and Functional Analysis of BnRALF10 in Immunity to Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2022; 13:877404. [PMID: 35592581 PMCID: PMC9113046 DOI: 10.3389/fpls.2022.877404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Rapid alkalinization factors (RALFs) were recently reported to be important players in plant immunity. Nevertheless, the signaling underlying RALF-triggered immunity in crop species against necrotrophic pathogens remains largely unknown. In this study, RALF family in the important oil crop oilseed rape (Brassica napus) was identified and functions of BnRALF10 in immunity against the devastating necrotrophic pathogen Sclerotinia sclerotiorum as well as the signaling underlying this immunity were revealed. The oilseed rape genome carried 61 RALFs, half of them were atypical, containing a less conserved YISY motif and lacking a RRXL motif or a pair of cysteines. Family-wide gene expression analyses demonstrated that patterns of expression in response to S. sclerotiorum infection and DAMP and PAMP treatments were generally RALF- and stimulus-specific. Most significantly responsive BnRALF genes were expressionally up-regulated by S. sclerotiorum, while in contrast, more BnRALF genes were down-regulated by BnPep5 and SsNLP1. These results indicate that members of BnRALF family are likely differentially involved in plant immunity. Functional analyses revealed that BnRALF10 provoked diverse immune responses in oilseed rape and stimulated resistance to S. sclerotiorum. These data support BnRALF10 to function as a DAMP to play a positive role in plant immunity. BnRALF10 interacted with BnFER. Silencing of BnFER decreased BnRALF10-induced reactive oxygen species (ROS) production and compromised rape resistance to S. sclerotiorum. These results back BnFER to be a receptor of BnRALF10. Furthermore, quantitative proteomic analysis identified dozens of BnRALF10-elicited defense (RED) proteins, which respond to BnRALF10 in protein abundance and play a role in defense. Our results revealed that BnRALF10 modulated the abundance of RED proteins to fine tune plant immunity. Collectively, our results provided some insights into the functions of oilseed rape RALFs and the signaling underlying BnRALF-triggered immunity.
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Affiliation(s)
- Yu-Han He
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhuo-Ran Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang University, Hangzhou, China
| | - Song-Yu Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xin-Zhong Cai
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
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Wang L, Liu F, Ju L, Xue B, Wang Y, Wang D, Hou D. Genome Structures and Evolution Analysis of Hsp90 Gene Family in Brassica napus Reveal the Possible Roles of Members in Response to Salt Stress and the Infection of Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2022; 13:854034. [PMID: 35463405 PMCID: PMC9022010 DOI: 10.3389/fpls.2022.854034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Heat shock proteins 90 (Hsp90s) are conserved proteins participating in the responses to heat stress and are found to be involved in different kinds of abiotic and biotic stresses. Brassica napus (B. napus) is an important heteropolyploid crop, producing edible oil. Salt stress is one of the most important hazards to the growth of rape in the world, while Sclerotinia stem rot is one of the most serious diseases, caused by Sclerotinia sclerotiorum (S. sclerotiorum). In this study, the evolution of Hsp90 genes and their responses to these two stresses were elucidated. Bioinformatic analysis through the whole genome of B. napus identified 35 Hsp90 gene family members. Five groups were obtained via phylogenetic analysis with the 35 Hsp genes, Hsps from its two ancestor species Brassica rapa, Brassica oleracea, and AtHsps. Gene structure and conservative motif analysis of these 35 Hsps indicated that the Hsps were relatively conservative in each group. Strong collinearity was also detected between the genomes of Brassica rapa, Brassica oleracea and B. napus, along with identifying syntenic gene pairs of Hsps among the three genomes. In addition, whole genome duplication was discovered as the main reason for the generation of BnHsp gene family. The analysis of cis-acting elements indicated that BnHsp90 might be involved in a variety of abiotic and biotic stress responses. Analysis of the expression pattern indicated that BnHsp90 participates in the responses of B. napus to salt stress and the infection of S. sclerotiorum. Fourteen and nine BnHsp90s were validated to be involved in the defense responses of B. napus against salt stress and S. sclerotiorum, respectively. Our results provide new insights for the roles of BnHsp90s in the responses of B. napus to salt stress and S. sclerotiorum.
