Cargando…

RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria

Guanine (G)-rich sequences in RNA can fold into diverse RNA G-quadruplex (rG4) structures to mediate various biological functions and cellular processes in eukaryotic organisms. However, the presence, locations, and functions of rG4s in prokaryotes are still elusive. We used QUMA-1, an rG4-specific...

Descripción completa

Detalles Bibliográficos
Autores principales: Shao, Xiaolong, Zhang, Weitong, Umar, Mubarak Ishaq, Wong, Hei Yuen, Seng, Zijing, Xie, Yingpeng, Zhang, Yingchao, Yang, Liang, Kwok, Chun Kit, Deng, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974567/
https://www.ncbi.nlm.nih.gov/pubmed/31964733
http://dx.doi.org/10.1128/mBio.02926-19
_version_ 1783490124821037056
author Shao, Xiaolong
Zhang, Weitong
Umar, Mubarak Ishaq
Wong, Hei Yuen
Seng, Zijing
Xie, Yingpeng
Zhang, Yingchao
Yang, Liang
Kwok, Chun Kit
Deng, Xin
author_facet Shao, Xiaolong
Zhang, Weitong
Umar, Mubarak Ishaq
Wong, Hei Yuen
Seng, Zijing
Xie, Yingpeng
Zhang, Yingchao
Yang, Liang
Kwok, Chun Kit
Deng, Xin
author_sort Shao, Xiaolong
collection PubMed
description Guanine (G)-rich sequences in RNA can fold into diverse RNA G-quadruplex (rG4) structures to mediate various biological functions and cellular processes in eukaryotic organisms. However, the presence, locations, and functions of rG4s in prokaryotes are still elusive. We used QUMA-1, an rG4-specific fluorescent probe, to detect rG4 structures in a wide range of bacterial species both in vitro and in live cells and found rG4 to be an abundant RNA secondary structure across those species. Subsequently, to identify bacterial rG4 sites in the transcriptome, the model Escherichia coli strain and a major human pathogen, Pseudomonas aeruginosa, were subjected to recently developed high-throughput rG4 structure sequencing (rG4-seq). In total, 168 and 161 in vitro rG4 sites were found in E. coli and P. aeruginosa, respectively. Genes carrying these rG4 sites were found to be involved in virulence, gene regulation, cell envelope synthesis, and metabolism. More importantly, biophysical assays revealed the formation of a group of rG4 sites in mRNAs (such as hemL and bswR), and they were functionally validated in cells by genetic (point mutation and lux reporter assays) and phenotypic experiments, providing substantial evidence for the formation and function of rG4s in bacteria. Overall, our study uncovers important regulatory functions of rG4s in bacterial pathogenicity and metabolic pathways and strongly suggests that rG4s exist and can be detected in a wide range of bacterial species.
format Online
Article
Text
id pubmed-6974567
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher American Society for Microbiology
record_format MEDLINE/PubMed
spelling pubmed-69745672020-02-04 RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria Shao, Xiaolong Zhang, Weitong Umar, Mubarak Ishaq Wong, Hei Yuen Seng, Zijing Xie, Yingpeng Zhang, Yingchao Yang, Liang Kwok, Chun Kit Deng, Xin mBio Research Article Guanine (G)-rich sequences in RNA can fold into diverse RNA G-quadruplex (rG4) structures to mediate various biological functions and cellular processes in eukaryotic organisms. However, the presence, locations, and functions of rG4s in prokaryotes are still elusive. We used QUMA-1, an rG4-specific fluorescent probe, to detect rG4 structures in a wide range of bacterial species both in vitro and in live cells and found rG4 to be an abundant RNA secondary structure across those species. Subsequently, to identify bacterial rG4 sites in the transcriptome, the model Escherichia coli strain and a major human pathogen, Pseudomonas aeruginosa, were subjected to recently developed high-throughput rG4 structure sequencing (rG4-seq). In total, 168 and 161 in vitro rG4 sites were found in E. coli and P. aeruginosa, respectively. Genes carrying these rG4 sites were found to be involved in virulence, gene regulation, cell envelope synthesis, and metabolism. More importantly, biophysical assays revealed the formation of a group of rG4 sites in mRNAs (such as hemL and bswR), and they were functionally validated in cells by genetic (point mutation and lux reporter assays) and phenotypic experiments, providing substantial evidence for the formation and function of rG4s in bacteria. Overall, our study uncovers important regulatory functions of rG4s in bacterial pathogenicity and metabolic pathways and strongly suggests that rG4s exist and can be detected in a wide range of bacterial species. American Society for Microbiology 2020-01-21 /pmc/articles/PMC6974567/ /pubmed/31964733 http://dx.doi.org/10.1128/mBio.02926-19 Text en Copyright © 2020 Shao et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Shao, Xiaolong
Zhang, Weitong
Umar, Mubarak Ishaq
Wong, Hei Yuen
Seng, Zijing
Xie, Yingpeng
Zhang, Yingchao
Yang, Liang
Kwok, Chun Kit
Deng, Xin
RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria
title RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria
title_full RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria
title_fullStr RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria
title_full_unstemmed RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria
title_short RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria
title_sort rna g-quadruplex structures mediate gene regulation in bacteria
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974567/
https://www.ncbi.nlm.nih.gov/pubmed/31964733
http://dx.doi.org/10.1128/mBio.02926-19
work_keys_str_mv AT shaoxiaolong rnagquadruplexstructuresmediategeneregulationinbacteria
AT zhangweitong rnagquadruplexstructuresmediategeneregulationinbacteria
AT umarmubarakishaq rnagquadruplexstructuresmediategeneregulationinbacteria
AT wongheiyuen rnagquadruplexstructuresmediategeneregulationinbacteria
AT sengzijing rnagquadruplexstructuresmediategeneregulationinbacteria
AT xieyingpeng rnagquadruplexstructuresmediategeneregulationinbacteria
AT zhangyingchao rnagquadruplexstructuresmediategeneregulationinbacteria
AT yangliang rnagquadruplexstructuresmediategeneregulationinbacteria
AT kwokchunkit rnagquadruplexstructuresmediategeneregulationinbacteria
AT dengxin rnagquadruplexstructuresmediategeneregulationinbacteria