Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

Abstract

Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins.

Mechanistic insights into transferable polymyxin resistance among gut bacteria

“…The identities of two chimeric MCR-1 versions (TM-MCR-1 and TM1-EptA) were determined using a Waters Q-ToF API-US Quad-ToF mass spectrometer connected to a Waters nano Acquity UPLC as described earlier (52,53). The expected protein bands were cut from the SDS-PAGE and digested with trypsin (G-Biosciences, St. Louis, MO).…”

Deciphering a unique biotin scavenging pathway with redundant genes in the probiotic bacterium Lactococcus lactis

“…It seemed unusual that L. lactis IL1403 with a small genome (2.37 Mb), which is estimated to be only half of the E. coli genome (4.64 Mb for MG1655) 9 , encodes numerous redundant (and/or duplicated) loci in the context of lipid metabolism as well as within the biotin utilization pathway. While unexpected, such an arrangement is not without precedent as a similar scenario was observed in Paracoccus 12 . This rare situation where redundant genes of biotin metabolism are present within the minimal genome of L. lactis might render some unknown physiological advantage, raising a possibility that it represents a relic of bacterial evolution and selection by its environmental niche 13 14 .…”

“…The birA 2 gene encodes a putative “simple” biotin protein ligase (BPL) that lacks the N-terminal DNA binding motif found in the putative dual-functional birA 1 ( Figs 1 and 2 ). While the presence of multiple copies of birA and bioY homologues is atypical, two copies of birA have been found in Francisella 16 and two different bioY orthologues are present in Paracoccus 12 . Apart from redundancies in birA and bioY , redundancy is also found within the fatty acid synthesis loci in L. lactis ( Table S1 ).…”

Crystal structure and acetylation of BioQ suggests a novel regulatory switch for biotin biosynthesis in Mycobacterium smegmatis

“…Quite similar to scenarios of BioQ, a TetR‐like transcription factor in Actinobacterium (Brune et al, ), the GntR‐type regulator, named as BioR, seems to compensate the loss of regulatory function of BirA in α‐proteobacteria species (Rodionov and Gelfand, ). Our subsequent studies defined that BioR is a functional repressor for biotin synthesis and its transport system in at least the following three species A. tumefaciens (Feng et al, ), B. melitensis (Feng et al, ), and Paracoccus denitrificans (Feng et al, ). Moreover, it seems very true that unexpected diversity can be assigned to the BioR regulatory networks (Feng et al, ; ; ).…”

“…Our subsequent studies defined that BioR is a functional repressor for biotin synthesis and its transport system in at least the following three species A. tumefaciens (Feng et al, ), B. melitensis (Feng et al, ), and Paracoccus denitrificans (Feng et al, ). Moreover, it seems very true that unexpected diversity can be assigned to the BioR regulatory networks (Feng et al, ; ; ). Obviously, the discovery of BioR and BirA α‐proteobacteria constituted another dipartite regulatory system to negotiate biotin metabolism.…”