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Affiliation(s)
- Long Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Fei Liu
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Lingyue Ju
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Bing Xue
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yongfeng Wang
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Daojie Wang
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- College of Agriculture, Henan University, Kaifeng, China
| | - Dianyun Hou
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
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Liu X, An L, Ren S, Zhou Y, Peng W. Comparative Proteomic Analysis Reveals Antibacterial Mechanism of Patrinia scabiosaefolia Against Methicillin Resistant Staphylococcus epidermidis. Infect Drug Resist 2022; 15:883-893. [PMID: 35281570 PMCID: PMC8912936 DOI: 10.2147/idr.s350715] [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: 11/22/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose As a kind of opportunist pathogen, Staphylococcus epidermidis (MRSE) can cause nosocomial infections and easily evolve into resistant bacteria. Among these, methicillin-resistant Staphylococcus epidermidis (MRSE) exhibit significantly higher rates. Our previous study showed that Patrinia scabiosaefolia (PS) possessed strong antibacterial activity against MRSE. However, the mechanism of PS against MRSE is not clear. Methods Here, a tandem mass tag-based (TMT) proteomic analysis was performed to elucidate the potential mechanism of PS against MRSE. We compared the differential expression proteins of MRSE under PS stress. Results Based on a fold change of >1.2 or < 1/1.2 (with p value set at <0.05), a total of 248 proteins (128 up-regulated proteins, 120 down-regulated proteins) were identified. Bioinformatic analysis showed that proteins including arginine deiminase (arcA), ornithine carbamoyltransferase (arcB) and carbamate kinase (arcC), serine–tRNA ligase (serS), phenylalanine–tRNA ligase beta and subunit (pheT), DltD (dlt), d-alanyl carrier protein (dlt), accumulation-associated protein (SasG), serine-aspartate repeat-containing protein C (SdrC) and hemin transport system permease protein HrtB (VraG) played important roles in mechanism of PS against MRSE. Conclusion In summary, these results indicated that arginine deiminase pathway (ADI) pathway, protein synthesis, cell wall synthesis, biofilm formation and uptake of iron were related to mechanisms of PS against MRSE. Our findings provide an insight into the the mechanism of PS against MRSE, and may be valuable in offering new targets to develop more anti-MRSE drugs.
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Affiliation(s)
- Xin Liu
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
- Correspondence: Xin Liu, College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China, Tel +8618886056643, Email
| | - Lili An
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Shuaijun Ren
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Yonghui Zhou
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Wei Peng
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
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9
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Teng Z, Yu Y, Zhu Z, Hong SB, Yang B, Zang Y. Melatonin elevated Sclerotinia sclerotiorum resistance via modulation of ATP and glucosinolate biosynthesis in Brassica rapa ssp. pekinensis. J Proteomics 2021; 243:104264. [PMID: 33992838 DOI: 10.1016/j.jprot.2021.104264] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/13/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
Sclerotinia stem rot is a common disease found in Brassica rapa that is caused by the necrotic plant pathogen Sclerotinia sclerotiorum. Melatonin (MT) has known biological activity and effectively relieved this type of Sclerotinia stem rot in B. rapa. To better understand the mechanisms behind MT-induced S. sclerotiorum resistance in B. rapa, we performed both proteomic and metabolomic analysis. Our results showed that during S. sclerotiorum infection, thiamine synthesis was activated and defended against it. In infected leaves, ribosomal synthesis-related proteins responded positively to MT treatment. Integrated proteomic and metabolomic analysis showed that amino acid metabolism was activated by MT treatment. After MT treatment, adenosine-triphosphate (ATP) content and the activity of antioxidant enzymes were both increased in B. rapa infected leaves. Cysteine synthase, sulfur transfer-related proteins, and glucosinolate (GS) were all increased after MT treatment in infected B. rapa leaves. Taken together, these results indicated that B. rapa leaves promoted thiamine formation to defend against S. sclerotiorum infection. Moreover, MT helped further induce antioxidant activation in B. rapa in an ATP-dependent manner and stimulating GS biosynthesis to well inhibit the S. sclerotiorum infection. SIGNIFICANCE: Melatonin (MT) has biological activity and effectively relieved the Sclerotinia stem rot of Brassica rapa caused by the necrotic plant pathogen Sclerotinia sclerotiorum. In order to reveal the molecular mechanisms of MT-induced S. sclerotiorum resistance in B. rapa, comprehensive proteomic and metabolomic analyses were conducted. The integration analysis of omic-data illustrated that the modulation of ATP and glucosinolate biosynthesis induced by MT administration helped to defend the infection of S. sclerotiorum in B. rapa. Our results will provide insights into MT-induced anti-fungal mechanism and therapeutic strategies to mitigate Sclerotinia stem rot of B. rapa, thereby increasing plant yield and decreasing economic losses.
