scholarly journals Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae

2021 ◽  
Vol 9 (8) ◽  
pp. 1780
Author(s):  
Raphael D. Isokpehi ◽  
Dominique S. McInnis ◽  
Antoinette M. Destefano ◽  
Gabrielle S. Johnson ◽  
Akimio D. Walker ◽  
...  
Keyword(s):  
Visual Analytics ◽  
Stress Proteins ◽  
Stress Protein ◽  
Inorganic Mercury ◽  
Food Sources ◽  
Aquatic Environments ◽  
Atp Binding ◽  
Binding Motif ◽  
Universal Stress Protein ◽  
Methylmercury Production

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.

scholarly journals Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qiong Jia ◽  
Xinling Hu ◽  
Dawei Shi ◽  
Yan Zhang ◽  
Meihao Sun ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Metabolic Pathways ◽  
Biochemical Analysis ◽  
Stress Proteins ◽  
Stress Protein ◽  
Human Monocyte ◽  
Dependent Manner ◽  
Proline Metabolism ◽  
Universal Stress Protein ◽  
Induced Proteins

Abstract The universal stress protein family is a family of stress-induced proteins. Universal stress proteins affect latency and antibiotic resistance in mycobacteria. Here, we showed that Mycobacterium smegmatis overexpressing M. tuberculosis universal stress protein Rv2624c exhibits increased survival in human monocyte THP-1 cells. Transcriptome analysis suggested that Rv2624c affects histidine metabolism, and arginine and proline metabolism. LC-MS/MS analysis showed that Rv2624c affects the abundance of arginine, a modulator of both mycobacteria and infected THP-1 cells. Biochemical analysis showed that Rv2624c is a nucleotide-binding universal stress protein, and an Rv2624c mutant incapable of binding ATP abrogated the growth advantage in THP-1 cells. Rv2624c may therefore modulate metabolic pathways in an ATP-dependent manner, changing the abundance of arginine and thus increasing survival in THP-1 cells.

scholarly journals Identification of Drought-Responsive Universal Stress Proteins in Viridiplantae

2011 ◽  
Vol 5 ◽  
pp. BBI.S6061 ◽  
Author(s):  
Raphael D. Isokpehi ◽  
Shaneka S. Simmons ◽  
Hari H.P. Cohly ◽  
Stephen I.N. Ekunwe ◽  
Gregorio B. Begonia ◽  
...  
Keyword(s):  
Stress Proteins ◽  
Stress Protein ◽  
Microarray Dataset ◽  
Water Deficit Stress ◽  
Binding Motif ◽  
Gene Transcript ◽  
Database Mining ◽  
Functional Annotations ◽  
Genes Encoding

Genes encoding proteins that contain the universal stress protein (USP) domain are known to provide bacteria, archaea, fungi, protozoa, and plants with the ability to respond to a plethora of environmental stresses. Specifically in plants, drought tolerance is a desirable phenotype. However, limited focused and organized functional genomic datasets exist on drought-responsive plant USP genes to facilitate their characterization. The overall objective of the investigation was to identify diverse plant universal stress proteins and Expressed Sequence Tags (ESTs) responsive to water-deficit stress. We hypothesize that cross-database mining of functional annotations in protein and gene transcript bioinformatics resources would help identify candidate drought-responsive universal stress proteins and transcripts from multiple plant species. Our bioinformatics approach retrieved, mined and integrated comprehensive functional annotation data on 511 protein and 1561 ESTs sequences from 161 viridiplantae taxa. A total of 32 drought-responsive ESTs from 7 plant genera Glycine, Hordeum, Manihot, Medicago, Oryza, Pinus and Triticum were identified. Two Arabidopsis USP genes At3g62550 and At3g53990 that encode ATP-binding motif were up-regulated in a drought microarray dataset. Further, a dataset of 80 simple sequence repeats (SSRs) linked to 20 singletons and 47 transcript assembles was constructed. Integrating the datasets on SSRs and drought-responsive ESTs identified three drought-responsive ESTs from bread wheat (BE604157), soybean (BM887317) and maritime pine (BX682209). The SSR sequence types were CAG, ATA and AT respectively. The datasets from cross-database mining provide organized resources for the characterization of USP genes as useful targets for engineering plant varieties tolerant to unfavorable environmental conditions.

scholarly journals Characterization of the thermotolerant cell. I. Effects on protein synthesis activity and the regulation of heat-shock protein 70 expression.

