Bacteria Are Not What They Eat: That Is Why They Are So Diverse

Parke, Donna; D’Argenio, David A.; Ornston, L N

doi:10.1128/jb.182.2.257-263.2000

Cited by 51 publications

(49 citation statements)

References 41 publications

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“…The functional significance of encoding transport systems with a decreased responsiveness to protocatechuate (in terms of gene expression) imparts an interesting physiological consequence. Protocatechuate (and particularly the metabolite b-carboxy-cis,cis-muconate) is toxic if allowed to accumulate intracellularly (Parke et al, 2000), and a highly expressed aromatic acid transport system may be maladaptive in an environment rich in protocatechuate and related compounds, particularly if the transport system has a high affinity for its substrate. For example, it has been proposed that a mutational hotspot in the protocatechuate uptake system vanK of Acinetobacter baylyi may enhance the adaptability of this species in a soil environment by providing a subset of the population with a decreased ability to transport protocatechuate and thus a greater resistance to protocatechuate exposure (D'Argenio et al, 1999;Parke et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

“…Protocatechuate (and particularly the metabolite b-carboxy-cis,cis-muconate) is toxic if allowed to accumulate intracellularly (Parke et al, 2000), and a highly expressed aromatic acid transport system may be maladaptive in an environment rich in protocatechuate and related compounds, particularly if the transport system has a high affinity for its substrate. For example, it has been proposed that a mutational hotspot in the protocatechuate uptake system vanK of Acinetobacter baylyi may enhance the adaptability of this species in a soil environment by providing a subset of the population with a decreased ability to transport protocatechuate and thus a greater resistance to protocatechuate exposure (D'Argenio et al, 1999;Parke et al, 2000). It is interesting to speculate that the preferential accumulation of mutations within PcaQ DNA-binding sites upstream of transport genes may reflect an adaptation to limit the active import of protocatechuate into the cell by limiting the expression of a relevant transport system.…”

Section: Discussionmentioning

confidence: 99%

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The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

et al. 2011

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The LysR protein PcaQ regulates the expression of genes encoding products relevant to the degradation of the aromatic acid protocatechuate (3,4-dihydroxybenzoate), and we have previously defined a PcaQ DNA-binding site located upstream of the target pcaDCHGB operon in Sinorhizobium meliloti. In this work, we show that PcaQ also regulates the expression of the S. meliloti smb20568-smb20787-smb20786-smb20785-smb20784 gene cluster, which is predicted to encode an ABC transport system. ABC transport systems have not been shown before to transport protocatechuate, and we have designated this gene cluster pcaMNVWX. The transcriptional start site of pcaM was mapped, and the predicted PcaQ DNA-binding site was located at −73 to −58 relative to this site. Results from electrophoretic mobility shift assays with purified PcaQ and from expression assays indicated that PcaQ activates expression of the transport system in the presence of protocatechuate. To investigate this transport system further, we generated a pcaM deletion mutant (predicted to encode the substrate-binding protein) and introduced a polar insertion mutation into pcaN, a gene that is predicted to encode a permease. These mutants grew poorly on protocatechuate, presumably because they fail to transport protocatechuate. Genome analyses revealed PcaQ-like DNA-binding sites encoded upstream of ABC transport systems in other members of the α-proteobacteria, and thus it appears likely that these systems are involved in the uptake of protocatechuate.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

et al. 2011

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“…The importance of transport proteins in defining the biological individuality of organisms harboring the ␤-ketoadipate pathway is becoming increasingly evident (35,49). Acinetobacter sp.…”

Section: Discussionmentioning

confidence: 99%

“…The pathway is biochemically conserved, and the structural genes encoding enzymes of the pathway are similar among the phylogenetically diverse organisms that possess it (24). Despite this mechanistic conservation, studies of a limited number of soil bacteria demonstrate a remarkable diversity of this pathway in terms of gene organization, regulation, inducing metabolites, and transport systems (reviewed in reference 35). This diversification may reflect the distinctive selection pressures faced by the organisms maintaining the pathway and thus may reveal characteristic features that are specific to the bacterial group in which the pathway resides (24,34).…”

mentioning

confidence: 99%

Diverse Organization of Genes of the β-Ketoadipate Pathway in Members of the Marine Roseobacter Lineage