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Affiliation(s)
- Zhiyan Teng
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agricultural and Food Science, Zhejiang A&F University, Wusu Street 666, Lin'an, Hangzhou 311300, China
| | - Youjian Yu
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agricultural and Food Science, Zhejiang A&F University, Wusu Street 666, Lin'an, Hangzhou 311300, China
| | - Zhujun Zhu
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agricultural and Food Science, Zhejiang A&F University, Wusu Street 666, Lin'an, Hangzhou 311300, China
| | - Seung-Beom Hong
- Department of Biotechnology, University of Houston Clear Lake, Houston, TX 77058-1098, USA
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China.
| | - Yunxiang Zang
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agricultural and Food Science, Zhejiang A&F University, Wusu Street 666, Lin'an, Hangzhou 311300, China.
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10
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Jia J, Jin J, Chen Q, Yuan Z, Li H, Bian J, Gui L. Eukaryotic expression, Co-IP and MS identify BMPR-1B protein-protein interaction network. Biol Res 2020; 53:24. [PMID: 32471519 PMCID: PMC7257232 DOI: 10.1186/s40659-020-00290-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/08/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND BMPR-1B is part of the transforming growth factor β super family and plays a pivotal role in ewe litter size. Functional loss of exon-8 mutations in the BMPR-1B gene (namely the FecB gene) can increase both the ewe ovulation rate and litter size. RESULTS This study constructed a eukaryotic expression system, prepared a monoclonal antibody, and characterized BMPR-1B/FecB protein-protein interactions (PPIs). Using Co-immunoprecipitation coupled to mass spectrometry (Co-IP/MS), 23 proteins were identified that specifically interact with FecB in ovary extracts of ewes. Bioinformatics analysis of selected PPIs demonstrated that FecB associated with several other BMPs, primarily via signal transduction in the ovary. FecB and its associated interaction proteins enriched the reproduction process via BMP2 and BMP4 pathways. Signal transduction was identified via Smads proteins and TGF-beta signaling pathway by analyzing the biological processes and pathways. Moreover, other target proteins (GDF5, GDF9, RhoD, and HSP 10) that interact with FecB and that are related to ovulation and litter size in ewes were identified. CONCLUSIONS In summary, this research identified a novel pathway and insight to explore the PPi network of BMPR-1B.
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Affiliation(s)
- Jianlei Jia
- grid.262246.60000 0004 1765 430XKey of Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China ,grid.262246.60000 0004 1765 430XCollege of Agriculture and Animal Husbandry, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China
| | - Jipeng Jin
- grid.262246.60000 0004 1765 430XKey of Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China ,grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou Gansu, 730070 China
| | - Qian Chen
- grid.262246.60000 0004 1765 430XCollege of Agriculture and Animal Husbandry, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China
| | - Zan Yuan
- grid.262246.60000 0004 1765 430XCollege of Agriculture and Animal Husbandry, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China
| | - Haiqin Li
- grid.262246.60000 0004 1765 430XCollege of Agriculture and Animal Husbandry, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China
| | - Junhao Bian
- grid.262246.60000 0004 1765 430XCollege of Agriculture and Animal Husbandry, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China
| | - Linsheng Gui
- grid.262246.60000 0004 1765 430XKey of Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China ,grid.262246.60000 0004 1765 430XCollege of Agriculture and Animal Husbandry, Qinghai University, 251#, Ningda Road, Chengbei District, Xining, Qinghai 810016 China
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11
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Hao X, Guo Z, Sun H, Liu X, Zhang Y, Zhang L, Sun W, Tian Y. Urinary protein biomarkers for pediatric medulloblastoma. J Proteomics 2020; 225:103832. [PMID: 32474013 DOI: 10.1016/j.jprot.2020.103832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/17/2020] [Accepted: 05/18/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVE To identify candidate urinary protein biomarkers to distinguish medulloblastoma (MB) patients from healthy patients or benign brain disease control patients. METHODS The tandem mass tag (TMT)-labeled quantitative proteomics approach was used to identify differential proteins in the urinary proteome of 9 pre- and postsurgery MB patients and 9 healthy control patients, respectively. Ingenuity pathway analysis was used for functional annotation of differential proteins. The biomarker candidates were validated by the parallel reaction monitoring (PRM) method in 112 samples (29 pre- and postsurgery MB patients, 26 healthy control patients, and 28 benign brain disease control patients). Receiver operating characteristic (ROC) curves were developed to evaluate candidate biomarkers. RESULTS A total of 114 differential proteins were found. Bioinformatic analysis revealed that the urinary proteome could reflect changes in MB. Seventeen candidate