Discovery of a Choline-Responsive Transcriptional Regulator in Burkholderia xenovorans

Martí‐Arbona, Ricardo; Maity, Tuhin; Dunbar, John; Ünkefer, Clifford J.; Unkefer, Pat J.

doi:10.5539/jmbr.v3n1p91

Cited by 2 publications

(2 citation statements)

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“…3 ) [ 45 - 49 ]. After uptake, choline is converted into glycine betaine by a family of oxidoreductases, such as BetA, BetB, and CMO [ 41 , 50 , 51 ]. In addition, L-ectoine synthase (EctC), a key enzyme in the production of ectoine, was also identified [ 52 ].…”

Section: Resultsmentioning

confidence: 99%

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18^T and NC20

Lee

Kim

2022

J. Microbiol. Biotechnol.

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Two novel, halotolerant strains of Martelella soudanensis , NC18 T and NC20, were isolated from deep subsurface sediment, deeply sequenced, and comparatively analyzed with related strains. Based on a phylogenetic analysis using 16S rRNA gene sequences, the two strains grouped with members of the genus Martelella . Here, we sequenced the complete genomes of NC18 T and NC20 to understand the mechanisms of their halotolerance. The genome sizes and G+C content of the strains were 6.1 Mb and 61.8 mol%, respectively. Moreover, NC18 T and NC20 were predicted to contain 5,849 and 5,830 genes, and 5,502 and 5,585 protein-coding genes, respectively. Both strains contain the identically predicted 6 rRNAs and 48 tRNAs. The harboring of halotolerant-associated genes revealed that strains NC18 T and NC20 might tolerate high salinity through the accumulation of potassium ions in a “salt-in” strategy induced by K + uptake protein (kup) and the K + transport system (trkAH and kdpFABC). These two strains also use the ectoine transport system (dctPQM), the glycine betaine transport system (proVWX), and glycine betaine uptake protein (opu) to accumulate “compatible solutes,” such as ectoine and glycine betaine, to protect cells from salt stress. This study reveals the halotolerance mechanism of strains NC18 T and NC20 in high salt environments and suggests potential applications for these halotolerant and halophilic strains in environmental biotechnology.

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Section: Resultsmentioning

confidence: 99%

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18^T and NC20

Lee

Kim

2022

J. Microbiol. Biotechnol.

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“…It does not restrict our investigation to a single organism in which gene clustering around the target TR might not have existed because of rearrangements, insertions or deletions of genetic material or other events. Recently, we reported the characterization of three TRs of unknown function in which we used a manual version of our approach to predict functionality and identify potential effector metabolites [ 29 , 38 , 39 ]. Our automated approach, Function Discovery V1.0 has also been effective in finding conserved genes clustered near our target genes and for ten randomly chosen TRs that have known effectors and functions (Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

Martí‐Arbona

Nowak‐Lovato

et al. 2014

BMC Genomics

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BackgroundThe clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity.ResultsA software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observed that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018.ConclusionThese studies provide the proof of concept and validation of a systematic approach to the discovery of the biological activity for proteins of unknown function, in this case a TR. Bxe_B3018 is a methylglyoxal responsive TR that controls the expression of an operon composed of a putative efflux system.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1142) contains supplementary material, which is available to authorized users.

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Discovery of a Choline-Responsive Transcriptional Regulator in Burkholderia xenovorans

Cited by 2 publications

References 9 publications

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18^T and NC20

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18^T and NC20

Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

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Discovery of a Choline-Responsive Transcriptional Regulator in Burkholderia xenovorans

Cited by 2 publications

References 9 publications

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20

Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

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Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18^T and NC20

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18^T and NC20