Dataset Information

Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans.

ABSTRACT: We have developed a stable isopropyl-beta-d-thiogalactopyranoside (IPTG)-inducible-expression plasmid, pIND4, which allows graduated levels of protein expression in the alphaproteobacteria Rhodobacter sphaeroides and Paracoccus denitrificans. pIND4 confers kanamycin resistance and combines the stable replicon of pMG160 with the lacI(q) gene from pYanni3 and the lac promoter, P(A1/04/03), from pJBA24.

SUBMITTER: Ind AC

PROVIDER: S-EPMC2765152 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans.

Ind Alice C AC Porter Steven L SL Brown Mostyn T MT Byles Elaine D ED de Beyer Jennifer A JA Godfrey Scott A SA Armitage Judith P JP

Applied and environmental microbiology 20090814 20

We have developed a stable isopropyl-beta-d-thiogalactopyranoside (IPTG)-inducible-expression plasmid, pIND4, which allows graduated levels of protein expression in the alphaproteobacteria Rhodobacter sphaeroides and Paracoccus denitrificans. pIND4 confers kanamycin resistance and combines the stable replicon of pMG160 with the lacI(q) gene from pYanni3 and the lac promoter, P(A1/04/03), from pJBA24. ...[more]

PMID: 19684165

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Project description:BackgroundThe genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data.ResultsThe analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles.ConclusionsOur analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results.

Dataset Information

Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans.

Publications

Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans.

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