biomarkers were validated by PRM. The combination of CADH1, FGFR4 and FIBB could be used to discriminate MB patients from healthy control patients with an area under the curve (AUC) of 0.973, and the combination of CADH1 and FIBB showed good discriminative power for differentiating MB from benign brain disease with an AUC of 0.884. CONCLUSION This report describes the first application of a TMT-PRM workflow to identify and validate MB-specific biomarkers in urine. These findings might contribute to the application of urinary proteomics for detecting and monitoring MB. BIOLOGICAL SIGNIFICANCE Medulloblastoma (MB) is among the most common pediatric brain malignancies. This tumor has a highly aggressive clinical course with a high tendency for relapses. Magnetic resonance imaging (MRI) is the major means of diagnosis and for radiographic surveillance after surgery. In MRI, sedation is often required in young children, which could expose them to a series of risks, including airway obstruction and even death. Aside from MRI, there is no reliable biomarker for clinical screening or monitoring of the disease. These facts introduce the clinical need of noninvasive biomarkers for early screening or monitoring of MB. This study is focused on the investigation of a marker panel based on urinary proteome, as a tool for the detection of MB in selected patients at risk. Upon evaluation of the marker model in an independent blinded set of 112 samples, the panel (CADH1, FGFR4 and FIBB) could be used to discriminate MB patients from healthy control patients with an area under the curve (AUC) of 0.973, and the combination of CADH1 and FIBB showed good discriminative power for differentiating MB from benign brain disease with an AUC of 0.884.
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Affiliation(s)
- Xiaolei Hao
- Department of Pediatric Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing Key Laboratory of Brain Tumor, China
| | - Zhengguang Guo
- Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Haidan Sun
- Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Xiaoyan Liu
- Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Yang Zhang
- Department of Pediatric Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing Key Laboratory of Brain Tumor, China
| | - Liwei Zhang
- Department of Pediatric Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing Key Laboratory of Brain Tumor, China
| | - Wei Sun
- Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China.
| | - Yongji Tian
- Department of Pediatric Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing Key Laboratory of Brain Tumor, China.
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12
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Mushtaq R, Shahzad K, Shah ZH, Alsamadany H, Alzahrani HAS, Alzahrani Y, Mujtaba T, Ahmed Z, Mansoor S, Bashir A. Isolation of biotic stress resistance genes from cotton (Gossypium arboreum) and their analysis in model plant tobacco (Nicotiana tabacum) for resistance against cotton leaf curl disease complex. J Virol Methods 2020; 276:113760. [PMID: 31712092 DOI: 10.1016/j.jviromet.2019.113760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/17/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
Cotton production is widely effected by Cotton Leaf Curl Virus (CLCuV) in world posing serious losses to cotton yield.The CRT genes from CLCuV resistant G. arboreum and CLCuV susceptible G. hirsutum were cloned and sequenced to know the differences of protein composition in both species. Molecular techniques were used to isolate full length putative biotic stress resistance genes from G. arboreum besides the analysis of identified novel genes in model plant tobacco (Nicotiana tabacum) for resistance to cotton leaf curl disease complex. It was found that transgenic plants over expressing Hydroperoxidelyase (HPL) genes exhibited higher enzyme activity than wild type. In addition the genome sequence information was used for the purpose of gene isolation. Even for the enhanced expression of Calreticulin (CRT), AOS and HPL in G. hirsutum, it still showed susceptibility against CLCuV suggesting alternative genes and pathways involved for the expression of resistance.
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Affiliation(s)
- Rakhshanda Mushtaq
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan; National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - Khurram Shahzad
- Department of Plant Breeding and Genetics, The University of Haripur, Pakistan.
| | - Zahid Hussain Shah
- Department of Plant Breeding and Genetics, PirMehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan.
| | - Hameed Alsamadany
- Department of Biological Sciences, King Abdulaziz University Jeddah Saudi Arabia.
| | - Hind A S Alzahrani
- College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia.
| | - Yahya Alzahrani
- Department of Biological Sciences, King Abdulaziz University Jeddah Saudi Arabia.
| | - Tahir Mujtaba
- Plant and Forest Biotechnology Umeå, Plant Science Centre, Swedish University of Agriculture Sciences, Umeå, Sweden.
| | - Zaheer Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad Pakistan.
| | - Shahid Mansoor
- National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - Aftab Bashir
- National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan; School of Life Sciences, Forman Christian College University, Lahore, Pakistan.
