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Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity

BACKGROUND: Ammonium is an important raw material for biomolecules and life activities, and the toxicity of ammonium is also an important ecological and agricultural issue. Ammonium toxicity in yeast has only recently been discovered, and information on its mechanism is limited. In recent years, env...

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Autores principales: Fu, Wenhao, Cao, Xiuling, An, Tingting, Zhao, Huihui, Zhang, Jie, Li, Danqi, Jin, Xuejiao, Liu, Beidong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9287935/
https://www.ncbi.nlm.nih.gov/pubmed/35840887
http://dx.doi.org/10.1186/s12864-022-08742-y
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author Fu, Wenhao
Cao, Xiuling
An, Tingting
Zhao, Huihui
Zhang, Jie
Li, Danqi
Jin, Xuejiao
Liu, Beidong
author_facet Fu, Wenhao
Cao, Xiuling
An, Tingting
Zhao, Huihui
Zhang, Jie
Li, Danqi
Jin, Xuejiao
Liu, Beidong
author_sort Fu, Wenhao
collection PubMed
description BACKGROUND: Ammonium is an important raw material for biomolecules and life activities, and the toxicity of ammonium is also an important ecological and agricultural issue. Ammonium toxicity in yeast has only recently been discovered, and information on its mechanism is limited. In recent years, environmental pollution caused by nitrogen-containing wastewater has been increasing. In addition, the use of yeast in bioreactors to produce nitrogen-containing compounds has been developed. Therefore, research on resistance mechanisms that allow yeast to grow under conditions of high concentrations of ammonium has become more and more important. RESULTS: To further understand the resistance mechanism of yeast to grow under high concentration of ammonium, we used NH(4)Cl to screen a yeast non-essential gene-deletion library. We identified 61 NH(4)Cl-sensitive deletion mutants from approximately 4200 mutants in the library, then 34 of them were confirmed by drop test analysis. Enrichment analysis of these 34 genes showed that biosynthesis metabolism, mitophagy, MAPK signaling, and other pathways may play important roles in NH(4)Cl resistance. Transcriptome analysis under NH(4)Cl stress revealed 451 significantly upregulated genes and 835 significantly downregulated genes. The genes are mainly enriched in: nitrogen compound metabolic process, cell wall, MAPK signaling pathway, mitophagy, and glycine, serine and threonine metabolism. CONCLUSIONS: Our results present a broad view of biological pathways involved in the response to NH(4)Cl stress, and thereby advance our understanding of the resistance genes and cellular transcriptional regulation under high concentration of ammonium. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08742-y.
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spelling pubmed-92879352022-07-17 Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity Fu, Wenhao Cao, Xiuling An, Tingting Zhao, Huihui Zhang, Jie Li, Danqi Jin, Xuejiao Liu, Beidong BMC Genomics Research BACKGROUND: Ammonium is an important raw material for biomolecules and life activities, and the toxicity of ammonium is also an important ecological and agricultural issue. Ammonium toxicity in yeast has only recently been discovered, and information on its mechanism is limited. In recent years, environmental pollution caused by nitrogen-containing wastewater has been increasing. In addition, the use of yeast in bioreactors to produce nitrogen-containing compounds has been developed. Therefore, research on resistance mechanisms that allow yeast to grow under conditions of high concentrations of ammonium has become more and more important. RESULTS: To further understand the resistance mechanism of yeast to grow under high concentration of ammonium, we used NH(4)Cl to screen a yeast non-essential gene-deletion library. We identified 61 NH(4)Cl-sensitive deletion mutants from approximately 4200 mutants in the library, then 34 of them were confirmed by drop test analysis. Enrichment analysis of these 34 genes showed that biosynthesis metabolism, mitophagy, MAPK signaling, and other pathways may play important roles in NH(4)Cl resistance. Transcriptome analysis under NH(4)Cl stress revealed 451 significantly upregulated genes and 835 significantly downregulated genes. The genes are mainly enriched in: nitrogen compound metabolic process, cell wall, MAPK signaling pathway, mitophagy, and glycine, serine and threonine metabolism. CONCLUSIONS: Our results present a broad view of biological pathways involved in the response to NH(4)Cl stress, and thereby advance our understanding of the resistance genes and cellular transcriptional regulation under high concentration of ammonium. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08742-y. BioMed Central 2022-07-15 /pmc/articles/PMC9287935/ /pubmed/35840887 http://dx.doi.org/10.1186/s12864-022-08742-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Fu, Wenhao
Cao, Xiuling
An, Tingting
Zhao, Huihui
Zhang, Jie
Li, Danqi
Jin, Xuejiao
Liu, Beidong
Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
title Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
title_full Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
title_fullStr Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
title_full_unstemmed Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
title_short Genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
title_sort genome-wide identification of resistance genes and transcriptome regulation in yeast to accommodate ammonium toxicity
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9287935/
https://www.ncbi.nlm.nih.gov/pubmed/35840887
http://dx.doi.org/10.1186/s12864-022-08742-y
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