Cover Image

Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology

Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL...

Full description

Saved in:
Bibliographic Details
Main Authors: Tripathi, Abhilash Kumar, Samanta, Dipayan, Saxena, Priya, Thakur, Payal, Rauniyar, Shailabh, Goh, Kian Mau, Sani, Rajesh Kumar
Format: Article
Language:English
Published: MDPI 2023
Subjects:
QD Chemistry
Online Access:http://eprints.utm.my/105770/1/GohKianMau2023_IdentificationofAHLSynthaseinDesulfovibriovulgarisHildenborough.pdf
http://eprints.utm.my/105770/
http://dx.doi.org/10.3390/catal13020364
Tags: Add Tag
No Tags, Be the first to tag this record!
id my.utm.105770
record_format eprints
spelling my.utm.1057702024-05-20T06:22:32Z http://eprints.utm.my/105770/ Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology Tripathi, Abhilash Kumar Samanta, Dipayan Saxena, Priya Thakur, Payal Rauniyar, Shailabh Goh, Kian Mau Sani, Rajesh Kumar QD Chemistry Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven a-helices and six ß sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation. MDPI 2023 Article PeerReviewed application/pdf en http://eprints.utm.my/105770/1/GohKianMau2023_IdentificationofAHLSynthaseinDesulfovibriovulgarisHildenborough.pdf Tripathi, Abhilash Kumar and Samanta, Dipayan and Saxena, Priya and Thakur, Payal and Rauniyar, Shailabh and Goh, Kian Mau and Sani, Rajesh Kumar (2023) Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology. Catalysts, 13 (2). pp. 1-18. ISSN 2073-4344 http://dx.doi.org/10.3390/catal13020364 DOI : 10.3390/catal13020364
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic QD Chemistry
spellingShingle QD Chemistry
Tripathi, Abhilash Kumar
Samanta, Dipayan
Saxena, Priya
Thakur, Payal
Rauniyar, Shailabh
Goh, Kian Mau
Sani, Rajesh Kumar
Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology
description Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven a-helices and six ß sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation.
format Article
author Tripathi, Abhilash Kumar
Samanta, Dipayan
Saxena, Priya
Thakur, Payal
Rauniyar, Shailabh
Goh, Kian Mau
Sani, Rajesh Kumar
author_facet Tripathi, Abhilash Kumar
Samanta, Dipayan
Saxena, Priya
Thakur, Payal
Rauniyar, Shailabh
Goh, Kian Mau
Sani, Rajesh Kumar
author_sort Tripathi, Abhilash Kumar
title Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology
title_short Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology
title_full Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology
title_fullStr Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology
title_full_unstemmed Identification of AHL synthase in Desulfovibrio vulgaris Hildenborough using an in-silico methodology
title_sort identification of ahl synthase in desulfovibrio vulgaris hildenborough using an in-silico methodology
publisher MDPI
publishDate 2023
url http://eprints.utm.my/105770/1/GohKianMau2023_IdentificationofAHLSynthaseinDesulfovibriovulgarisHildenborough.pdf
http://eprints.utm.my/105770/
http://dx.doi.org/10.3390/catal13020364
_version_ 1800082660978065408
score 13.211869

Similar Items