Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12

Psychrophilic yeast Glaciozyma antarctica PI12 was isolated from Antarctica. However, the information related to psychrophilic yeast and genus Glaciozyma is limited. Therefore, characterization of growth, cell doubling time, cell division, aerobic and partial anaerobic respiration system, morphology...

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Main Author:	Koh, Joseph Soon Peng
Format:	Thesis
Language:	English English
Published:	2016
Subjects:	QK504-(638) Cryptogams
Online Access:	https://eprints.ums.edu.my/id/eprint/39421/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/39421/2/FULLTEXT.pdf
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spelling	my-ums-ep.394212024-08-05T02:55:12Z Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12 2016 Koh, Joseph Soon Peng QK504-(638) Cryptogams Psychrophilic yeast Glaciozyma antarctica PI12 was isolated from Antarctica. However, the information related to psychrophilic yeast and genus Glaciozyma is limited. Therefore, characterization of growth, cell doubling time, cell division, aerobic and partial anaerobic respiration system, morphology and the growth at -12oC, -7oC and - 5oC were carried out. Our result showed that G. antarctica PI12 formed whitish creamy colony on PDA media, and has an optimal growth temperature of 12oC in YPD media. Its cell doubling time is 15.8 hours per generation, and the cell division occurs on either poles of the cell. G. antarctica PI12 can grow under both aerobic and partially anaerobic conditions, but with a faster growth at aerobic condition. Little is known about the other genes which are involved in the cold adaptation of G. antarctica PI12. Therefore, to understand the adaptation strategies of G. antarctica PI12, RNA-seq was carried out followed by a de novo assembly of G. antarctica PI12 transcriptome using the Trinity assembly package. Thermal stresses such as -12oC, 0oC, 16oC and 20oC were used to induce a maximum number of expressed genes by G. antarctica PI12. We have obtained approximately 465 million of reads using the paired-end Illumina sequencing platform. These reads was assembled into 6,301 unique genes, which comprised of a total of 46,196 unique transcripts (UT) sequences (mean sequence length ~1, 555 bp) including 29,885 UTs with coding sequence (CDS). Our data provide the first comprehensive sequence resource available for functional genomics studies in G. antarctica PI12. Besides, the gene expression patterns of G. antarctica PI12 in response to rapid temperature shifts were determined. 205 and 206 genes were affected when the cells were rapidly shifted from 12oC to 0oC or -12oC in minimal media, and YPD media. When the cells were rapidly shifted from 12oC to 16oC and 20oC, 116 genes were expressed. We grouped the genes obtained from minimal media and YPD into the early cold response (ECR, 0oC for six hours); late cold response (LCR, 0oC for 24 hours); early freeze response (EFR, -12oC for six hours); and late freeze response (LFR, -12oC for 24 hours). On the other hand, we grouped expressed genes in the heat shock response to the early heat response (EHR, 16oC for six hours); and late heat response (LHR, 16oC and 20oC for 24 hours); early heat response (EHR, 20oC for six hours); and late heat response (LHR, 20oC for 24 hours). Interestingly, there are groups of genes expressed consistently according to the time incubation at six and 24 hours. The result implies that the thermal specific early and late responses are mediated by a different and yet uncharacterized regulatory proteins. An adaptation model of G. antarctica PI12 which involved three components, namely the inactivation, the adaptive and the cell death was constructed based on the results, it indicates the complexity of the adaptation strategy of G. antarctica PI12 to adapt to a changing temperature. 2016 Thesis https://eprints.ums.edu.my/id/eprint/39421/ https://eprints.ums.edu.my/id/eprint/39421/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/39421/2/FULLTEXT.pdf text en validuser dphil doctoral Universiti Malaysia Sabah Institut Penyelidikan Bioteknologi
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QK504-(638) Cryptogams
spellingShingle	QK504-(638) Cryptogams Koh, Joseph Soon Peng Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12
description	Psychrophilic yeast Glaciozyma antarctica PI12 was isolated from Antarctica. However, the information related to psychrophilic yeast and genus Glaciozyma is limited. Therefore, characterization of growth, cell doubling time, cell division, aerobic and partial anaerobic respiration system, morphology and the growth at -12oC, -7oC and - 5oC were carried out. Our result showed that G. antarctica PI12 formed whitish creamy colony on PDA media, and has an optimal growth temperature of 12oC in YPD media. Its cell doubling time is 15.8 hours per generation, and the cell division occurs on either poles of the cell. G. antarctica PI12 can grow under both aerobic and partially anaerobic conditions, but with a faster growth at aerobic condition. Little is known about the other genes which are involved in the cold adaptation of G. antarctica PI12. Therefore, to understand the adaptation strategies of G. antarctica PI12, RNA-seq was carried out followed by a de novo assembly of G. antarctica PI12 transcriptome using the Trinity assembly package. Thermal stresses such as -12oC, 0oC, 16oC and 20oC were used to induce a maximum number of expressed genes by G. antarctica PI12. We have obtained approximately 465 million of reads using the paired-end Illumina sequencing platform. These reads was assembled into 6,301 unique genes, which comprised of a total of 46,196 unique transcripts (UT) sequences (mean sequence length ~1, 555 bp) including 29,885 UTs with coding sequence (CDS). Our data provide the first comprehensive sequence resource available for functional genomics studies in G. antarctica PI12. Besides, the gene expression patterns of G. antarctica PI12 in response to rapid temperature shifts were determined. 205 and 206 genes were affected when the cells were rapidly shifted from 12oC to 0oC or -12oC in minimal media, and YPD media. When the cells were rapidly shifted from 12oC to 16oC and 20oC, 116 genes were expressed. We grouped the genes obtained from minimal media and YPD into the early cold response (ECR, 0oC for six hours); late cold response (LCR, 0oC for 24 hours); early freeze response (EFR, -12oC for six hours); and late freeze response (LFR, -12oC for 24 hours). On the other hand, we grouped expressed genes in the heat shock response to the early heat response (EHR, 16oC for six hours); and late heat response (LHR, 16oC and 20oC for 24 hours); early heat response (EHR, 20oC for six hours); and late heat response (LHR, 20oC for 24 hours). Interestingly, there are groups of genes expressed consistently according to the time incubation at six and 24 hours. The result implies that the thermal specific early and late responses are mediated by a different and yet uncharacterized regulatory proteins. An adaptation model of G. antarctica PI12 which involved three components, namely the inactivation, the adaptive and the cell death was constructed based on the results, it indicates the complexity of the adaptation strategy of G. antarctica PI12 to adapt to a changing temperature.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Koh, Joseph Soon Peng
author_facet	Koh, Joseph Soon Peng
author_sort	Koh, Joseph Soon Peng
title	Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12
title_short	Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12
title_full	Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12
title_fullStr	Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12
title_full_unstemmed	Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12
title_sort	analysis of the cold adaptation strategy of antarctic yeast glaciozyma antarctica pi12
granting_institution	Universiti Malaysia Sabah
granting_department	Institut Penyelidikan Bioteknologi
publishDate	2016
url	https://eprints.ums.edu.my/id/eprint/39421/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/39421/2/FULLTEXT.pdf
_version_	1811770509503758336

Analysis of the cold adaptation strategy of antarctic yeast Glaciozyma antarctica PI12

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