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Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.

Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O - Microbiol Insights (2014)

Bottom Line: The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease.Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling.Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Bethune-Cookman University, Daytona Beach, FL, USA.

ABSTRACT
The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus, and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

No MeSH data available.


Related in: MedlinePlus

Transcription units and functional associations of arsenic resistance operon in Bacteroides thetaiotaomicron VPI-5482. The web pages for the transcription units are http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-83 and http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-442.
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f4-mbi-7-2014-025: Transcription units and functional associations of arsenic resistance operon in Bacteroides thetaiotaomicron VPI-5482. The web pages for the transcription units are http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-83 and http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-442.

Mentions: The integration of data fields from several data sources was accomplished through visual analytics tasks. Figure 2 is a visualization that integrates the data on binary code; body site; genome; and the availability of Pfam annotations and abundance (number of genes) for 12 reference genomes sequenced by the HMP. Several patterns can be identified from Figure 2. As gastrointestinal pre-systemic metabolism is an essential step of arsenic metabolism in humans, we further investigated the abundance of arsenic resistance genes in 43 Bacteroides genomes (Fig. 3). There were several noteworthy findings from the visualization including (i) multiple copies of arsA, arsD, and arsR were observed in the genomes of Bacteroides intestinalis 341, DSM 17393, and B. thetaiotaomicron VPI-5482; (ii) all the Bacteroides genomes did not include the annotation for arsB (Pfam2040, arsB); and (iii) in 21 Bacteroides genomes, only one arsC gene per genome was annotated. Clearly, the B. intestinalis and B. thetaiotaomicron strains have multiple arsA, arsD, and arsR, which is indicative of the presence of at least two arsenic resistance operons. The genomic context of the genes in the arsenic operons of B. thetaiotaomicron is presented in Figure 4. Further analysis of the Pfam domain composition of the three genes annotated with the Pfam for the arsA gene revealed that two genes (BT_0116 and BT_0802) had only the Pfam02374 annotation, whereas BT_3895 had a protein domain annotation of Pfam02374 (arsA) and Pfam10609 (ParA/MinD ATPase like).


Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.

Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O - Microbiol Insights (2014)

Transcription units and functional associations of arsenic resistance operon in Bacteroides thetaiotaomicron VPI-5482. The web pages for the transcription units are http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-83 and http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-442.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4230230&req=5

f4-mbi-7-2014-025: Transcription units and functional associations of arsenic resistance operon in Bacteroides thetaiotaomicron VPI-5482. The web pages for the transcription units are http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-83 and http://biocyc.org/BTHE226186/NEW-IMAGE?type=OPERON&object=TUJXV-442.
Mentions: The integration of data fields from several data sources was accomplished through visual analytics tasks. Figure 2 is a visualization that integrates the data on binary code; body site; genome; and the availability of Pfam annotations and abundance (number of genes) for 12 reference genomes sequenced by the HMP. Several patterns can be identified from Figure 2. As gastrointestinal pre-systemic metabolism is an essential step of arsenic metabolism in humans, we further investigated the abundance of arsenic resistance genes in 43 Bacteroides genomes (Fig. 3). There were several noteworthy findings from the visualization including (i) multiple copies of arsA, arsD, and arsR were observed in the genomes of Bacteroides intestinalis 341, DSM 17393, and B. thetaiotaomicron VPI-5482; (ii) all the Bacteroides genomes did not include the annotation for arsB (Pfam2040, arsB); and (iii) in 21 Bacteroides genomes, only one arsC gene per genome was annotated. Clearly, the B. intestinalis and B. thetaiotaomicron strains have multiple arsA, arsD, and arsR, which is indicative of the presence of at least two arsenic resistance operons. The genomic context of the genes in the arsenic operons of B. thetaiotaomicron is presented in Figure 4. Further analysis of the Pfam domain composition of the three genes annotated with the Pfam for the arsA gene revealed that two genes (BT_0116 and BT_0802) had only the Pfam02374 annotation, whereas BT_3895 had a protein domain annotation of Pfam02374 (arsA) and Pfam10609 (ParA/MinD ATPase like).

Bottom Line: The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease.Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling.Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Bethune-Cookman University, Daytona Beach, FL, USA.

ABSTRACT
The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus, and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

No MeSH data available.


Related in: MedlinePlus