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13
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Li S, Fang X, Han S, Zhu T, Zhu H. Differential Proteome Analysis of Hybrid Bamboo (Bambusa pervariabilis × Dendrocalamopsis grandis) Under Fungal Stress (Arthrinium phaeospermum). Sci Rep 2019; 9:18681. [PMID: 31822726 PMCID: PMC6904554 DOI: 10.1038/s41598-019-55229-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/22/2019] [Indexed: 12/24/2022] Open
Abstract
In this study, TMT (tandem mass tag)-labeled quantitative protein technology combined with LC–MS/MS (liquid chromatography-mass spectrometry/mass spectrometry) was used to isolate and identify the proteins of the hybrid bamboo (Bambusa pervariabilis × Dendrocalamopsis grandis) and the bamboo inoculated with the pathogenic fungi Arthrinium phaeospermum. A total of 3320 unique peptide fragments were identified after inoculation with either A. phaeospermum or sterile water, and 1791 proteins were quantified. A total of 102 differentially expressed proteins were obtained, of which 66 differential proteins were upregulated and 36 downregulated in the treatment group. Annotation and enrichment analysis of these peptides and proteins using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases with bioinformatics software showed that the differentially expressed protein functional annotation items were mainly concentrated on biological processes and cell components. The LC–PRM/MS (liquid chromatography-parallel reaction monitoring/mass spectrometry) quantitative analysis technique was used to quantitatively analyze 11 differential candidate proteins obtained by TMT combined with LC–MS/MS. The up–down trend of 10 differential proteins in the PRM results was consistent with that of the TMT quantitative analysis. The coincidence rate of the two results was 91%, which confirmed the reliability of the proteomic results. Therefore, the differentially expressed proteins and signaling pathways discovered here may be the further concern for the bamboo-pathogen interaction studies.
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Affiliation(s)
- Shujiang Li
- College of Forestry, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xinmei Fang
- College of Forestry, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
| | - Hanmingyue Zhu
- College of Forestry, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
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14
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Visconti S, D'Ambrosio C, Fiorillo A, Arena S, Muzi C, Zottini M, Aducci P, Marra M, Scaloni A, Camoni L. Overexpression of 14-3-3 proteins enhances cold tolerance and increases levels of stress-responsive proteins of Arabidopsis plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110215. [PMID: 31623776 DOI: 10.1016/j.plantsci.2019.110215] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 05/13/2023]
Abstract
14-3-3 proteins are a family of conserved proteins present in eukaryotes as several isoforms, playing a regulatory role in many cellular and physiological processes. In plants, 14-3-3 proteins have been reported to be involved in the response to stress conditions, such as drought, salt and cold. In the present study, 14-3-3ε and 14-3-3ω isoforms, which were representative of ε and non-ε phylogenetic groups, were overexpressed in Arabidopsis thaliana plants; the effect of their overexpression was investigated on H+-ATPase activation and plant response to cold stress. Results demonstrated that H+-ATPase activity was increased in 14-3-3ω-overexpressing plants, whereas overexpression of both 14-3-3 isoforms brought about cold stress tolerance, which was evaluated through ion leakage, lipid peroxidation, osmolyte synthesis, and ROS production assays. A dedicated tandem mass tag (TMT)-based proteomic analysis demonstrated that different proteins involved in the plant response to cold or oxidative stress were over-represented in 14-3-3ε-overexpressing plants.
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Affiliation(s)
- Sabina Visconti
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Chiara D'Ambrosio
- Proteomics & Mass Spectrometry Laboratory ISPAAM, National Research Council, 80147, Naples, Italy.
