Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion

Tripathi, Abhilash Kumar; Thakur, Payal; Saxena, Priya; Rauniyar, Shailabh; Gopalakrishnan, Vinoj; Singh, Ram Nageena; Gadhamshetty, Venkataramana; Gnimpieba, Etienne Z.; Jasthi, Bharat K.; Sani, Rajesh K.

doi:10.3389/fmicb.2021.754140

Cited by 40 publications

(12 citation statements)

References 156 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These include the production of hydrogen sulfide, ammonia, and some organic and inorganic acids [ 2 ]. Several MIC mechanisms have been described, including chemical MIC (CMIC) and electrical MIC (EMIC) [ 3 ]. Metal corrosion by the production of corrosive metabolites such as hydrogen sulfide is known as CMIC, whereas the corrosion involving direct electron transfer between bacteria and metal is known as EMIC [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

et al. 2023

Self Cite

View full text Add to dashboard Cite

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB’s role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.

show abstract

Section: Introductionmentioning

confidence: 99%

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…Cu and other heavy-metal toxicity in the environment have been addressed previously using sulfate-reducing bacteria (SRB) [4,[16][17][18]. SRB are heterotrophic anaerobic microorganisms that oxidize simple organic compounds by reducing sulfate to sulfide [19]. The sulfide thus generated can easily remove heavy metals such as Cu from contaminated sites by forming metal sulfide complexes [16].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

Tripathi

Saxena

Thakur

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.

show abstract

“…Another important enzyme in SRBs is the sulfite reductase enzyme, which has three subunits encoded by dsvABC genes. Another important enzyme in the function of SRB bacteria is ATP sulfurylase, which is encoded by the sat gene and plays a key role in the uptake of sulfate activated by APS sulfurylase (Tripathi et al, 2021;Li et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

The antibiofilm and antibacterial effects of medicinal plant extracts on isolated sulfate-reducing bacteria from orthodontic appliances

KALBASSI¹,

YARAHMADI

MOHAMMADIFARD

et al. 2022

Food Sci. Technol

View full text Add to dashboard Cite

Sulfate-Reducing Bacteria (SRB) are a heterogeneous group of oral microflorae that cause dental caries, destructive periodontal infections, and biofilms on fixed orthodontic appliances. Plant extracts as a source of antibacterial components may have acceptable activity against SRB strains and their biofilm development. Our study aimed at determining the antibiofilm, antimicrobial efficacy, and cytotoxicity of Iran's endemic plants against pathogenic SRB. Plantago ovata, Terminalia chebula, Eugenia caryophyllata, and Aloe vera extracts were prepared according to standard methods. Patients and orthodontic appliances samples were collected, and SRB strains were isolated using standard tests and 16S rRNA analysis. The extracts' antimicrobial, antibiofilm activity, and cytotoxicity were determined using dilution broth micro, crystal violet staining, and MTT method, respectively. Biofilm involved gene expression of strains determined using Real-time PCR. Three SRB isolates harboring target genes were identified using 16S rDNA that showed a more than 90% of similarity to Desulfomicrobium orale spp. All investigated extracts showed good activity against SRB isolates. T. chebula, E. caryophyllata, and A. vera showed promising antibiofilm activity, and their subMIC concentrations downregulated biofilm-forming related genes in all isolates. T. Chebula had the lowest cytotoxicity, followed by E. caryophyllata and A. vera. T. Chebula also showed the best average selectivity index (SI) of 17.9, followed by E. caryophyllata (12.52). Extracts investigated in the present study had good antibacterial and antibiofilm activity against isolated sulfate-reducing bacteria isolated from patients' orthodontic appliances. Most of these extracts may be potential candidates for the development of antibacterial drugs.

show abstract

Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion

Cited by 40 publications

References 156 publications

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

The antibiofilm and antibacterial effects of medicinal plant extracts on isolated sulfate-reducing bacteria from orthodontic appliances

Contact Info

Product

Resources

About