Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism
Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especiall...
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BioMed Central
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Online Access: | http://tubdok.tub.tuhh.de/handle/11420/1410 https://nbn-resolving.org/urn:nbn:de:gbv:830-88216549 https://doi.org/10.15480/882.1407 |
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fttuhamburg:oai:tore.tuhh.de:11420/1410 2023-10-01T03:56:59+02:00 Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism Schäfers, Christian Blank, Saskia Wiebusch, Sigrid Elleuche, Skander Antranikian, Garabed 2017-02-03 application/pdf http://tubdok.tub.tuhh.de/handle/11420/1410 https://nbn-resolving.org/urn:nbn:de:gbv:830-88216549 https://doi.org/10.15480/882.1407 en eng BioMed Central Standards in genomic sciences 1944-3277 Open Access Publizieren 2016 - 2017 / Technische Universität Hamburg-Harburg Standards in genomic sciences 12 (2017), 1:22 http://tubdok.tub.tuhh.de/handle/11420/1410 urn:nbn:de:gbv:830-88216549 doi:10.15480/882.1407 11420/1410 2-s2.0-85011343867 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ 4.0 false whole genome sequence de novo assembly Thermus Thermus brockianus xylan degradation xylose metabolism Thermophiles single molecule real-time sequencing 570: Biowissenschaften Biologie 570 Journal Article Other 2017 fttuhamburg https://doi.org/10.15480/882.1407 2023-09-03T22:14:13Z Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures. Here we analyze the first whole genome sequence of T. brockianus strain GE-1. Insights of the genome sequence and the methodologies that were applied during de novo assembly and annotation are given in detail. The finished genome shows a phred quality value of QV50. The complete genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and 66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified encoding key enzymes for xylan depolymerization and xylose metabolism. This is in agreement with the growth experiments in which xylan is utilized as sole source of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding protein XylF, the xylose isomerase XylA catalyzing the first step of xylose metabolism and the xylulokinase XylB, responsible for the second step of xylose metabolism. Our data indicate that an ancestor of T. brockianus obtained the ability to use xylose as alternative carbon source by horizontal gene transfer. Article in Journal/Newspaper Iceland TUHH Open Research (TORE - Technische Universität Hamburg) Geysir ENVELOPE(-20.277,-20.277,64.307,64.307) |
institution |
Open Polar |
collection |
TUHH Open Research (TORE - Technische Universität Hamburg) |
op_collection_id |
fttuhamburg |
language |
English |
topic |
whole genome sequence de novo assembly Thermus Thermus brockianus xylan degradation xylose metabolism Thermophiles single molecule real-time sequencing 570: Biowissenschaften Biologie 570 |
spellingShingle |
whole genome sequence de novo assembly Thermus Thermus brockianus xylan degradation xylose metabolism Thermophiles single molecule real-time sequencing 570: Biowissenschaften Biologie 570 Schäfers, Christian Blank, Saskia Wiebusch, Sigrid Elleuche, Skander Antranikian, Garabed Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism |
topic_facet |
whole genome sequence de novo assembly Thermus Thermus brockianus xylan degradation xylose metabolism Thermophiles single molecule real-time sequencing 570: Biowissenschaften Biologie 570 |
description |
Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures. Here we analyze the first whole genome sequence of T. brockianus strain GE-1. Insights of the genome sequence and the methodologies that were applied during de novo assembly and annotation are given in detail. The finished genome shows a phred quality value of QV50. The complete genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and 66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified encoding key enzymes for xylan depolymerization and xylose metabolism. This is in agreement with the growth experiments in which xylan is utilized as sole source of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding protein XylF, the xylose isomerase XylA catalyzing the first step of xylose metabolism and the xylulokinase XylB, responsible for the second step of xylose metabolism. Our data indicate that an ancestor of T. brockianus obtained the ability to use xylose as alternative carbon source by horizontal gene transfer. |
format |
Article in Journal/Newspaper |
author |
Schäfers, Christian Blank, Saskia Wiebusch, Sigrid Elleuche, Skander Antranikian, Garabed |
author_facet |
Schäfers, Christian Blank, Saskia Wiebusch, Sigrid Elleuche, Skander Antranikian, Garabed |
author_sort |
Schäfers, Christian |
title |
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism |
title_short |
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism |
title_full |
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism |
title_fullStr |
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism |
title_full_unstemmed |
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism |
title_sort |
complete genome sequence of thermus brockianus ge-1 reveals key enzymes of xylan/xylose metabolism |
publisher |
BioMed Central |
publishDate |
2017 |
url |
http://tubdok.tub.tuhh.de/handle/11420/1410 https://nbn-resolving.org/urn:nbn:de:gbv:830-88216549 https://doi.org/10.15480/882.1407 |
long_lat |
ENVELOPE(-20.277,-20.277,64.307,64.307) |
geographic |
Geysir |
geographic_facet |
Geysir |
genre |
Iceland |
genre_facet |
Iceland |
op_relation |
Standards in genomic sciences 1944-3277 Open Access Publizieren 2016 - 2017 / Technische Universität Hamburg-Harburg Standards in genomic sciences 12 (2017), 1:22 http://tubdok.tub.tuhh.de/handle/11420/1410 urn:nbn:de:gbv:830-88216549 doi:10.15480/882.1407 11420/1410 2-s2.0-85011343867 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ 4.0 false |
op_doi |
https://doi.org/10.15480/882.1407 |
_version_ |
1778527718224166912 |