RNA G-quadruplex structures mediate gene regulation in bacteria

Shao，Xiaolong1; Zhang，Weitong1; Umar，Mubarak Ishaq2; Wong，Hei Yuen2; Seng，Zijing3; Xie，Yingpeng1; Zhang，Yingchao1; Yang，Liang4; Kwok，Chun Kit2,5; Deng，Xin1,5

2020

10.1128/mBio.02926-19

mBio   影响因子和分区

2161-2129

2150-7511

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. IMPORTANCE G-quadruplex in RNA (rG4) mediates various biological functions and cellular processes in eukaryotic organisms. However, the presence, locations, and functions of rG4 are still elusive in prokaryotes. Here, we found that rG4 is an abundant RNA secondary structure across a wide range of bacterial species. Subsequently, the transcriptome-wide rG4 structure sequencing (rG4-seq) revealed that the model E. coli strain and a major human pathogen, P. aeruginosa, have 168 and 161 in vitro rG4 sites, respectively, involved in virulence, gene regulation, cell envelope, and metabolism. We further verified the regulatory functions of two rG4 sites in bacteria (hemL and bswR). Overall, this finding strongly suggests that rG4s play key regulatory roles in a wide range of bacterial species.

Bacteria Gene regulation Nucleic acid structures Prokaryotes RNA G-quadruplexes (rG4) Transcriptome-wide

SCI

英语

其他

Shenzhen Basic Research Project[JCYJ20180507181642811]

Microbiology

Microbiology

WOS:000518763400091

AMER SOC MICROBIOLOGY

2-s2.0-85078262558

Scopus

1.Department of Biomedical Sciences,City University of Hong Kong,Kowloon Tong,Hong Kong
2.Department of Chemistry,City University of Hong Kong,Kowloon Tong,Hong Kong
3.Singapore Centre for Environmental Life Sciences Engineering (SCELSE),Nanyang Technological University,Singapore
4.School of Medicine,Southern University of Science and Technology (SUSTech),Shenzhen,China
5.Shenzhen Research Institute of City University of Hong Kong,Shenzhen,China

Shao，Xiaolong,Zhang，Weitong,Umar，Mubarak Ishaq,et al. RNA G-quadruplex structures mediate gene regulation in bacteria[J]. mBio,2020,11(1).

Shao，Xiaolong.,Zhang，Weitong.,Umar，Mubarak Ishaq.,Wong，Hei Yuen.,Seng，Zijing.,...&Deng，Xin.(2020).RNA G-quadruplex structures mediate gene regulation in bacteria.mBio,11(1).

Shao，Xiaolong,et al."RNA G-quadruplex structures mediate gene regulation in bacteria".mBio 11.1(2020).