1
|
Fan B, Wang C, Ding X, Zhu B, Song X, Borriss R. AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5520604. [PMID: 31219564 PMCID: PMC6585148 DOI: 10.1093/database/baz071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/27/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
Since its isolation 20 years ago, many studies have been devoted to Bacillus velezensis FZB42 (former name Bacillus amyloliquefaciens subsp. plantarum FZB42), which has been gradually accepted as a model organism for Gram-positive rhizobacteria. FZB42 is different from another widely studied bacterial strain, Bacillus subtilis 168, in its many features that are closely associated with plants. FZB42 represents a large group of Bacillus isolates that are beneficial to plants and of great importance in agriculture. In this work a database for FZB42 named 'AmyloWiki' is built to integrate all information of FZB42 available to date. The information includes the genomic, transcriptomic, proteomic, post-translational data as well as FZB42 unique genes, protein regulators, mutant availability, publications and etc. The website is built up with PHP and MySQL with a function of keyword searching, browsing, data-downloading and other functions.
Collapse
Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Bingyao Zhu
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, 10115 Berlin, Germany, and Nord Reet UG, Marienstr. 27a, 17489 Greifswald, Germany
| |
Collapse
|
2
|
Fan B, Wang C, Song X, Ding X, Wu L, Wu H, Gao X, Borriss R. Bacillus velezensis FZB42 in 2018: The Gram-Positive Model Strain for Plant Growth Promotion and Biocontrol. Front Microbiol 2018; 9:2491. [PMID: 30386322 PMCID: PMC6198173 DOI: 10.3389/fmicb.2018.02491] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022] Open
Abstract
Bacillus velezensis FZB42, the model strain for Gram-positive plant-growth-promoting and biocontrol rhizobacteria, has been isolated in 1998 and sequenced in 2007. In order to celebrate these anniversaries, we summarize here the recent knowledge about FZB42. In last 20 years, more than 140 articles devoted to FZB42 have been published. At first, research was mainly focused on antimicrobial compounds, apparently responsible for biocontrol effects against plant pathogens, recent research is increasingly directed to expression of genes involved in bacteria–plant interaction, regulatory small RNAs (sRNAs), and on modification of enzymes involved in synthesis of antimicrobial compounds by processes such as acetylation and malonylation. Till now, 13 gene clusters involved in non-ribosomal and ribosomal synthesis of secondary metabolites with putative antimicrobial action have been identified within the genome of FZB42. These gene clusters cover around 10% of the whole genome. Antimicrobial compounds suppress not only growth of plant pathogenic bacteria and fungi, but could also stimulate induced systemic resistance (ISR) in plants. It has been found that besides secondary metabolites also volatile organic compounds are involved in the biocontrol effect exerted by FZB42 under biotic (plant pathogens) and abiotic stress conditions. In order to facilitate easy access to the genomic data, we have established an integrating data bank ‘AmyloWiki’ containing accumulated information about the genes present in FZB42, available mutant strains, and other aspects of FZB42 research, which is structured similar as the famous SubtiWiki data bank.
Collapse
Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany.,Nord Reet UG, Greifswald, Germany
| |
Collapse
|
3
|
Fan B, Li YL, Li L, Peng XJ, Bu C, Wu XQ, Borriss R. Malonylome analysis of rhizobacterium Bacillus amyloliquefaciens FZB42 reveals involvement of lysine malonylation in polyketide synthesis and plant-bacteria interactions. J Proteomics 2016; 154:1-12. [PMID: 27939684 DOI: 10.1016/j.jprot.2016.11.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/24/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
Using the combination of affinity enrichment and high-resolution LC-MS/MS analysis, we performed a large-scale lysine malonylation analysis in the model representative of Gram-positive plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens FZB42. Altogether, 809 malonyllysine sites in 382 proteins were identified. The bioinformatic analysis revealed that lysine malonylation occurs on the proteins involved in a variety of biological functions including central carbon metabolism, fatty acid biosynthesis and metabolism, NAD(P) binding and translation machinery. A group of proteins known to be implicated in rhizobacterium-plant interaction were also malonylated; especially, the enzymes responsible for antibiotic production including polyketide synthases (PKSs) and nonribosomal peptide synthases (NRPSs) were highly malonylated. Furthermore, our analysis showed malonylation occurred on proteins structure with higher surface accessibility and appeared to be conserved in many bacteria but not in archaea. The results provide us valuable insights into the potential roles of lysine malonylation in governing bacterial metabolism and cellular processes. BIOLOGICAL SIGNIFICANCE Although in mammalian cells some important findings have been discovered that protein malonylation is related to basic metabolism and chronic disease, few studies have been performed on prokaryotic malonylome. In this study, we determined the malonylation profiles of Bacillus amyloliquefaciens FZB42, a model organism of Gram-positive plant growth-promoting rhizobacteria. FZB42 is known for the extensive investigations on its strong ability of producing antimicrobial polyketides and its potent activities of stimulating plant growth. Our analysis shows that malonylation is highly related to the polyketide synthases and the proteins involved bacterial interactions with plants. The results not only provide one of the first malonylomes for exploring the biochemical nature of bacterial proteins, but also shed light on the better understanding of bacterial antibiotic biosynthesis and plant-microbe interaction.
Collapse
Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
| | - Yu-Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
| | - Lei Li
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
| | - Xiao-Jun Peng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China.
| | - Chen Bu
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China.
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
| | - Rainer Borriss
- Fachgebiet Phytomedizin, Albrecht Daniel Thaer Institut für Agrar- und Gartenbauwissenschaften, Lebenswissenschaftliche Fakultät, Humboldt Universität zu Berlin, 14195 Berlin, Germany.
| |
Collapse
|