title: Malonylome analysis of rhizobacterium Bacillus amyloliquefaciens FZB42 reveals involvement of lysine malonylation in polyketide synthesis and plant-bacteria interactions.
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.
  
  
  
  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.
authors.affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China. Electronic address: fanben2000@gmail.com.
authors.forename: Ben
authors.initials: B
authors.lastname: Fan
authors.affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China. Electronic address: lyj.lylo@163.com.
authors.forename: Yu-Long
authors.initials: YL
authors.lastname: Li
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany. Electronic address: lei.li1@uni-wuerzburg.de.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.affiliation: Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China. Electronic address: xiaojun_peng@ptm-biolab.com.
authors.forename: Xiao-Jun
authors.initials: XJ
authors.lastname: Peng
authors.affiliation: Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China. Electronic address: chen_bu@ptm-biolab.com.
authors.forename: Chen
authors.initials: C
authors.lastname: Bu
authors.affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China. Electronic address: xqwu2015@gmail.com.
authors.forename: Xiao-Qin
authors.initials: XQ
authors.lastname: Wu
authors.affiliation: Fachgebiet Phytomedizin, Albrecht Daniel Thaer Institut für Agrar- und Gartenbauwissenschaften, Lebenswissenschaftliche Fakultät, Humboldt Universität zu Berlin, 14195 Berlin, Germany. Electronic address: rainer.borriss@rz.hu-berlin.de.
authors.forename: Rainer
authors.initials: R
authors.lastname: Borriss
mesh_terms: D000069977:Bacillus amyloliquefaciens / Q000737:chemistry* / Q000378:metabolism; D001419:Bacteria / Q000166:cytology / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D019295:Computational Biology; D016937:Gram-Positive Endospore-Forming Rods; D008239:Lysine / Q000378:metabolism; D008314:Malonates / Q000378:metabolism*; D010944:Plants / Q000378:metabolism / Q000382:microbiology*; D061065:Polyketides / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D008314:Malonates; D061065:Polyketides; C030290:malonic acid; D008239:Lysine
keywords: Bacillus amyloliquefaciens; FZB42; Malonylation; Malonylome; Plant-microbe interaction; Polyketide synthetase