| | - Anna Fiorillo
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Simona Arena
- Proteomics & Mass Spectrometry Laboratory ISPAAM, National Research Council, 80147, Naples, Italy
| | - Carlo Muzi
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Michela Zottini
- Department of Biology, University of Padova, 35131, Padova, Italy
| | - Patrizia Aducci
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Mauro Marra
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory ISPAAM, National Research Council, 80147, Naples, Italy
| | - Lorenzo Camoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
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15
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Zhou X, Peng LY, Wang ZC, Wang W, Zhu Z, Huang XH, Chen LB, Song QS, Bao YY. Identification of novel antimicrobial peptides from rice planthopper, Nilaparvata lugens. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 113:103215. [PMID: 31449847 DOI: 10.1016/j.ibmb.2019.103215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/14/2019] [Accepted: 08/18/2019] [Indexed: 05/08/2023]
Abstract
In this study, two novel antibacterial peptide genes, termed lugensin A and B were identified and characterized from a rice sap-sucking hemipteran insect pest, the brown planthopper, Nilaparvata lugens. Lugensin gene expression was significantly induced by Gram-negative and Gram-positive bacterial stains under the regulation of a signal receptor, the long peptidoglycan recognition protein (PGRP-LC) in the IMD pathway. Knockdown of PGRP-LC by RNAi eliminated bacterium induced Lugensin gene expression. Lugensins had the apparent antibacterial activities against Escherichia coli K12, Bacillus subtilis and the rice bacterial brown stripe pathogen Acidovorax avenae subsp. avenae (Aaa) strain RS-1. Lugensins inhibited bacterial proliferation by disrupting the integrity of the bacterial membranes. Scanning electron microscopy revealed abnormal membrane morphology of the recombinant Lugensin-treated bacteria. Lugensins induced complete cell disruption of E. coli K12 and B. subtilis strains while formed the holes on the cell surface of Aaa RS-1 strain. Immunofluorescence showed that Lugensins localized in the cell membrane of E. coli K12 while accumulated in the cytosol of B. subtilis. Differently, Lugensins remained in both the cell membrane and the cytosol of Aaa RS-1 strain, suggesting different action modes of Lugensins to different microbes. This is the first report of the novel antibacterial peptides found in the rice sap-sucking hemipteran insect species.
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Affiliation(s)
- Xiang Zhou
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lu-Yao Peng
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe-Chao Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhen Zhu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Hui Huang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li-Bo Chen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qi-Sheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, USA.
| | - Yan-Yuan Bao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
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16
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Yuan L, Wang J, Xie S, Zhao M, Nie L, Zheng Y, Zhu S, Hou J, Chen G, Wang C. Comparative Proteomics Indicates That Redox Homeostasis Is Involved in High- and Low-Temperature Stress Tolerance in a Novel Wucai ( Brassica campestris L.) Genotype. Int J Mol Sci 2019; 20:ijms20153760. [PMID: 31374822 PMCID: PMC6696267 DOI: 10.3390/ijms20153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
The genotype WS-1, previously identified from novel wucai germplasm, is tolerant to both low-temperature (LT) and high-temperature (HT) stress. However, it is unclear which signal transduction pathway or acclimation mechanisms are involved in the temperature-stress response. In this study, we used the proteomic method of tandem mass tag (TMT) coupled with liquid chromatography-mass spectrometry (LC-MS/MS) to identify 1022 differentially expressed proteins (DEPs) common to WS-1, treated with either LT or HT. Among these 1022 DEPs, 172 were upregulated in response to both LT and HT, 324 were downregulated in response to both LT and HT, and 526 were upregulated in response to one temperature stress and downregulated in response to the other. To illustrate the common regulatory pathway in WS-1, 172 upregulated DEPs were further analyzed. The redox homeostasis, photosynthesis, carbohydrate metabolism, heat-shockprotein, and chaperones and signal transduction pathways were identified to be associated with temperature stress tolerance in wucai. In addition, 35S:BcccrGLU1 overexpressed in Arabidopsis, exhibited higher reduced glutathione (GSH) content and reduced glutathione/oxidized glutathione (GSH/GSSG) ratio and less oxidative damage under temperature stress. This result is consistent with the dynamic regulation of the relevant proteins involved in redox homeostasis. These data demonstrate that maintaining redox homeostasis is an important common regulatory pathway for tolerance to temperature stress in novel wucai germplasm.
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Affiliation(s)
- Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jie Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Shilei Xie
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Mengru Zhao
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Libing Nie
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Yushan Zheng
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Shidong Zhu
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinfeng Hou
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China.
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China.
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China.
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17
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Analysis of Proteins Associated with Quality Deterioration of Grouper Fillets Based on TMT Quantitative Proteomics during Refrigerated Storage. Molecules 2019; 24:molecules24142641. [PMID: 31330849 PMCID: PMC6680736 DOI: 10.3390/molecules24142641] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/02/2023] Open
Abstract
A TMT (Tandem Mass Tag)-based strategy was applied to elucidate proteins that change in proteomes of grouper fillets during refrigerated storage. In addition, quality analyses on pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) for grouper fillets were performed. A total of 64 differentially significant expressed proteins (DSEPs) were found in the results in the Day 0 vs. Day 6 group comparison and the Day 0 vs. Day 12 group comparison. It is worth mentioning that more proteome changes were found in the Day 0 vs. Day 12 comparisons. Bioinformatics was utilized to analyze the DSEP. UniProt Knowledgebase (UniProtKB), Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein interaction network analysis were adopted. All DSEPs were classified into seven areas by function: binding proteins, calcium handling, enzymes, heat shock protein, protein turnover, structural proteins and miscellaneous. The numbers of proteins that correlated closely with pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) were 4, 3, 6 and 8, respectively.
