Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase

Abstract

Rhizobium etli CE3 grown in succinate-ammonium minimal medium (MM) excreted outer membrane vesicles (OMVs) with diameters of 40 to 100 nm. Proteins from the OMVs and the periplasmic space were isolated from 6 and 24 h cultures and identified by proteome analysis. A total of 770 proteins were identified: 73.8 and 21.3 % of these occurred only in the periplasm and OMVs, respectively, and only 4.9 % were found in both locations. The majority of proteins found in either location were present only at 6 or 24 h: in the periplasm and OMVs, only 24 and 9 % of proteins, respectively, were present at both sampling times, indicating a time-dependent differential sorting of proteins into the two compartments. The OMVs contained proteins with physiologically varied roles, including Rhizobium adhering proteins (Rap), polysaccharidases, polysaccharide export proteins, auto-aggregation and adherence proteins, glycosyl transferases, peptidoglycan binding and cross-linking enzymes, potential cell wall-modifying enzymes, porins, multidrug efflux RND family proteins, ABC transporter proteins and heat shock proteins. As expected, proteins with known periplasmic localizations (phosphatases, phosphodiesterases, pyrophosphatases) were found only in the periplasm, along with numerous proteins involved in amino acid and carbohydrate metabolism and transport. Nearly one-quarter of the proteins present in the OMVs were also found in our previous analysis of the R. etli total exproteome of MM-grown cells, indicating that these nanoparticles are an important mechanism for protein excretion in this species.

Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach

“…The proteins with predicted transmembrane helices different from the short transmembrane helix in the N-terminus were excluded. These enrichment levels of periplasmic proteins are in line or above previous publications [21,22,23,24]. Undoubtedly, some extent of cell lysis occurred during preparation of periplasmic protein fractions, in that known cytoplasmic proteins were recovered, accounting for the 54.3% (Table S2).…”

Cracking Open Bacterial Membrane Vesicles

“…As we have reviewed here, biochemical approaches are powerful tools for elucidating the composition, biogenesis, and function of MVs. Proteomic and lipidomic analyses indicate that the composition of MVs depends on the growth conditions (Choi et al, 2014;Kim et al, 2016;Wagner et al, 2018;Taboada et al, 2019), suggesting that the MVs are heterogenous and their functions differ depending on the environment. On the other hand, recent studies have shown different pathways of MV formation, which lead to different MV compositions.…”

Microbiota–host communications: Bacterial extracellular vesicles as a common language

“…One of the obstacles to progress in the field is a lack of standardized methodology in the isolation and purification of EVs, as well as a lack of well-defined identification of individual markers present on bacterial EVs [ 5 ]. EV composition and size can change drastically, depending on growth conditions [ 88 , 126 , 127 ] and on strains even within the same species [ 128 ].…”