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Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined t...

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Autores principales: Costa, Ohana Y.A., Zerillo, Marcelo M., Zühlke, Daniela, Kielak, Anna M., Pijl, Agata, Riedel, Katharina, Kuramae, Eiko E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074687/
https://www.ncbi.nlm.nih.gov/pubmed/32059463
http://dx.doi.org/10.3390/microorganisms8020244
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author Costa, Ohana Y.A.
Zerillo, Marcelo M.
Zühlke, Daniela
Kielak, Anna M.
Pijl, Agata
Riedel, Katharina
Kuramae, Eiko E.
author_facet Costa, Ohana Y.A.
Zerillo, Marcelo M.
Zühlke, Daniela
Kielak, Anna M.
Pijl, Agata
Riedel, Katharina
Kuramae, Eiko E.
author_sort Costa, Ohana Y.A.
collection PubMed
description The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin–antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
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spelling pubmed-70746872020-03-20 Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses Costa, Ohana Y.A. Zerillo, Marcelo M. Zühlke, Daniela Kielak, Anna M. Pijl, Agata Riedel, Katharina Kuramae, Eiko E. Microorganisms Article The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin–antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth. MDPI 2020-02-12 /pmc/articles/PMC7074687/ /pubmed/32059463 http://dx.doi.org/10.3390/microorganisms8020244 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Costa, Ohana Y.A.
Zerillo, Marcelo M.
Zühlke, Daniela
Kielak, Anna M.
Pijl, Agata
Riedel, Katharina
Kuramae, Eiko E.
Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
title Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
title_full Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
title_fullStr Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
title_full_unstemmed Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
title_short Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
title_sort responses of acidobacteria granulicella sp. wh15 to high carbon revealed by integrated omics analyses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074687/
https://www.ncbi.nlm.nih.gov/pubmed/32059463
http://dx.doi.org/10.3390/microorganisms8020244
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