Bacterial chromate reduction: A review of important genomic, proteomic, and bioinformatic analysis

Pradhan, Sukanta Kumar; Singh, Nihar Ranjan; Rath, Bhagwat Prasad; Thatoi, Hrudayanath

doi:10.1080/10643389.2016.1258912

Cited by 45 publications

(26 citation statements)

References 104 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…E . antarcticum B7 resistance to chromium confers advantages to its adaptation and may be a future target in bioremediation trials against this toxic metal [ 85 , 86 ].…”

Section: Resultsmentioning

confidence: 99%

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance

et al. 2018

View full text Add to dashboard Cite

Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.

show abstract

“…E . antarcticum B7 resistance to chromium confers advantages to its adaptation and may be a future target in bioremediation trials against this toxic metal [ 85 , 86 ].…”

Section: Resultsmentioning

confidence: 99%

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Therefore, compared to high-throughput metagenomic methods, the phenotype test is a straightforward way to evaluate heavy metal contamination conditions. Microbial Cr (VI) remediation ability is related to Cr remediation related genes and proteins in microorganisms ( Pradhan et al, 2016 ). Although chrA and yieF were not found in the XGD and LJX samples, the microbial communities of these three sites also exhibited Cr (VI) reduction ability.…”

Section: Discussionmentioning

confidence: 99%

“…Although chrA and yieF were not found in the XGD and LJX samples, the microbial communities of these three sites also exhibited Cr (VI) reduction ability. This may be due to the function of other Cr (VI) reductases, such as SOD, catalase, NemA, and LpDH ( Thatoi et al, 2014 ; Pradhan et al, 2016 ). Although the riparian soil samples were incubated in the laboratory, the copies of chrA and yieF did not change after incubation.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River

Pei

et al. 2018

Front. Microbiol.

View full text Add to dashboard Cite

The Yellow River is the most important water resource in northern China. In the recent past, heavy metal contamination has become severe due to industrial processes and other anthropogenic activities. In this study, riparian soil samples with varying levels of chromium (Cr) pollution severity were collected along the Gansu industrial reach of the Yellow River, including samples from uncontaminated sites (XC, XGU), slightly contaminated sites (LJX, XGD), and heavily contaminated sites (CG, XG). The Cr concentrations of these samples varied from 83.83 mg⋅kg-1 (XGU) to 506.58 mg⋅kg-1 (XG). The chromate [Cr (VI)] reducing ability in the soils collected in this study followed the sequence of the heavily contaminated > slightly contaminated > the un-contaminated. Common Cr remediation genes chrA and yieF were detected in the XG and CG samples. qRT-PCR results showed that the expression of chrA was up-regulated four and threefold in XG and CG samples, respectively, whereas the expression of yieF was up-regulated 66- and 7-fold in the same samples after 30 min treatment with Cr (VI). The copy numbers of chrA and yieF didn’t change after 35 days incubation with Cr (VI). The microbial communities in the Cr contaminated sampling sites were different from those in the uncontaminated samples. Especially, the relative abundances of Firmicutes and Bacteroidetes were higher while Actinobacteria was lower in the contaminated group than uncontaminated group. Further, potential indicator species, related to Cr such as Cr-remediation genera (Geobacter, PSB-M-3, Flavobacterium, and Methanosarcina); the Cr-sensitive genera (Skermanella, Iamia, Arthrobacter, and Candidatus Nitrososphaera) were also identified. These data revealed that Cr shifted microbial composition and function. Further, Cr (VI) reducing ability could be related with the expression of Cr remediation genes.

show abstract

“…Chromium exists in two major oxidation states in the environment, trivalent (+ 3) and hexavalent (+ 6) chromium, both stable and water-soluble [26]. Various sources of chromium include textile-dyeing industries, tanneries, electroplating, wood preservation, and petroleum refining [27,28]. Due to its soluble nature, chromium can actively enter cells and damage their constituents [29].…”

Section: Introductionmentioning

confidence: 99%

Cellular response of Brevibacterium casei #NIOSBA88 to arsenic and chromium—a proteomic approach

Shah

Damare

2020

Braz J Microbiol

View full text Add to dashboard Cite

Cellular response against different heavy metal stress differs with the metal. Arsenic and chromium are heavy metals and toxic to living systems. The concentration of these metals in seawater is very low. However, due to their solubility in nature, they actively enter cells via various transport mechanisms and cause damage to the cells. Brevibacterium casei #NIOSBA88, a marine-derived, gram-positive isolate was multi-metal tolerant. Proteomic analysis of this isolate in response to arsenic and chromium resulted in the identification of total 2549 proteins, out of which 880 proteins were found to be commonly expressed at 750 mgL −1 arsenic and 100 mgL −1 chromium and in absence of both the metals. In contrast, 533, 212, and 270 proteins were found to be unique in the absence of any metal, 750 mgL −1 of arsenic and 100 mgL −1 of chromium respectively. Proteins such as antibiotic biosynthesis monooxygenase, ArsR family transcriptional regulator, cytochrome C oxidase subunit II, and thioredoxin reductase were exclusively expressed only in response to arsenic and chromium. Other proteins like superoxide dismutase, lipid hydroperoxide reductase, and thioredoxin-disulfide reductase were found to be upregulated in response to both the metals. Most of the proteins involved in the normal cell functioning were found to be downregulated. Major metabolic functions affected include amino acid metabolism, carbohydrate metabolism, translation, and energy metabolism. Peptide mass fingerprinting of Brevibacterium casei #NIOSBA88 exposed to arsenic and chromium respectively revealed the deleterious effect of these metals on the bacterium and its strategy to overcome the stress.

show abstract

Bacterial chromate reduction: A review of important genomic, proteomic, and bioinformatic analysis

Cited by 45 publications

References 104 publications

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance

Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River

Cellular response of Brevibacterium casei #NIOSBA88 to arsenic and chromium—a proteomic approach

Contact Info

Product

Resources

About