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Conference Paper: RNA-Seq analysis of the degradation of haloacetate by Burkholderia caribensis MBA4

TitleRNA-Seq analysis of the degradation of haloacetate by Burkholderia caribensis MBA4
Authors
Issue Date2014
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/wps/find/journaldescription.cws_home/713354/description#description
Citation
The 16th European Congress on Biotechnology (ECB16), Edinburgh, Scotland, 13-16 July 2014. In New Biotechnology, 2014, v. 31 n. Suppl., p. S153 How to Cite?
AbstractBurkholderia caribensis strain MBA4 was isolated for its ability to utilize monobromoacetate as carbon and energy source. This bacterium produced an inducible haloacid dehalogenase that transforms monohaloacetate to glycolate and to glyoxylate by glycolate oxidase. Genomic analysis of the bacterium showed that it contains three glycolate oxidases: ETY79679-81, ETY80271-3 and ETY84258-60. Transcriptomic analysis showed that ETY79679-81 was expressed constitutively to a reads per kilobase transcript per million reads (RPKM) value of around 100 no matter the substrate was pyruvate, glycolate or chloroacetate. ETY80271-3 gave values of 7 in pyruvate-, 867 in chloroacetate- and 1260 in glycolate-grown cells. ETY84258-60 gave values of 20 in pyruvate-, 1880 in chloroacetate- and 178 in glycolate-grown cells. A malate synthase G gene, ETY84261, was found downstream of ETY84258-60. Apparently, ETY80271-3 converted glycolate to glyoxylate and through the glycerate pathway to pyruvate. When MBA4 was grown on chloroacetate, gene products of ETY84258-61 were mainly used and malate was generated. Putative regulator GlcC genes, ETY80275 and ETY84257, can be found upstream of ETY80271-3 and ETY84258-60, respectively. The expression profiles of these glycolate oxidases suggested that both GlcC were activated by glycolate and chloroacetate with ETY80275 more responsive to glycolate and ETY84257 more reactive towards chloroacetate. While the relative transcript levels of ETY80275 were rather stable, expression of ETY84257 was enhanced in glycolate- and even more in chloroacetate-grown cells. The characterization of the degradation of haloacetate by B. caribensis MBA4 is made possible with the use of RNA-seq analysis.
Persistent Identifierhttp://hdl.handle.net/10722/205056
ISSN
2015 Impact Factor: 3.199
2015 SCImago Journal Rankings: 1.092

 

DC FieldValueLanguage
dc.contributor.authorTsang, JSHen_US
dc.contributor.authorPan, Yen_US
dc.contributor.authorZheng, Nen_US
dc.date.accessioned2014-09-20T01:19:58Z-
dc.date.available2014-09-20T01:19:58Z-
dc.date.issued2014en_US
dc.identifier.citationThe 16th European Congress on Biotechnology (ECB16), Edinburgh, Scotland, 13-16 July 2014. In New Biotechnology, 2014, v. 31 n. Suppl., p. S153en_US
dc.identifier.issn1871-6784-
dc.identifier.urihttp://hdl.handle.net/10722/205056-
dc.description.abstractBurkholderia caribensis strain MBA4 was isolated for its ability to utilize monobromoacetate as carbon and energy source. This bacterium produced an inducible haloacid dehalogenase that transforms monohaloacetate to glycolate and to glyoxylate by glycolate oxidase. Genomic analysis of the bacterium showed that it contains three glycolate oxidases: ETY79679-81, ETY80271-3 and ETY84258-60. Transcriptomic analysis showed that ETY79679-81 was expressed constitutively to a reads per kilobase transcript per million reads (RPKM) value of around 100 no matter the substrate was pyruvate, glycolate or chloroacetate. ETY80271-3 gave values of 7 in pyruvate-, 867 in chloroacetate- and 1260 in glycolate-grown cells. ETY84258-60 gave values of 20 in pyruvate-, 1880 in chloroacetate- and 178 in glycolate-grown cells. A malate synthase G gene, ETY84261, was found downstream of ETY84258-60. Apparently, ETY80271-3 converted glycolate to glyoxylate and through the glycerate pathway to pyruvate. When MBA4 was grown on chloroacetate, gene products of ETY84258-61 were mainly used and malate was generated. Putative regulator GlcC genes, ETY80275 and ETY84257, can be found upstream of ETY80271-3 and ETY84258-60, respectively. The expression profiles of these glycolate oxidases suggested that both GlcC were activated by glycolate and chloroacetate with ETY80275 more responsive to glycolate and ETY84257 more reactive towards chloroacetate. While the relative transcript levels of ETY80275 were rather stable, expression of ETY84257 was enhanced in glycolate- and even more in chloroacetate-grown cells. The characterization of the degradation of haloacetate by B. caribensis MBA4 is made possible with the use of RNA-seq analysis.-
dc.languageengen_US
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/wps/find/journaldescription.cws_home/713354/description#description-
dc.relation.ispartofNew Biotechnologyen_US
dc.titleRNA-Seq analysis of the degradation of haloacetate by Burkholderia caribensis MBA4en_US
dc.typeConference_Paperen_US
dc.identifier.emailTsang, JSH: jshtsang@hku.hken_US
dc.identifier.authorityTsang, JSH=rp00792en_US
dc.identifier.doi10.1016/j.nbt.2014.05.2001en_US
dc.identifier.hkuros238574en_US
dc.identifier.volume31en_US
dc.identifier.issueSuppl.-
dc.identifier.spageS153en_US
dc.identifier.epageS153en_US
dc.publisher.placeNetherlands-

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