Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8

Abstract

A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells.

Metabolomic and proteomic changes induced by growth inhibitory concentrations of copper in the biofilm-forming marine bacteriumPseudoalteromonas lipolytica

“…The metabolic differences observed between planktonic and biofilm cultures of P. lipolytica TC8 were expected. 31 The present results showed that, in the Cu concentration range tested, the culture mode had more influence on the metabolome than Cu exposure. Moreover, metabolic profiles of biofilm and planktonic cultures did not converge under Cu stress.…”

“…In P. lipolytica TC8, this type of compounds was previously shown to be more specifically biosynthesized in biofilms than in planktonic cultures. 31 Seven metabolites were under-expressed in planktonic Cu-1400 conditions and not expressed in biofilm samples. Almost all were ornithine lipids (OLs) (VIPs n°16 to 19, 24 and 30) and most of them (except VIP n°19) exhibited slightly shorter saturated or mono-unsaturated acyl chains than the OL (VIP n°35) significantly more produced at the highest Cu concentration (Cu-1400).…”

“…The whole metabolomic process (quenching, cell extraction, LC-MS analysis, data extraction and treatment) was performed as previously described. 30,31 Briefly, the extraction step was performed with ethyl acetate [solvent/bacterial culture, 2:1 (v/v)]. This mixture was shaken (1 min) and sonicated (30 min) at 20°C.…”

“…Sample preparation, digestion, nano-LC-MS/MS, database search and data analysis were then conducted as previously described. 31 Briefly, planktonic and biofilm cultures were centrifuged two times (4000 g) at 4°C during 15 min. The resulting pellets were then suspended in a lysis buffer [10 mM Tris-HCl, pH 8.0; buffer/pellet, 5:1 (v/v)] with protease inhibitors (Sigma-Aldrich, St Quentin-Fallavier, France).…”

“…Thanks to the clustering observed in the heatmap ( Figure 1B), 21 of them were considered as characteristic of a phenotype and/or a Cu exposure condition. A molecular formula was determined for 21 of them and eleven were putatively identified thanks to previous works 30,31 (Table S2). Five metabolites were over-produced in planktonic Cu-1400 conditions.…”