Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction

Rückert, Christian; Koch, Daniel J.; Rey, Daniel A.; Albersmeier, Andreas; Mormann, Sascha; Pühler, Alfred; Kalinowski, Jörn

doi:10.1186/1471-2164-6-121

Cited by 60 publications

(52 citation statements)

References 50 publications

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“…thermopropionicum has a gene cluster that encodes transporters and enzymes for sulfur anions (Supplemental Table S5). Its gene content is similar to those annotated as assimilatory sulfate-reducing gene clusters in Clostridium acetobutylicum (AE001437) and other bacteria (Rückert et al 2005). On the other hand, gene clusters considered to be necessary for dissimilatory sulfate reduction, such as those for transmembrane electron transport complexes (Haveman et al 2004), are not found in P. thermopropionicum.…”

Section: Metabolismmentioning

confidence: 65%

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

Kosaka¹,

Kato²,

Shimoyama³

et al. 2008

Genome Res.

107

100

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The anaerobic biodegradation of organic matter is accomplished by sequential syntrophic catabolism by microbes in different niches. Pelotomaculum thermopropionicum is a representative syntrophic bacterium that catalyzes the intermediate bottleneck step in the anaerobic-biodegradation process, whereby volatile fatty acids (VFAs) and alcohols produced by upstream fermenting bacteria are converted to acetate, hydrogen, and carbon dioxide (substrates for downstream methanogenic archaea). To reveal genomic features that contribute to our understanding of the ecological niche and evolution of P. thermopropionicum, we sequenced its 3,025,375-bp genome and performed comparative analyses with genomes of other community members available in the databases. In the genome, 2920 coding sequences (CDSs) were identified. These CDSs showed a distinct distribution pattern in the functional categories of the Clusters of Orthologous Groups database, which is considered to reflect the niche of this organism. P. thermopropionicum has simple catabolic pathways, in which the propionate-oxidizing methylmalonyl-CoA pathway constitutes the backbone and is linked to several peripheral pathways. Genes for most of the important catabolic enzymes are physically linked to those for PAS-domain-containing regulators, suggesting that the catabolic pathways are regulated in response to environmental conditions and/or global cellular situations rather than specific substrates. Comparative analyses of codon usages revealed close evolutionary relationships between P. thermopropionicum and other niche members, while it was distant from phylogenetically related sugar-fermenting bacteria. These analyses suggest that P. thermopropionicum has evolved as a syntrophy specialist by interacting with niche-associated microbes.

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Section: Metabolismmentioning

confidence: 65%

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

Kosaka¹,

Kato²,

Shimoyama³

et al. 2008

Genome Res.

107

100

View full text Add to dashboard Cite

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“…The siroheme prosthetic group is known to be essential for the function of sulfite-reductases, which convert sulfite (derived from sulfate) to sulfide [67]. Thus, cluster 4 proteins may be involved in the uptake of sulfate or other sulfur-based compounds, a suggestion supported by sequence similarity between cluster 4 proteins and CysZ of Corynebacterium glutamicum , a putative sulfate transporter [16]. …”

Section: Resultsmentioning

confidence: 99%

“…A putative sulfate uptake porter termed CysZ (TC# 2.A.102.6.1) was also shown to belong to the TSUP family. As for TauE, its mechanism of action is unknown [16]. Yet another homologue, SafE1 (TC# 2.A.102.2.2), was proposed to be a sulfoacetate exporter [17].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins

Shlykov¹,

Zheng²,

Chen³

et al. 2012

Biochimica et Biophysica Acta (BBA) - Biomembranes

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The ubiquitous sequence diverse 4-Toluene Sulfonate Uptake Permease (TSUP) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. Prokaryotic members of the TSUP family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. Despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. We show that the prototypical eight TMS topology arose from an intragenic duplication of a four TMS unit. Possibly, a two TMS α-helical hairpin structure was the precursor of the 4 TMS repeat unit. Genome context analyses confirmed the proposal of a sulfur-based compound transport role for many TSUP homologues, but functional outliers appear to be prevalent as well. Preliminary results suggest that the TSUP family is a member of a large novel superfamily that includes rhodopsins, integral membrane chaperone proteins, transmembrane electron flow carriers and several transporter families. All of these proteins probably arose via the same pathway: 2 → 4 → 8 TMSs followed by loss of a TMS either at the N- or C-terminus, depending on the family, to give the more frequent 7 TMS topology.

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“…cysZ is a conserved, non-essential gene that encodes an inner membrane protein involved in sulfate transport [35], [36]. It is not surprising that sulfate transporter proteins would be highly abundant as this is a key nutrient for cells during all phases of growth.…”

Section: Discussionmentioning

confidence: 99%

Novel Genetic Tools for Diaminopimelic Acid Selection in Virulence Studies of Yersinia pestis

et al. 2011

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Molecular studies of bacterial virulence are enhanced by expression of recombinant DNA during infection to allow complementation of mutants and expression of reporter proteins in vivo. For highly pathogenic bacteria, such as Yersinia pestis, these studies are currently limited because deliberate introduction of antibiotic resistance is restricted to those few which are not human treatment options. In this work, we report the development of alternatives to antibiotics as tools for host-pathogen research during Yersinia pestis infections focusing on the diaminopimelic acid (DAP) pathway, a requirement for cell wall synthesis in eubacteria. We generated a mutation in the dapA-nlpB(dapX) operon of Yersinia pestis KIM D27 and CO92 which eliminated the expression of both genes. The resulting strains were auxotrophic for diaminopimelic acid and this phenotype was complemented in trans by expressing dapA in single and multi-copy. In vivo, we found that plasmids derived from the p15a replicon were cured without selection, while selection for DAP enhanced stability without detectable loss of any of the three resident virulence plasmids. The dapAX mutation rendered Y. pestis avirulent in mouse models of bubonic and septicemic plague which could be complemented when dapAX was inserted in single or multi-copy, restoring development of disease that was indistinguishable from the wild type parent strain. We further identified a high level, constitutive promoter in Y. pestis that could be used to drive expression of fluorescent reporters in dapAX strains that had minimal impact to virulence in mouse models while enabling sensitive detection of bacteria during infection. Thus, diaminopimelic acid selection for single or multi-copy genetic systems in Yersinia pestis offers an improved alternative to antibiotics for in vivo studies that causes minimal disruption to virulence.

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Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction

Cited by 60 publications

References 50 publications

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins

Novel Genetic Tools for Diaminopimelic Acid Selection in Virulence Studies of Yersinia pestis

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