title: Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.
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.
authors.affiliation: Department of Biology, Bethune-Cookman University, Daytona Beach, FL, USA.
authors.forename: Raphael D
authors.initials: RD
authors.lastname: Isokpehi
authors.affiliation: RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson, MS, USA.
authors.forename: Udensi K
authors.initials: UK
authors.lastname: Udensi
authors.affiliation: Department of Biology, Jackson State University, Jackson, MS, USA. ; Department of Computer Science, Jackson State University, Jackson, MS, USA.
authors.forename: Shaneka S
authors.initials: SS
authors.lastname: Simmons
authors.affiliation: Jarvis Christian College, Hawkins, TX, USA.
authors.forename: Antoinesha L
authors.initials: AL
authors.lastname: Hollman
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
authors.forename: Antia E
authors.initials: AE
authors.lastname: Cain
authors.affiliation: H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
authors.forename: Samson A
authors.initials: SA
authors.lastname: Olofinsae
authors.affiliation: H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
authors.forename: Oluwabukola A
authors.initials: OA
authors.lastname: Hassan
authors.affiliation: H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
authors.forename: Zainab A
authors.initials: ZA
authors.lastname: Kashim
authors.affiliation: H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
authors.forename: Ojochenemi A
authors.initials: OA
authors.lastname: Enejoh
authors.affiliation: H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
authors.forename: Deborah E
authors.initials: DE
authors.lastname: Fasesan
authors.affiliation: H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
authors.forename: Oyekanmi
authors.initials: O
authors.lastname: Nashiru
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