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18
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Quantitative proteomics analysis reveals resistance differences of banana cultivar 'Brazilian' to Fusarium oxysporum f. sp. cubense races 1 and 4. J Proteomics 2019; 203:103376. [PMID: 31078632 DOI: 10.1016/j.jprot.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 12/29/2022]
Abstract
Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases in banana production. Foc is classified into three physiological races. However, the resistance mechanisms of banana against different Foc races are poorly understood. In this study, we performed a comparative proteomics analysis to investigate the resistance mechanisms of 'Brazilian' against Foc1 and Foc4. The proteomes of 'Brazilian' roots inoculated with Foc1 and Foc4 and mock inoculated control at 48 h were analyzed using TMT based quantitative analysis technique. A total of 7325 unique protein species were identified, of which 689, 744, and 1222 protein species were differentially accumulated in Foc1 vs. CK, Foc4 vs. CK, and Foc1 vs. Foc4, respectively. The differential accumulations of candidate protein species were further confirmed by RT-qPCR, PRM, and physiological and biochemical assays. Bioinformatics analysis revealed that the differentially abundance protein species (DAPS) related to pattern recognition receptors, plant cell wall modification, redox homeostasis, and defense responses were differentially accumulated after Foc1 and Foc4 infection, suggesting that 'Brazilian' differed in resistance to the two Foc races. Our study lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level. SIGNIFICANCE: The banana fusarium wilt disease is one of the most destructive disease of banana and is caused by Fusarium oxysporum f. sp. cubense (Foc). Foc is classified into three physiological races, namely, Foc1, Foc2, and Foc4. Among these races, Foc1 and Foc4 are widely distributed in south China and significantly lose yield. Although both physiological races (Foc1 and Foc4) can invade the Cavendish banana cultivar 'Brazilian', they have significant pathogenicity differences. Unfortunately, how the resistance differences are produced between two races is still largely unclear to date. In this study, we addressed this issue by performing TMT-based comparative quantitative proteomics analysis of 'Brazilian' roots after inoculation with Foc1 and Foc4 as well as sterile water as the control. We revealed that the series of protein species associated with pattern recognition receptors, plant cell wall modification, redox homeostasis, pathogenesis, phytohormones and signal transduction, plant secondary metabolites and programmed cell death etc. were involved in the response to Foc infection. Notably, the potential role of lipid signaling in banana defense against Foc are not reported previously but rather unveiled for the first time in this study. The current study represents the most extensive analysis of the protein profile of 'Brazilian' in response to Foc inoculation and includes for the first time the results from comparison quantitative proteomics analysis between plants inoculated with a pathogenic strain Foc4 and a nonpathogenic strain Foc1 of 'Brazilian', which will lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level.
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Wang Z, Ma LY, Cao J, Li YL, Ding LN, Zhu KM, Yang YH, Tan XL. Recent Advances in Mechanisms of Plant Defense to Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2019; 10:1314. [PMID: 31681392 PMCID: PMC6813280 DOI: 10.3389/fpls.2019.01314] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/20/2023]
Abstract
Sclerotinia sclerotiorum (Lib.) de Bary is an unusual pathogen which has the broad host range, diverse infection modes, and potential double feeding lifestyles of both biotroph and necrotroph. It is capable of infecting over 400 plant species found worldwide and more than 60 names have agriculturally been used to refer to diseases caused by this pathogen. Plant defense to S. sclerotiorum is a complex biological process and exhibits a typical quantitative disease resistance (QDR) response. Recent studies using Arabidopsis thaliana and crop plants have obtained new advances in mechanisms used by plants to cope with S. sclerotiorum infection. In this review, we focused on our current understanding on plant defense mechanisms against this pathogen, and set up a model for the defense process including three stages: recognition of this pathogen, signal transduction and defense response. We also have a particular interest in defense signaling mediated by diverse signaling molecules. We highlight the current challenges and unanswered questions in both the defense process and defense signaling. Essentially, we discussed candidate resistance genes newly mapped by using high-throughput experiments in important crops, and classified these potential gene targets into different stages of the defense process, which will broaden our understanding of the genetic architecture underlying quantitative resistance to S. sclerotiorum. We proposed that more powerful mapping population(s) will be required for accurate and reliable QDR gene identification.
