Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics

ABSTRACT Thiocyanate (N=C−S−) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate i...

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Autores principales:	Tom Berben, Cherel Balkema, Dimitry Y. Sorokin, Gerard Muyzer
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	chemolithoautotrophs chemostat RNA-Seq soda lakes Thioalkalivibrio thiocyanate Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/5713402e6bbf4b348e110efde9099cd1
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spelling	oai:doaj.org-article:5713402e6bbf4b348e110efde9099cd12021-12-02T19:48:49ZAnalysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics10.1128/mSystems.00102-172379-5077https://doaj.org/article/5713402e6bbf4b348e110efde9099cd12017-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00102-17https://doaj.org/toc/2379-5077ABSTRACT Thiocyanate (N=C−S−) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems (copCD, ABC-type transporters), a putative electron acceptor (fccAB), and a two-component regulatory system (histidine kinase and a σ54-responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB, genes involved in sulfite oxidation through the reverse sulfidogenesis pathway. IMPORTANCE Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.Tom BerbenCherel BalkemaDimitry Y. SorokinGerard MuyzerAmerican Society for MicrobiologyarticlechemolithoautotrophschemostatRNA-Seqsoda lakesThioalkalivibriothiocyanateMicrobiologyQR1-502ENmSystems, Vol 2, Iss 6 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	chemolithoautotrophs chemostat RNA-Seq soda lakes Thioalkalivibrio thiocyanate Microbiology QR1-502
spellingShingle	chemolithoautotrophs chemostat RNA-Seq soda lakes Thioalkalivibrio thiocyanate Microbiology QR1-502 Tom Berben Cherel Balkema Dimitry Y. Sorokin Gerard Muyzer Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics
description	ABSTRACT Thiocyanate (N=C−S−) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems (copCD, ABC-type transporters), a putative electron acceptor (fccAB), and a two-component regulatory system (histidine kinase and a σ54-responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB, genes involved in sulfite oxidation through the reverse sulfidogenesis pathway. IMPORTANCE Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.
format	article
author	Tom Berben Cherel Balkema Dimitry Y. Sorokin Gerard Muyzer
author_facet	Tom Berben Cherel Balkema Dimitry Y. Sorokin Gerard Muyzer
author_sort	Tom Berben
title	Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics
title_short	Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics
title_full	Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics
title_fullStr	Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics
title_full_unstemmed	Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics
title_sort	analysis of the genes involved in thiocyanate oxidation during growth in continuous culture of the haloalkaliphilic sulfur-oxidizing bacterium <named-content content-type="genus-species">thioalkalivibrio thiocyanoxidans</named-content> arh 2<sup>t</sup> using transcriptomics
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/5713402e6bbf4b348e110efde9099cd1
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Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <named-content content-type="genus-species">Thioalkalivibrio thiocyanoxidans</named-content> ARh 2<sup>T</sup> Using Transcriptomics

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