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

Abstract

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.

Characteristics of the bovicin HJ50 gene cluster in Streptococcus bovis HJ50

“…34 % identity to the putative ABC transporter in Clostridium perfringens SM101 (Myers et al, 2006). ORF2 showed 22 % identity to the ABC transporter protein found in Silicibacter pomeroyi DSS-3 (Buchan et al, 2004), and 25 % identity to SpaE encoded on the subtilin locus of Bacillus subtilis A1/3 (Chung & Hansen, 1992). These results suggested that bovE, bovF, ORF1 and ORF2 might form an ABC-transporter-like complex which contributes to self-protection of S. bovis HJ50 from bovicin HJ50.…”

Binding Site Determinants for the LysR-Type Transcriptional Regulator PcaQ in the Legume Endosymbiont Sinorhizobium meliloti

“…Enzymes involved in the protocatechuate branch of the ␤-ketoadipate pathway in S. meliloti are encoded within the pcaDCHGB and pcaIJF operons, which are subject to regulation by products encoded by pcaQ and pcaR, respectively (23). The regulator encoded by pcaQ is a member of the LysR-type transcriptional regulator (LTTR) superfamily, and PcaQ homologues are present in many species of ␣-proteobacteria (3,4,7,23,34,36,37).LysR-type regulators comprise one of the largest groups of prokaryotic transcriptional regulators characterized to date; these proteins regulate a diverse range of regulons, including genes whose products are involved in nitrogen and carbon fixation, biofilm formation, the oxidative stress response, bacterial virulence, and the catabolism of various compounds, including aromatic acids (10,16,19,22,23,28,34,46,47,51,55,57). LTTR proteins consist of a conserved helix-turn-helix DNA binding motif located in the N-terminal portion of the polypeptide, whereas the C terminus includes an inducer binding site.…”

The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria

“…Together with the fact that many IS-like elements and transposase genes are flanked with the pca gene cluster, it suggests that the b-ketoadipate pathway genes may be acquired via transposition events and subsequently distributed among actinobacteria via the horizontal transfer of plasmids. Eulberg et al (1998) first found a pcaL gene that encoded a merged enzyme with b-ketoadipate enol-lactone hydrolase and c-carboxymuconolactone decarboxylase in the rhodococcal pca gene cluster, although these two enzymes are encoded by separate genes, pcaD and pcaC, respectively, in most proteobacteria (Buchan et al, 2004). In addition, Iwagami et al (2000) identified the pcaL gene homologue in the streptomycete pca gene cluster (strain 2065).…”

“…1). In the case of the proteobacteria, this pathway is biochemically conserved among phylogenetically different strains, but operon organization, regulatory proteins, coinducer molecules and transport proteins for the pathway are remarkably diverse, most likely reflecting subtle aspects of niche adaptation (Buchan et al, 2004;Parke, 1997;Parke et al, 2000). In contrast, there is still little information available concerning protocatechuate catabolic gene clusters from actinobacteria (Eaton, 2001;Eulberg et al, 1998;Iwagami et al, 2000).…”

“…1). The b-ketoadipate pathway, in particular, is considered to be a good model system for studying mechanisms of evolution in an ecologically important catabolic pathway (Buchan et al, 2004;Parke et al, 2000). Following initial ortho-cleavage by protocatechuate 3,4-dioxygenase (PcaHG), five additional enzymes, i.e.…”