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Isokpehi RD, Udensi UK, Simmons SS, et al. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. Microbiol Insights. 2014;7:25-34doi: 10.4137/MBI.S18076.
Isokpehi, R. D., Udensi, U. K., Simmons, S. S., Hollman, A. L., Cain, A. E., Olofinsae, S. A., Hassan, O. A., Kashim, Z. A., Enejoh, O. A., Fasesan, D. E., & Nashiru, O. (2014). Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. Microbiology insights, 725-34. https://doi.org/10.4137/MBI.S18076
Isokpehi, Raphael D, et al. "Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes." Microbiology insights vol. 7 (2014): 25-34. doi: https://doi.org/10.4137/MBI.S18076
Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. Microbiol Insights. 2014 Nov 11;7:25-34. doi: 10.4137/MBI.S18076. eCollection 2014. PMID: 25452698; PMCID: PMC4230230.
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Microbiol Insights. 2014 Nov 11;7:25-34. doi: 10.4137/MBI.S18076. eCollection 2014.

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

Microbiology insights

Raphael D Isokpehi, Udensi K Udensi, Shaneka S Simmons, Antoinesha L Hollman, Antia E Cain, Samson A Olofinsae, Oluwabukola A Hassan, Zainab A Kashim, Ojochenemi A Enejoh, Deborah E Fasesan, Oyekanmi Nashiru

Affiliations

  1. Department of Biology, Bethune-Cookman University, Daytona Beach, FL, USA.
  2. RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson, MS, USA.
  3. Department of Biology, Jackson State University, Jackson, MS, USA. ; Department of Computer Science, Jackson State University, Jackson, MS, USA.
  4. Jarvis Christian College, Hawkins, TX, USA.
  5. Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
  6. H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.

PMID: 25452698 PMCID: PMC4230230 DOI: 10.4137/MBI.S18076

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.

Keywords: Bacteroides; Bacteroidetes; Human Microbiome Project; arsenate; arsenic; arsenite; bioinformatics; genomes; gut microbiota; heavy metal transport; human symbiont; mercuric transport; secondary data analysis; visual analytics

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