Abstract
Microorganisms secrete into their extracellular environment numerous compounds that are required for their survival. Many of these compounds could be of great interest for biotechnology applications and their genes used in synthetic biology design. The secreted proteins and the components of the translocation systems themselves can be scrutinized in-depth by the most recent proteomic tools. While the secretomes of pathogens are well-documented, those of non-pathogens remain largely to be established. Here, we present the analysis of the exoproteome from the marine bacterium Ruegeria pomeroyi DSS-3 grown in standard laboratory conditions. We used a shotgun approach consisting of trypsin digestion of the exoproteome, and identification of the resulting peptides by liquid chromatography coupled to tandem mass spectrometry. Three different proteins that have domains homologous to those observed in RTX toxins were uncovered and were semi-quantified as the most abundantly secreted proteins. One of these proteins clearly stands out from the catalogue, representing over half of the total exoproteome. We also listed many soluble proteins related to ABC and TRAP transporters implied in the uptake of nutrients. The Ruegeria pomeroyi DSS-3 case-study illustrates the power of the shotgun nano-LC-MS/MS strategy to decipher the exoproteome from marine bacteria and to contribute to environmental proteomics.
Highlights
Marine microorganisms have defined the chemistry of the oceans and atmosphere, and represent a large proportion of the biological diversity on Earth
Three proteins far-related to RTX-like toxins were detected as the most abundant proteins, one of them representing over 50% of the total exoproteome
To investigate the exoproteome of R. pomeroyi DSS-3, we setup a novel shotgun proteomic approach that could quickly identify and semi-quantify the major proteins found in the extracellular medium for a given growth condition
Summary
Marine microorganisms have defined the chemistry of the oceans and atmosphere, and represent a large proportion of the biological diversity on Earth. R. pomeroyi DSS-3 is the first roseobacterium with a sequenced genome and has served as a model organism for studying the ecophysiological strategies of heterotrophic marine bacteria [7,8,9]. The exoproteomes of many bacteria remain unknown, despite the high interest some of the secreted proteins could have for biotechnological use. Eight translocation systems though the cytoplasmic membrane and eight though the outer membrane have been described in gram-negative bacteria (reviewed in [17]) Three of the former translocation systems (type I, III and IV) can carry out the secretion of proteins directly though the gram-negative bilayer. Protein analysis considering integrative aspects should be taken into account In this respect, the LocateP tool, developed for gram-positive bacteria, is an interesting predictor [23]. Three proteins far-related to RTX-like toxins were detected as the most abundant proteins, one of them representing over 50% of the total exoproteome
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