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Schott AS, Behr J, Geißler AJ, Kuster B, Hahne H, Vogel RF. Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19. J Proteome Res 2017; 16:3816-3829. [PMID: 28862000 DOI: 10.1021/acs.jproteome.7b00474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.
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Affiliation(s)
- Ann-Sophie Schott
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Jürgen Behr
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany
| | - Andreas J Geißler
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany.,Chair of Proteomics and Bioanalytics, Technische Universität München , Freising 85354, Germany.,Center for Integrated Protein Science Munich, Freising 85354, Germany
| | | | - Rudi F Vogel
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
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Offline pentafluorophenyl (PFP)-RP prefractionation as an alternative to high-pH RP for comprehensive LC-MS/MS proteomics and phosphoproteomics. Anal Bioanal Chem 2017; 409:4615-4625. [PMID: 28555341 DOI: 10.1007/s00216-017-0407-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 01/21/2023]
Abstract
Technological advances in liquid chromatography and tandem mass spectrometry (LC-MS/MS) have enabled comprehensive analyses of proteins and their post-translational modifications from cell culture and tissue samples. However, sample complexity necessitates offline prefractionation via a chromatographic method that is orthogonal to online reversed-phase high-performance liquid chromatography (RP-HPLC). This additional fractionation step improves target identification rates by reducing the complexity of the sample as it is introduced to the instrument. A commonly employed offline prefractionation method is high pH reversed-phase (Hi-pH RP) chromatography. Though highly orthogonal to online RP-HPLC, Hi-pH RP relies on buffers that interfere with electrospray ionization. Thus, samples that are prefractionated using Hi-pH RP are typically desalted prior to LC-MS/MS. In the present work, we evaluate an alternative offline prefractionation method, pentafluorophenyl (PFP)-based reversed-phase chromatography. Importantly, PFP prefractionation results in samples that are dried prior to analysis by LC-MS/MS. This reduction in sample handling relative to Hi-pH RP results in time savings and could facilitate higher target identification rates. Here, we have compared the performances of PFP and Hi-pH RP in offline prefractionation of peptides and phosphopeptides that have been isolated from human cervical carcinoma (HeLa) cells. Given the prevalence of isobaric mass tags for peptide quantification, we evaluated PFP chromatography of peptides labeled with tandem mass tags. Our results suggest that PFP is a viable alternative to Hi-pH RP for both peptide and phosphopeptide offline prefractionation.
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Huang HJ, Liu CW, Huang XH, Zhou X, Zhuo JC, Zhang CX, Bao YY. Screening and Functional Analyses of Nilaparvata lugens Salivary Proteome. J Proteome Res 2016; 15:1883-96. [PMID: 27142481 DOI: 10.1021/acs.jproteome.6b00086] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Most phloem-feeding insects secrete gelling and watery saliva during the feeding process. However, the functions of salivary proteins are poorly understood. In this study, our purpose was to reveal the components and functions of saliva in a rice sap-sucking insect pest, Nilaparvata lugens. The accomplishment of the whole genome and transcriptome sequencing in N. lugens would be helpful for elucidating the gene information and expression specificity of the salivary proteins. In this study, we have, for the first time, identified the abundant protein components from gelling and watery saliva in a monophagous sap-sucking insect species through shotgun proteomic detection combined with the genomic and transcriptomic analysis. Eight unknown secreted proteins were limited to N. lugens, indicating species-specific saliva components. A group of annexin-like proteins first identified in the secreted saliva displayed different domain structure and expression specificity with typical insect annexins. Nineteen genes encoding five annexin-like proteins, six salivaps (salivary glands-specific proteins with unknown function), seven putative enzymes, and a mucin-like protein showed salivary gland-specific expression pattern, suggesting their importance in the physiological mechanisms of salivary gland and saliva in this insect species. RNA interference revealed that salivap-3 is a key protein factor in forming the salivary sheath, while annexin-like5 and carbonic anhydrase are indispensable for N. lugens survival. These novel findings will greatly help to clarify the detailed functions of salivary proteins in the physiological process of N. lugens and elucidate the interaction mechanisms between N. lugens and the rice plant, which could provide important targets for the future management of rice pests.
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Affiliation(s)
- Hai-Jian Huang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
| | - Cheng-Wen Liu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
| | - Xiao-Hui Huang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
| | - Xiang Zhou
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
| | - Chuan-Xi Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
| | - Yan-Yuan Bao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China
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