Interactive Analytics for Complex Cognitive Activities on Information             from Annotations of Prokaryotic Genomes

Isokpehi, Raphael D.; Wootson, Kiara M.; Smith-McInnis, Dominique R.; Simmons, Shaneka S.

doi:10.22369/issn.2153-4136/8/2/5

Cited by 1 publication

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References 40 publications

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“…Our report provides findings from protein sequence analytics to guide further research on the molecular functions, biological processes and cellular components associated with Desulfovibrionaceae universal stress proteins (USPs). In our prior publications, we have applied bioinformatics and developed visual analytics resources to understand the universal stress proteins of taxonomic groups namely viridiplantae, Bacillus , Schistosoma , Alcanivorax , Brucella and Lactobacillus [ 35 , 41 , 42 , 43 , 44 , 45 , 46 ]. In this report, we have made noteworthy findings on a collection of 719 Desulfovibrionaceae USPs regarding (1) protein domain arrangement; and (2) functional amino acid residues ( Figure 1 ).…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae

et al. 2021

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The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments.

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