Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis

sRNAs represent a powerful class of regulators that influences multiple mRNA targets in response to environmental changes. However, very few direct sRNA–sRNA interactions have been deeply studied in any organism. Zymomonas mobilis is a bacterium with unique ethanol-producing metabolic pathways in wh...

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Main Authors: Runhua Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongfu Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-03-01
Series:Frontiers in Bioengineering and Biotechnology
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fbioe.2020.00155/full
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spelling doaj-a67bdf4df24a4b1b9e69edc7e2581f102020-11-25T03:30:12ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852020-03-01810.3389/fbioe.2020.00155511156Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilisRunhua Han0Katie Haning1Juan C. Gonzalez-Rivera2Yongfu Yang3Runxia Li4Seung Hee Cho5Ju Huang6Bobi A. Simonsen7Shihui Yang8Lydia M. Contreras9Lydia M. Contreras10McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United StatesMcKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United StatesMcKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United StatesState Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, ChinaState Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, ChinaInstitute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United StatesState Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, ChinaMcKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United StatesState Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, ChinaMcKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United StatesInstitute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United StatessRNAs represent a powerful class of regulators that influences multiple mRNA targets in response to environmental changes. However, very few direct sRNA–sRNA interactions have been deeply studied in any organism. Zymomonas mobilis is a bacterium with unique ethanol-producing metabolic pathways in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that two sRNAs (Zms4 and Zms6) are upregulated under ethanol stress and have significant impacts on ethanol tolerance and production in Z. mobilis. We conducted multi-omics analysis (combining transcriptomics and sRNA-immunoprecipitation) to map gene networks under the influence of their regulation. We confirmed that Zms4 and Zms6 bind multiple RNA targets and regulate their expressions, influencing many downstream pathways important to ethanol tolerance and production. In particular, Zms4 and Zms6 interact with each other as well as many other sRNAs, forming a novel sRNA–sRNA direct interaction network. This study thus uncovers a sRNA network that co-orchestrates multiple ethanol related pathways through a diverse set of mRNA targets and a large number of sRNAs. To our knowledge, this study represents one of the largest sRNA–sRNA direct interactions uncovered so far.https://www.frontiersin.org/article/10.3389/fbioe.2020.00155/fullZymomonas mobilissmall RNAsRNA interactionsintegrated omicsethanol tolerance
collection DOAJ
language English
format Article
sources DOAJ
author Runhua Han
Katie Haning
Juan C. Gonzalez-Rivera
Yongfu Yang
Runxia Li
Seung Hee Cho
Ju Huang
Bobi A. Simonsen
Shihui Yang
Lydia M. Contreras
Lydia M. Contreras
spellingShingle Runhua Han
Katie Haning
Juan C. Gonzalez-Rivera
Yongfu Yang
Runxia Li
Seung Hee Cho
Ju Huang
Bobi A. Simonsen
Shihui Yang
Lydia M. Contreras
Lydia M. Contreras
Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Frontiers in Bioengineering and Biotechnology
Zymomonas mobilis
small RNA
sRNA interactions
integrated omics
ethanol tolerance
author_facet Runhua Han
Katie Haning
Juan C. Gonzalez-Rivera
Yongfu Yang
Runxia Li
Seung Hee Cho
Ju Huang
Bobi A. Simonsen
Shihui Yang
Lydia M. Contreras
Lydia M. Contreras
author_sort Runhua Han
title Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
title_short Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
title_full Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
title_fullStr Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
title_full_unstemmed Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
title_sort multiple small rnas interact to co-regulate ethanol tolerance in zymomonas mobilis
publisher Frontiers Media S.A.
series Frontiers in Bioengineering and Biotechnology
issn 2296-4185
publishDate 2020-03-01
description sRNAs represent a powerful class of regulators that influences multiple mRNA targets in response to environmental changes. However, very few direct sRNA–sRNA interactions have been deeply studied in any organism. Zymomonas mobilis is a bacterium with unique ethanol-producing metabolic pathways in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that two sRNAs (Zms4 and Zms6) are upregulated under ethanol stress and have significant impacts on ethanol tolerance and production in Z. mobilis. We conducted multi-omics analysis (combining transcriptomics and sRNA-immunoprecipitation) to map gene networks under the influence of their regulation. We confirmed that Zms4 and Zms6 bind multiple RNA targets and regulate their expressions, influencing many downstream pathways important to ethanol tolerance and production. In particular, Zms4 and Zms6 interact with each other as well as many other sRNAs, forming a novel sRNA–sRNA direct interaction network. This study thus uncovers a sRNA network that co-orchestrates multiple ethanol related pathways through a diverse set of mRNA targets and a large number of sRNAs. To our knowledge, this study represents one of the largest sRNA–sRNA direct interactions uncovered so far.
topic Zymomonas mobilis
small RNA
sRNA interactions
integrated omics
ethanol tolerance
url https://www.frontiersin.org/article/10.3389/fbioe.2020.00155/full
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