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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

Visualization of binary-encoded matrix for relevance of genomes with genes for arsenic operon, aquaporin, and universal stress protein. Data were obtained from the Integrated Microbial Genomes. Black square, relevance annotated for genome; white square, relevance not annotated for genome. When relevance data were not available, we entered a “Not_Reported” for data processing.
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Related In: Results  -  Collection


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f1-mbi-7-2014-025: Visualization of binary-encoded matrix for relevance of genomes with genes for arsenic operon, aquaporin, and universal stress protein. Data were obtained from the Integrated Microbial Genomes. Black square, relevance annotated for genome; white square, relevance not annotated for genome. When relevance data were not available, we entered a “Not_Reported” for data processing.

Mentions: A seven-digit binary code was assigned to 3,274 genomes (119 archaea, 3033 bacteria, and 122 eukaryota) obtained from the IMG system. The order of the seven Pfam families in the binary code is ArsA, ArsB, ArsC, ArsD, ArsR, Aqp, and Usp (Table 1). As functional annotations of genes could change, we selected only genomes that have the complete profile (111111111). A total of 62 microbial genomes from 18 genera had a binary code in which all the seven Pfam families were present. We further grouped the genomes according to their relevance (eg, agriculture, biotechnology, human pathogen, and medical) to help direct further research. A subset of 57 genomes with the complete profile was mapped to 22 assignments of relevance. Additionally, five genomes did not have an assignment of relevance and their assignment was designated “Not_Reported”. A visualization of the matrix of 23-digit binary signatures was constructed for 62 genomes (Fig. 1).


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)

Visualization of binary-encoded matrix for relevance of genomes with genes for arsenic operon, aquaporin, and universal stress protein. Data were obtained from the Integrated Microbial Genomes. Black square, relevance annotated for genome; white square, relevance not annotated for genome. When relevance data were not available, we entered a “Not_Reported” for data processing.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1-mbi-7-2014-025: Visualization of binary-encoded matrix for relevance of genomes with genes for arsenic operon, aquaporin, and universal stress protein. Data were obtained from the Integrated Microbial Genomes. Black square, relevance annotated for genome; white square, relevance not annotated for genome. When relevance data were not available, we entered a “Not_Reported” for data processing.
Mentions: A seven-digit binary code was assigned to 3,274 genomes (119 archaea, 3033 bacteria, and 122 eukaryota) obtained from the IMG system. The order of the seven Pfam families in the binary code is ArsA, ArsB, ArsC, ArsD, ArsR, Aqp, and Usp (Table 1). As functional annotations of genes could change, we selected only genomes that have the complete profile (111111111). A total of 62 microbial genomes from 18 genera had a binary code in which all the seven Pfam families were present. We further grouped the genomes according to their relevance (eg, agriculture, biotechnology, human pathogen, and medical) to help direct further research. A subset of 57 genomes with the complete profile was mapped to 22 assignments of relevance. Additionally, five genomes did not have an assignment of relevance and their assignment was designated “Not_Reported”. A visualization of the matrix of 23-digit binary signatures was constructed for 62 genomes (Fig. 1).

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