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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.789442018-09-19T05:12:45Z http://eprints.utm.my/id/eprint/78944/ Gene amplification and sequencing of hemicellulase using culture dependent technique 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 NonPeerReviewed application/pdf en http://eprints.utm.my/id/eprint/78944/1/NurNazwaSaimonMFBME2016.pdf Saimon, Nur Nazwa (2016) Gene amplification and sequencing of hemicellulase using culture dependent technique. Masters thesis, Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering. http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:109606
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
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
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
publishDate 2016
url http://eprints.utm.my/id/eprint/78944/1/NurNazwaSaimonMFBME2016.pdf
http://eprints.utm.my/id/eprint/78944/
http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:109606
_version_ 1643658052676616192
score 13.211869

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