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

• 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
• Institution: Universiti Teknologi Malaysia

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.