Diminished Redundancy of Outer Membrane Factor Proteins in Rhizobiales: A &lt;i&gt;nodT&lt;/i&gt; Homolog Is Essential for Free-Living &lt;i&gt;Rhizobium etli&lt;/i&gt;

Hernández-Mendoza, Armando; Nava, Noreide; Santana, Olivia; Abreu‐Goodger, Cei; Tovar, Anibal; Quinto, Carmen

doi:10.1159/000103594

Cited by 9 publications

(9 citation statements)

References 89 publications

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“…The NodT protein belongs to the family of outer membrane proteins from the RND (resistance-nodulation-cell division) efflux system, which is involved in the diverse adaptive processes, including plant-microbe interactions [48]. Chromosomal copies of nodT are essential for bacteria viability outside the plants [49], but the use of a single nodT chromosomal copy for symbiotic purposes could not be effective enough. nodT demonstrates a DD-based evolutionary scenario, including duplication, neofunctionalization, and clustering into the nod regulon.…”

Section: Discussionmentioning

confidence: 99%

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

Chirak

Kimeklis

Karasev

et al. 2019

Genes

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Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (>90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (<60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive "Afghan" peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the "gain-and-loss of sym genes" and the "compaction of sym cluster" strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.

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Section: Discussionmentioning

confidence: 99%

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

Chirak

Kimeklis

Karasev

et al. 2019

Genes

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“…Nodulation protein NodT RHE_RS17445 is a chromosomally encoded OM lipoprotein that is not involved in Nod factor synthesis or transport. A functional nodT is essential for the viability of R. etli CE3, where NodT is proposed to play a role in chromosome segregation or maintaining OM stability rather than as an export pump [67]. The dicarboxylate transporter RHE_RS15195 (DctA) is expected to be a symbiotically essential gene in R. etli, since rhizobial mutants defective in dicarboxylate transport are unable to fix nitrogen [68].…”

Section: Omv-localized Proteins Of Physiological Interestmentioning

confidence: 99%

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

et al. 2019

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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.

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“…The authors proposed that NodTch may play a role in outer membrane stability or in chromosome segregation instead of, or in addition to, drug efflux [30]. …”

Section: Comparison Of the Secretome Of R Etli During Exponential Anmentioning

confidence: 99%

The extracellular proteome of Rhizobium etli CE3 in exponential and stationary growth phase

2010

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BackgroundThe extracellular proteome or secretome of symbiotic bacteria like Rhizobium etli is presumed to be a key element of their infection strategy and survival. Rhizobia infect the roots of leguminous plants and establish a mutually beneficial symbiosis. To find out the possible role of secreted proteins we analyzed the extracellular proteome of R. etli CE3 in the exponential and stationary growth phases in minimal medium, supplemented with succinate-ammonium.ResultsThe extracellular proteins were obtained by phenol extraction and identified by LC-ESI MS/MS. We identified 192 and 191 proteins for the exponential and stationary phases respectively. Using the software Signal P, we predicted signal peptides for 12.95% and 35.60% of the proteins identified in the exponential and stationary phases, respectively, which could therefore be secreted by the Sec pathway. For the exponential growth phase, we found in abundance proteins like the ribosomal proteins, toxins and proteins belonging to the group "defence mechanisms". For the stationary growth phase, we found that the most abundant proteins were those with unknown function, and in many of these we identified characteristic domains of proteases and peptidases.ConclusionsOur study provided the first dataset of the secretome of R. etli and its modifications, which may lead to novel insights into the adaptive response of different stages of growth. In addition, we found a high number of proteins with unknown function; these proteins could be analyzed in future research to elucidate their role in the extracellular proteome of R. etli.

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Diminished Redundancy of Outer Membrane Factor Proteins in Rhizobiales: A <i>nodT</i> Homolog Is Essential for Free-Living <i>Rhizobium etli</i>

Cited by 9 publications

References 89 publications

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

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

The extracellular proteome of Rhizobium etli CE3 in exponential and stationary growth phase

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