A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)

For many years, researchers have studied the social lives of bacteria to understand intra- and inter-species interactions. Cell-cell communication, also known as quorum sensing (QS), is used by bacteria to coordinate their behaviour in response to environmental conditions. The QS system in Streptoco...

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Main Author:	Raja Farhana Raja Khairuddin
Format:	thesis
Language:	eng
Published:	2014
Subjects:	T Technology (General)
Online Access:	https://ir.upsi.edu.my/detailsg.php?det=1450
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spelling	oai:ir.upsi.edu.my:14502020-02-27 A computational approach to studying the evolution of streptococcal quorum sensing systems (IR) 2014 Raja Farhana Raja Khairuddin T Technology (General) For many years, researchers have studied the social lives of bacteria to understand intra- and inter-species interactions. Cell-cell communication, also known as quorum sensing (QS), is used by bacteria to coordinate their behaviour in response to environmental conditions. The QS system in Streptococcus species is well known to regulate competence. Studies show that Streptococcus pneumoniae has two homologous QS systems: 1) the competence (Com) system that regulates competence; and 2) a bacteriocin-like peptide (Blp) system that regulates the production of bacteriocins. Both functions are widespread in the genus. In S. pneumoniae, the Blp QS system shares a common ancestor and has similar features to the Com QS system. However, the evolutionary relationship between these QS systems remains obscure. SUCRE methodology was developed to identify the QS homologous genes in the streptococcal species. SUCRE uses four complementary approaches: homology search, putative gene finding, regulon construction, and evolutionary analysis. The performance of SUCRE was assessed in comparison with other orthology detection methods. SUCRE is precise in identifying the QS homologous genes and has similar performance to OrthoMCL. The QS system structures are found to be conserved across the streptococcal species. A streptococcal species phylogeny was constructed from the ribosomal and tRNA synthetase gene families. Using the QS genes identified from SUCRE and the streptococcal species phylogeny, the study infers the evolution of the QS systems in Streptococcus species. The study shows that the QS systems evolved as a regulon unit. The paralogous relationship between each of the QS systems suggests that duplication has a huge influence on functional divergence of the QS systems in the genus. Although, horizontal gene transfer (HGT) is commonly found in bacteria, little evidence is found to support that the effect of HGT on the functional divergence of the QS systems in this genus. However, the QS regulon genes of the same QS system are found to be nonvertically transferred across species that signifies that the HGT event promotes the sequence variation between these genes. 2014 thesis https://ir.upsi.edu.my/detailsg.php?det=1450 https://ir.upsi.edu.my/detailsg.php?det=1450 text eng closedAccess Doctoral Universiti Pendidikan Sultan Idris Fakulti Seni, Komputeran dan Industri Kreatif N/A
institution	Universiti Pendidikan Sultan Idris
collection	UPSI Digital Repository
language	eng
topic	T Technology (General)
spellingShingle	T Technology (General) Raja Farhana Raja Khairuddin A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)
description	For many years, researchers have studied the social lives of bacteria to understand intra- and inter-species interactions. Cell-cell communication, also known as quorum sensing (QS), is used by bacteria to coordinate their behaviour in response to environmental conditions. The QS system in Streptococcus species is well known to regulate competence. Studies show that Streptococcus pneumoniae has two homologous QS systems: 1) the competence (Com) system that regulates competence; and 2) a bacteriocin-like peptide (Blp) system that regulates the production of bacteriocins. Both functions are widespread in the genus. In S. pneumoniae, the Blp QS system shares a common ancestor and has similar features to the Com QS system. However, the evolutionary relationship between these QS systems remains obscure. SUCRE methodology was developed to identify the QS homologous genes in the streptococcal species. SUCRE uses four complementary approaches: homology search, putative gene finding, regulon construction, and evolutionary analysis. The performance of SUCRE was assessed in comparison with other orthology detection methods. SUCRE is precise in identifying the QS homologous genes and has similar performance to OrthoMCL. The QS system structures are found to be conserved across the streptococcal species. A streptococcal species phylogeny was constructed from the ribosomal and tRNA synthetase gene families. Using the QS genes identified from SUCRE and the streptococcal species phylogeny, the study infers the evolution of the QS systems in Streptococcus species. The study shows that the QS systems evolved as a regulon unit. The paralogous relationship between each of the QS systems suggests that duplication has a huge influence on functional divergence of the QS systems in the genus. Although, horizontal gene transfer (HGT) is commonly found in bacteria, little evidence is found to support that the effect of HGT on the functional divergence of the QS systems in this genus. However, the QS regulon genes of the same QS system are found to be nonvertically transferred across species that signifies that the HGT event promotes the sequence variation between these genes.
format	thesis
qualification_name
qualification_level	Doctorate
author	Raja Farhana Raja Khairuddin
author_facet	Raja Farhana Raja Khairuddin
author_sort	Raja Farhana Raja Khairuddin
title	A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)
title_short	A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)
title_full	A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)
title_fullStr	A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)
title_full_unstemmed	A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)
title_sort	computational approach to studying the evolution of streptococcal quorum sensing systems (ir)
granting_institution	Universiti Pendidikan Sultan Idris
granting_department	Fakulti Seni, Komputeran dan Industri Kreatif
publishDate	2014
url	https://ir.upsi.edu.my/detailsg.php?det=1450
_version_	1747832973378453504

A computational approach to studying the evolution of streptococcal quorum sensing systems (IR)

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