Regulation of Sulfur Assimilation Pathways in Burkholderia cenocepacia through Control of Genes by the SsuR Transcription Factor

Łochowska, Anna; Iwanicka-Nowicka, Roksana; Zielak, Agata; Modelewska, Anna; Thomas, Mark S.; Hryniewicz, Monika M.

doi:10.1128/jb.00483-10

Cited by 15 publications

(13 citation statements)

References 36 publications

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“…This is well supported by the identification of Bradyrhizobium , Caulobacter , and Burkholderia as biomarkers (Supplementary Fig. S2 , Supplementary Tables S2 and S5 ), all which are known to be involved in sulfur metabolism 72 , 73 and house homologous genes for the same. The pathogenic Burkholderia , a taxonomic biomarker for Tb samples (Supplementary Fig.…”

Section: Discussionsupporting

confidence: 53%

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Mukherjee

Chettri

Langpoklakpam

et al. 2017

Sci Rep

121

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Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

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Section: Discussionsupporting

confidence: 53%

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Mukherjee

Chettri

Langpoklakpam

et al. 2017

Sci Rep

121

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show abstract

“…This is well supported by the identification of Bradyrhizobium , Caulobacter , and Burkholderia as biomarkers (Fig. 4, Supplementary Table S2), all which are known to be involved in sulfur metabolism 66,67 and house homologous genes for the same. Interestingly, a number of biomarkers identified here for the taiga samples such as Phenylobacterium , Sphingomonadaceae, Novosphingobium and Rhodococcus were detected as “habitat specialists” in oil contaminated taiga samples by Yang et al 68 .…”

Section: Discussionsupporting

confidence: 58%

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies

Mukherjee

Chettri

Langpoklakpam

et al. 2016

Preprint

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18 Microbial remediation of oil polluted habitats remains one of the foremost methods for 19 restoration of petroleum hydrocarbon contaminated environments. The development of 20 effective bioremediation strategies however, require an extensive understanding of the 21 36 37 38 39 40 41 42 43 48 during production, operational use, and transportation. The development, effectiveness and 49 availability of technologies and strategies pose a significant challenge for the remediation, 50 rehabilitation and restoration of these contaminated environments. Many of the 51 technologies developed and in use for the restoration of oil contaminated environments 52 exploit the potential of biological systems, in particular microbial systems, to use these toxic 53 compounds as substrates for growth. Hence, much of the research conducted on 54 bioremediation has concentrated on the capabilities of a single or couple of microbes 55 exhibiting robust and effective growth using petroleum hydrocarbons. However, in the 56 environment, bioremediation is often a complex process involving co-metabolism, cross-57 induction, inhibition and non-interaction among microbes 1-3 , possibly as petroleum 58 hydrocarbons are a mixture of organic pollutants and therefore are used differently by 59 different microbes. These findings, along with others, established bioremediation as a 60 process mediated by a consortium of microbes rather than a few. Thus, characterization of 61 microbial communities of oil contaminated environments could potentially provide 62 guidelines for effective remediation and restoration of such environments. 63 Until recently, it was only possible to study a handful of microorganisms of interest 64 isolated from source materials (as blood, soil, water or air), given the restrictions of the 65 composition of culture media which cannot reflect and mimic the dynamic nutrient fluxes of 66 the source environment. Indeed, only 1% of microorganisms were found to be cultivable 67 4 using a set of media from the highly characterized soil rhizosphere 4 . The advent of high 68 throughput massively-parallel sequencing methods has however, allowed us to investigate 69 the entire complement of organisms inhabiting a certain environment. These next-70 generation sequencing methods (NGS) include a variety of methods to holistically study any 71 biological system such as amplicon sequencing (for variant identification and phylogenetic 72 surveys), whole genome shotgun sequencing (single organism genome and metagenomes) 73 and RNA-Seq (transcriptomes, metatranscriptomes and identification of non-regular RNAs). 74 These powerful methods have ushered in rapid advances in bioinformatics approaches 75 leading to development of software capable of handling huge amounts of data and offering 76 meaningful biological interpretations of the same. Although a technological breakthrough in 77 modern science, a number of NGS methods as metagenomic and transcriptomic/ 78 metatranscriptomic sequencing are still expensive and hence, most studies on ecologic...

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“…encoding enzymes involved in the aliphatic sulfonate assimilation pathway (25,40). BLAST analysis reveals that B. phytofirmans possesses two enzymes that have 23 and 26% identity to the CysB and SsuR transcriptional regulators, respectively.…”

Section: Characterization Of a Pdo-rhodanese Fusion Proteinmentioning

confidence: 99%

Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase–rhodanese fusion protein functions in sulfur assimilation

Motl

Skiba

Kabil

et al. 2017

Journal of Biological Chemistry

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Hydrogen sulfide (HS) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts HS to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.

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Regulation of Sulfur Assimilation Pathways in Burkholderia cenocepacia through Control of Genes by the SsuR Transcription Factor

Cited by 15 publications

References 36 publications

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies

Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase–rhodanese fusion protein functions in sulfur assimilation

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