Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption

The genus Jeotgalibacillus under the family of Planococcaceae is one of the understudy genera. In this project, a bacterium strain D5 was isolated from Desaru beach, Johor. This study aimed to characterize strain D5 from morphological, physiological and biochemical aspects, in addition to examine th...

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Main Author:	Yaakop, Amira Suriaty
Format:	Thesis
Language:	English
Published:	2017
Subjects:	QH Natural history
Online Access:	http://eprints.utm.my/id/eprint/79238/1/AmiraSuriatyYaakopPFBME2017.pdf
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spelling	my-utm-ep.792382018-10-14T08:39:44Z Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption 2017 Yaakop, Amira Suriaty QH Natural history The genus Jeotgalibacillus under the family of Planococcaceae is one of the understudy genera. In this project, a bacterium strain D5 was isolated from Desaru beach, Johor. This study aimed to characterize strain D5 from morphological, physiological and biochemical aspects, in addition to examine the genomic feature and RNA expression response under saline stress. To achieve this objective, polyphasic analyses (phenotypic and genotypic), genome sequencing and RNA-Seq-based transcriptome analyses were performed. The result showed that strain D5 was mostly similar to Jeotgalibacillus alimentarius DSM 18867T with 99.87% 16S rRNA sequence similarity, and lower in similarity to other species. Strain D5 is distinguished from the other Jeotgalibacillus type strains due to the differences in phenotypic and genotypic characteristics which include morphology, endospore position, and shape, acid production from carbohydrates, tolerance to NaCl, fatty acid composition, DNA G+C content and DNA–DNA relatedness values. The D5 was proposed as a new type strain with the name of J. malaysiensis (DSM 28777T =KCTC 33350T). The complete genome of J. malaysiensis (3.52 Mbp) was sequenced using PacBio RS II sequencing system and was compared with draft genomes of J. alimentarius, J. campisalis, and J. soli. In total, 224 complete metabolic pathways were detected in J. malaysiensis genome, which include glycolysis, Krebs cycle, TCA cycle, pentose phosphate and others. J. malaysiensis shared 1,158 orthologous genes with the other Jeotgalibacillus spp. Which are involved in central metabolism, such as genes for flagellar activity, amino acid transport, translation, ribosomal structure, and biogenesis. To understand the mechanism of osmotic adaptation in J. malaysiensis, cells were cultivated in marine broth supplemented with 2% NaCl (control), saline stress of 10% and 20% (w/v) NaCl. The pairwise differentially expressed gene (DEGs) detected during the osmotic upshift were analyzed and categorized according to eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) groups. At 10% (w/v) NaCl, 195 genes were differentially expressed while at 20 % (w/v) NaCl, 166 DEGs were differentially expressed. Osmotic stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. J. malaysiensis apply a combination of approaches which include utilization of the TRK system for the regulation of K+ uptake, uptake and synthesis of various osmoprotectants especially proline and glutamate. As a conclusion, this study has provided new insights into the biology of this genus and showed that J. malaysiensis established halotolerance via a global cooperative mechanism, rather than by one single approach. 2017 Thesis http://eprints.utm.my/id/eprint/79238/ http://eprints.utm.my/id/eprint/79238/1/AmiraSuriatyYaakopPFBME2017.pdf application/pdf en public phd doctoral Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering Faculty of Biosciences and Medical Engineering
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	QH Natural history
spellingShingle	QH Natural history Yaakop, Amira Suriaty Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
description	The genus Jeotgalibacillus under the family of Planococcaceae is one of the understudy genera. In this project, a bacterium strain D5 was isolated from Desaru beach, Johor. This study aimed to characterize strain D5 from morphological, physiological and biochemical aspects, in addition to examine the genomic feature and RNA expression response under saline stress. To achieve this objective, polyphasic analyses (phenotypic and genotypic), genome sequencing and RNA-Seq-based transcriptome analyses were performed. The result showed that strain D5 was mostly similar to Jeotgalibacillus alimentarius DSM 18867T with 99.87% 16S rRNA sequence similarity, and lower in similarity to other species. Strain D5 is distinguished from the other Jeotgalibacillus type strains due to the differences in phenotypic and genotypic characteristics which include morphology, endospore position, and shape, acid production from carbohydrates, tolerance to NaCl, fatty acid composition, DNA G+C content and DNA–DNA relatedness values. The D5 was proposed as a new type strain with the name of J. malaysiensis (DSM 28777T =KCTC 33350T). The complete genome of J. malaysiensis (3.52 Mbp) was sequenced using PacBio RS II sequencing system and was compared with draft genomes of J. alimentarius, J. campisalis, and J. soli. In total, 224 complete metabolic pathways were detected in J. malaysiensis genome, which include glycolysis, Krebs cycle, TCA cycle, pentose phosphate and others. J. malaysiensis shared 1,158 orthologous genes with the other Jeotgalibacillus spp. Which are involved in central metabolism, such as genes for flagellar activity, amino acid transport, translation, ribosomal structure, and biogenesis. To understand the mechanism of osmotic adaptation in J. malaysiensis, cells were cultivated in marine broth supplemented with 2% NaCl (control), saline stress of 10% and 20% (w/v) NaCl. The pairwise differentially expressed gene (DEGs) detected during the osmotic upshift were analyzed and categorized according to eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) groups. At 10% (w/v) NaCl, 195 genes were differentially expressed while at 20 % (w/v) NaCl, 166 DEGs were differentially expressed. Osmotic stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. J. malaysiensis apply a combination of approaches which include utilization of the TRK system for the regulation of K+ uptake, uptake and synthesis of various osmoprotectants especially proline and glutamate. As a conclusion, this study has provided new insights into the biology of this genus and showed that J. malaysiensis established halotolerance via a global cooperative mechanism, rather than by one single approach.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Yaakop, Amira Suriaty
author_facet	Yaakop, Amira Suriaty
author_sort	Yaakop, Amira Suriaty
title	Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
title_short	Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
title_full	Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
title_fullStr	Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
title_full_unstemmed	Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
title_sort	genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption
granting_institution	Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering
granting_department	Faculty of Biosciences and Medical Engineering
publishDate	2017
url	http://eprints.utm.my/id/eprint/79238/1/AmiraSuriatyYaakopPFBME2017.pdf
_version_	1747818179812392960

Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption

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