Gene amplification and sequencing of hemicellulase using culture dependent technique

The present study aims to discover hemicellulase genes from thermophilic bacteria of Anoxybacillus gonensis G2T and Halothermobacillus malaysiensis RA using culture dependent technique. The hemicellulase genes with the amplicon size of 2118 bp, 1143 bp, 1554 bp and 2190 bp from A. gonensis G2T and H...

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Main Author:	Saimon, Nur Nazwa
Format:	Thesis
Language:	English
Published:	2016
Subjects:	TP Chemical technology
Online Access:	http://eprints.utm.my/id/eprint/78944/1/NurNazwaSaimonMFBME2016.pdf
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spelling	my-utm-ep.789442018-09-19T05:12:45Z Gene amplification and sequencing of hemicellulase using culture dependent technique 2016-09 Saimon, Nur Nazwa TP Chemical technology The present study aims to discover hemicellulase genes from thermophilic bacteria of Anoxybacillus gonensis G2T and Halothermobacillus malaysiensis RA using culture dependent technique. The hemicellulase genes with the amplicon size of 2118 bp, 1143 bp, 1554 bp and 2190 bp from A. gonensis G2T and H. malaysiensis RA were successfully obtained. Bioinformatics analyse of primary, secondary structure and tertiary structure of these proteins were performed by using bioinformatics tools. Beta-xylosidase from A. gonensis G2T and alpha-glucuronidase from H. malaysiensis RA are intracellular proteins. While, endo-1,4-beta-xylanase and alpha-N-arabinofuranosidase from H. malaysiensis RA have signal peptide and secreted as extracellular protein. I-TASSER and Swiss Model server were used to model the tertiary structure of hemicellulase. Good structures were generated after energy minimization through YASARA server. Using Neighbor-Joining method, the phylogenetic analysis reveals that beta-xylosidase from A. gonensis G2T (bxAg) is closely related with beta-xylosidase from Geobacillus sp. WSUCF1; endo-1,4-beta-xylanase from H. malaysiensis RA (ebxHm) is distantly related with endo-1,4-beta-xylanase from Xanthomonas translucens pv translucens, family GH10 Maribacter dokdonensis DSW-8 and Saccharicrinis fermentans DSM 9555JCM 21142; alpha-N-arabinofuranosidase from H. malaysiensis RA (anaHm) is closely related with alpha-N-arabinofuranosidase from Gemmatimonas sp. SG8 28; and alpha-glucuronidase from H. malaysiensis RA (agHm) is distantly related with alpha-glucuronidase from Sphingomonas sp.WG, Caulobacter vibrioides, Xanthomonas oryzae pv. oryzae and Stenotrophomonas maltophilia. 2016-09 Thesis http://eprints.utm.my/id/eprint/78944/ http://eprints.utm.my/id/eprint/78944/1/NurNazwaSaimonMFBME2016.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:109606 masters 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	TP Chemical technology
spellingShingle	TP Chemical technology Saimon, Nur Nazwa Gene amplification and sequencing of hemicellulase using culture dependent technique
description	The present study aims to discover hemicellulase genes from thermophilic bacteria of Anoxybacillus gonensis G2T and Halothermobacillus malaysiensis RA using culture dependent technique. The hemicellulase genes with the amplicon size of 2118 bp, 1143 bp, 1554 bp and 2190 bp from A. gonensis G2T and H. malaysiensis RA were successfully obtained. Bioinformatics analyse of primary, secondary structure and tertiary structure of these proteins were performed by using bioinformatics tools. Beta-xylosidase from A. gonensis G2T and alpha-glucuronidase from H. malaysiensis RA are intracellular proteins. While, endo-1,4-beta-xylanase and alpha-N-arabinofuranosidase from H. malaysiensis RA have signal peptide and secreted as extracellular protein. I-TASSER and Swiss Model server were used to model the tertiary structure of hemicellulase. Good structures were generated after energy minimization through YASARA server. Using Neighbor-Joining method, the phylogenetic analysis reveals that beta-xylosidase from A. gonensis G2T (bxAg) is closely related with beta-xylosidase from Geobacillus sp. WSUCF1; endo-1,4-beta-xylanase from H. malaysiensis RA (ebxHm) is distantly related with endo-1,4-beta-xylanase from Xanthomonas translucens pv translucens, family GH10 Maribacter dokdonensis DSW-8 and Saccharicrinis fermentans DSM 9555JCM 21142; alpha-N-arabinofuranosidase from H. malaysiensis RA (anaHm) is closely related with alpha-N-arabinofuranosidase from Gemmatimonas sp. SG8 28; and alpha-glucuronidase from H. malaysiensis RA (agHm) is distantly related with alpha-glucuronidase from Sphingomonas sp.WG, Caulobacter vibrioides, Xanthomonas oryzae pv. oryzae and Stenotrophomonas maltophilia.
format	Thesis
qualification_level	Master's degree
author	Saimon, Nur Nazwa
author_facet	Saimon, Nur Nazwa
author_sort	Saimon, Nur Nazwa
title	Gene amplification and sequencing of hemicellulase using culture dependent technique
title_short	Gene amplification and sequencing of hemicellulase using culture dependent technique
title_full	Gene amplification and sequencing of hemicellulase using culture dependent technique
title_fullStr	Gene amplification and sequencing of hemicellulase using culture dependent technique
title_full_unstemmed	Gene amplification and sequencing of hemicellulase using culture dependent technique
title_sort	gene amplification and sequencing of hemicellulase using culture dependent technique
granting_institution	Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering
granting_department	Faculty of Biosciences and Medical Engineering
publishDate	2016
url	http://eprints.utm.my/id/eprint/78944/1/NurNazwaSaimonMFBME2016.pdf
_version_	1747818109791633408

Gene amplification and sequencing of hemicellulase using culture dependent technique

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