Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria

Jason T. Bouvier, Natalia V. Sernova, Salehe Ghasempur, Irina A. Rodionova, Matthew W. Vetting, Nawar F. Al-Obaidi, Steven C. Almo, John Alan Gerlt, Dmitry A. Rodionov

Research output: Contribution to journalArticle

Abstract

We used comparative genomics to reconstruct D-galacturonic and D-glucuronic acid catabolic pathways and associated transcriptional regulons involving the tripartite ATP-independent periplasmic (TRAP) family transporters that bind hexuronates in proteobacteria. The reconstructed catabolic network involves novel transcription factors, catabolic enzymes, and transporters for utilization of both hexuronates and aldarates (D-glucarate and meso-galactarate). The reconstructed regulons for a novel GntR family transcription factor, GguR, include the majority of hexuronate/aldarate utilization genes in 47 species from the Burkholderiaceae, Comamonadaceae, Halomonadaceae, and Pseudomonadaceae families. GudR, GulR, and UdhR are additional local regulators of some hexuronate/aldarate utilization genes in some of the above-mentioned organisms. The predicted DNA binding motifs of GguR and GudR regulators from Ralstonia pickettii and Polaromonas were validated by in vitro binding assays. Genes from the GulR- and GguR-controlled loci were differentially expressed in R. pickettii grown on hexuronates and aldarates. By a combination of bioinformatics and experimental techniques we identified a novel variant of the oxidative pathway for hexuronate utilization, including two previously uncharacterized subfamilies of lactone hydrolases (UxuL and UxuF). The genomic context of respective genes and reconstruction of associated pathways suggest that both enzymes catalyze the conversion of D-galactaro- and D-glucaro-1,5-lactones to the ring-opened aldarates. The activities of the purified recombinant enzymes, UxuL and UxuF, from four proteobacterial species were directly confirmed and kinetically characterized. The inferred novel aldarate-specific transporter from the tripartite tricarboxylate transporter (TTT) family transporter TctC was confirmed to bind D-glucarate in vitro. This study expands our knowledge of bacterial carbohydrate catabolic pathways by identifying novel families of catabolic enzymes, transcriptional regulators, and transporters. IMPORTANCE Hexuronate catabolic pathways and their transcriptional networks are highly variable among different bacteria. We identified novel transcriptional regulators that control the hexuronate and aldarate utilization genes in four families of proteobacteria. By regulon reconstruction and genome context analysis we identified several novel components of the common hexuronate/aldarate utilization pathways, including novel uptake transporters and catabolic enzymes. Two novel families of lactonases involved in the oxidative pathway of hexuronate catabolism were characterized. Novel transcriptional regulons were validated via in vitro binding assays and gene expression studies with Polaromonas and Ralstonia species. The reconstructed catabolic pathways are interconnected with each other metabolically and coregulated via the GguR regulons in proteobacteria.

Original languageEnglish (US)
Article numbere00431-18
JournalJournal of bacteriology
Volume201
Issue number2
DOIs
StatePublished - Jan 1 2019

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Regulon
Proteobacteria
Metabolic Networks and Pathways
Ralstonia pickettii
Enzymes
Genes
Lactones
Burkholderiaceae
Halomonadaceae
Pseudomonadaceae
Transcription Factors
Comamonadaceae
Ralstonia
Glucuronic Acid
Nucleotide Motifs
Gene Regulatory Networks
Hydrolases
Genomics
Computational Biology
Adenosine Triphosphate

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

Bouvier, J. T., Sernova, N. V., Ghasempur, S., Rodionova, I. A., Vetting, M. W., Al-Obaidi, N. F., ... Rodionov, D. A. (2019). Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria. Journal of bacteriology, 201(2), [e00431-18]. https://doi.org/10.1128/JB.00431-18

Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria. / Bouvier, Jason T.; Sernova, Natalia V.; Ghasempur, Salehe; Rodionova, Irina A.; Vetting, Matthew W.; Al-Obaidi, Nawar F.; Almo, Steven C.; Gerlt, John Alan; Rodionov, Dmitry A.

In: Journal of bacteriology, Vol. 201, No. 2, e00431-18, 01.01.2019.

Research output: Contribution to journalArticle

Bouvier, JT, Sernova, NV, Ghasempur, S, Rodionova, IA, Vetting, MW, Al-Obaidi, NF, Almo, SC, Gerlt, JA & Rodionov, DA 2019, 'Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria', Journal of bacteriology, vol. 201, no. 2, e00431-18. https://doi.org/10.1128/JB.00431-18
Bouvier JT, Sernova NV, Ghasempur S, Rodionova IA, Vetting MW, Al-Obaidi NF et al. Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria. Journal of bacteriology. 2019 Jan 1;201(2). e00431-18. https://doi.org/10.1128/JB.00431-18
Bouvier, Jason T. ; Sernova, Natalia V. ; Ghasempur, Salehe ; Rodionova, Irina A. ; Vetting, Matthew W. ; Al-Obaidi, Nawar F. ; Almo, Steven C. ; Gerlt, John Alan ; Rodionov, Dmitry A. / Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria. In: Journal of bacteriology. 2019 ; Vol. 201, No. 2.
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