Buchan¹,

Neidle

Moran³

2004

Appl Environ Microbiol

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Members of the Roseobacter lineage, an ecologically important marine clade within the class ␣-Proteobacteria, harbor genes for the protocatechuate branch of the ␤-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. The genes of this pathway are typically clustered, although gene order varies among organisms. Here we characterize genes linked to pcaH and -G, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the Roseobacter lineage (pairwise 16S rRNA gene sequence identities, 92 to 99%). Sequence analysis of genomic fragments revealed five unique pca gene arrangements. Identical gene organization was found for isolates demonstrating species-level identity (i.e., >99% 16S rRNA gene similarity). In one isolate, six functionally related genes were clustered: pcaQ, pobA, pcaD, pcaC, pcaH, and pcaG. The remaining seven isolates lacked at least one of these genes in their clusters, although the relative order of the remaining genes was preserved. Three genes (pcaC, -H, and -G) were physically linked in all isolates. A highly conserved open reading frame (ORF) was found immediately downstream of pcaG in all eight isolates. Reverse transcription-PCR analysis of RNA from one isolate, Silicibacter pomeroyi DSS-3, provides evidence that this ORF is coexpressed with upstream pca genes. The absence of this ORF in similar bacterial pca gene clusters from diverse microbes suggests a niche-specific role for its protein product in Roseobacter group members. Collectively, these comparisons of bacterial pca gene organization illuminate a complex evolutionary history and underscore the widespread ecological importance of the encoded ␤-ketoadipate pathway.

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“…Instead of enhancing 4-ABS biotransformation, the accumulation of 4-sulfocatechol in the pcaG2 mutant RK1 during 4-ABS bioconversion led to an incomplete 4-ABS biotransformation (Gan et al, 2011a). It is conceivable that instead of being a repressor in the sad operon, a high concentration of 4-sulfocatechol is toxic to the cell, as is observed for some diphenolic compounds such as catechol and protocatechuate (Park et al, 2001;Parke et al, 2000), thereby reducing the overall bacterial fitness and 4-ABS biodegradation efficiency. The results from the transcription study suggest the presence of a transcriptional regulator(s) for the sadABD operon, thus warranting future studies focusing on the identification of this transcriptional regulator(s) and characterization of its DNA-binding site(s) and substrate range.…”

Section: Expression Systemmentioning

confidence: 99%

Cloning and functional analysis of the genes coding for 4-aminobenzenesulfonate 3,4-dioxygenase from Hydrogenophaga sp. PBC

2012

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The gene coding for the oxygenase component, sadA, of 4-aminobenzenesulfonate (4-ABS) 3,4-dioxygenase in Hydrogenophaga sp. PBC was previously identified via transposon mutagenesis. Expression of wild-type sadA in trans restored the ability of the sadA mutant to grow on 4-ABS. The inclusion of sadB and sadD, coding for a putative glutamine-synthetase-like protein and a plant-type ferredoxin, respectively, further improved the efficiency of 4-ABS degradation. Transcription analysis using the gfp promoter probe plasmid showed that sadABD was expressed during growth on 4-ABS and 4-sulfocatechol. Heterologous expression of sadABD in Escherichia coli led to the biotransformation of 4-ABS to a metabolite which shared a similar retention time and UV/vis profile with 4-sulfocatechol. The putative reductase gene sadC was isolated via degenerate PCR and expression of sadC and sadABD in E. coli led to maximal 4-ABS biotransformation. In E. coli, the deletion of sadB completely eliminated dioxygenase activity while the deletion of sadC or sadD led to a decrease in dioxygenase activity. Phylogenetic analysis of SadB showed that it is closely related to the glutamine-synthetase-like proteins involved in the aniline degradation pathway. This is the first discovery, to our knowledge, of the functional genetic components for 4-ABS aromatic ring hydroxylation in the bacterial domain.

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Bacteria Are Not What They Eat: That Is Why They Are So Diverse

Cited by 51 publications

References 41 publications

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

Diverse Organization of Genes of the β-Ketoadipate Pathway in Members of the Marine Roseobacter Lineage

Cloning and functional analysis of the genes coding for 4-aminobenzenesulfonate 3,4-dioxygenase from Hydrogenophaga sp. PBC

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