1988 ◽  
Vol 106 (4) ◽  
pp. 1105-1116 ◽  
Author(s):  
L A Mizzen ◽  
W J Welch
Keyword(s):  
Protein Synthesis ◽  
Heat Shock ◽  
Stress Proteins ◽  
Stress Protein ◽  
Shock Treatment ◽  
Heat Shock Treatment ◽  
Normal Medium ◽  
Growth Environment ◽  
Mammalian Cell Lines ◽  
C 30

Exposure of mammalian cells to a nonlethal heat-shock treatment, followed by a recovery period at 37 degrees C, results in increased cell survival after a subsequent and otherwise lethal heat-shock treatment. Here we characterize this phenomenon, termed acquired thermotolerance, at the level of translation. In a number of different mammalian cell lines given a severe 45 degrees C/30-min shock and then returned to 37 degrees C, protein synthesis was completely inhibited for as long as 5 h. Upon resumption of translational activity, there was a marked induction of heat-shock (or stress) protein synthesis, which continued for several hours. In contrast, cells first made thermotolerant (by a pretreatment consisting of a 43 degrees C/1.5-h shock and further recovery at 37 degrees C) and then presented with the 45 degrees C/30-min shock exhibited considerably less translational inhibition and an overall reduction in the amount of subsequent stress protein synthesis. The acquisition and duration of such "translational tolerance" was correlated with the expression, accumulation, and relative half-lives of the major stress proteins of 72 and 73 kD. Other agents that induce the synthesis of the stress proteins, such as sodium arsenite, similarly resulted in the acquisition of translational tolerance. The probable role of the stress proteins in the acquisition of translational tolerance was further indicated by the inability of the amino acid analogue, L-azetidine 2-carboxylic acid, an inducer of nonfunctional stress proteins, to render cells translationally tolerant. If, however, analogue-treated cells were allowed to recover in normal medium, and hence produce functional stress proteins, full translational tolerance was observed. Finally, we present data indicating that the 72- and 73-kD stress proteins, in contrast to the other major stress proteins (of 110, 90, and 28 kD), are subject to strict regulation in the stressed cell. Quantitation of 72- and 73-kD synthesis after heat-shock treatment under a number of conditions revealed that "titration" of 72/73-kD synthesis in response to stress may represent a mechanism by which the cell monitors its local growth environment.

scholarly journals Effects of the Bacterial Extract OM-85 on Phagocyte Functions and the Stress Response

1994 ◽  
Vol 3 (2) ◽  
pp. 143-148 ◽  
Author(s):  
S. Baladi ◽  
S. Kantengwa ◽  
Y. R. A. Donati ◽  
B. S. Polla
Keyword(s):  
Stress Response ◽  
Respiratory Burst ◽  
Stress Proteins ◽  
Human Peripheral Blood ◽  
Stress Protein ◽  
Blood Monocytes ◽  
Bacterial Extract ◽  
Heat Shock Stress ◽  
Intracellular Expression ◽  
Glucose Regulated Protein

The effects of the bacterial extract OM-85 on the respiratory burst, intracellular calcium and the stress response have been investigated in human peripheral blood monocytes from normal donors. Activation of the respiratory burst during bacterial phagocytosis has been previously associated with heat shock/stress proteins synthesis. Whereas OM-85 stimulated superoxide production and increased Ca2+mobilization, it fared to induce synthesis of classical HSPs. The lack of stress protein induction was observed even in the presence of iron which potentiates both oxidative injury and stress protein induction during bacterial phagocytosis. However OM-85 induced a 75–78 kDa protein, which is likely to be a glucose regulated protein (GRP78), and enhanced intracellular expression of interleukin-lβ precursor.

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