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...
Main Authors: | , , , , , , , , , |
---|---|
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 |
id |
doaj-a67bdf4df24a4b1b9e69edc7e2581f10 |
---|---|
record_format |
Article |
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 |
work_keys_str_mv |
AT runhuahan multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT katiehaning multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT juancgonzalezrivera multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT yongfuyang multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT runxiali multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT seungheecho multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT juhuang multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT bobiasimonsen multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT shihuiyang multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT lydiamcontreras multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis AT lydiamcontreras multiplesmallrnasinteracttocoregulateethanoltoleranceinzymomonasmobilis |
_version_ |
1724576843164549120 |