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- Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria
- Yubin Yang, Hana Hyeon, Minju Joo, Kangseok Lee, Eunkyoung Shin
- J. Microbiol. 2025;63(4):e2501027. Published online April 2, 2025
- DOI: https://doi.org/10.71150/jm.2501027
- 369 View
- 34 Download
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Abstract
PDF -
The escalating antibiotic resistance crisis poses a significant challenge to global public health, threatening the efficacy of current treatments and driving the emergence of multidrug-resistant pathogens. Among the various factors associated with bacterial antibiotic resistance, small regulatory RNAs (sRNAs) have emerged as pivotal post-transcriptional regulators which orchestrate bacterial adaptation to antibiotic pressure via diverse mechanisms. This review consolidates the current knowledge on sRNA-mediated mechanisms, focusing on drug uptake, drug efflux systems, lipopolysaccharides, cell wall modification, biofilm formation, and mutagenesis. Recent advances in transcriptomics and functional analyses have revealed novel sRNAs and their regulatory networks, expanding our understanding of resistance mechanisms. These findings highlight the potential of targeting sRNA-mediated pathways as an innovative therapeutic strategy to combat antibiotic resistance, and offer promising avenues for managing challenging bacterial infections.
Journal Articles
- Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
- Dayeong Bae , Hana Hyeon , Eunkyoung Shin , Ji&# , Kangseok Lee
- J. Microbiol. 2023;61(2):211-220. Published online February 22, 2023
- DOI: https://doi.org/10.1007/s12275-023-00013-z
- 65 View
- 0 Download
- 1 Web of Science
- 1 Crossref
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Abstract
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RNase E is an essential enzyme in Escherichia coli. The cleavage site of this single-stranded specific endoribonuclease is
well-characterized in many RNA substrates. Here, we report that the upregulation of RNase E cleavage activity by a mutation
that affects either RNA binding (Q36R) or enzyme multimerization (E429G) was accompanied by relaxed cleavage specificity.
Both mutations led to enhanced RNase E cleavage in RNA I, an antisense RNA of ColE1-type plasmid replication,
at a major site and other cryptic sites. Expression of a truncated RNA I with a major RNase E cleavage site deletion at the
5′-end (RNA I-
5) resulted in an approximately twofold increase in the steady-state levels of RNA I-
5 and the copy number
of ColE1-type plasmid in E. coli cells expressing wild-type or variant RNase E compared to those expressing RNA I. These
results
indicate that RNA I- 5 does not efficiently function as an antisense RNA despite having a triphosphate group at the 5′-end, which protects the RNA from ribonuclease attack. Our study suggests that increased cleavage rates of RNase E lead to relaxed cleavage specificity on RNA I and the inability of the cleavage product of RNA I as an antisense regulator in vivo does not stem from its instability by having 5′-monophosphorylated end. -
Citations
Citations to this article as recorded by
- Engineering an Escherichia coli based in vivo mRNA manufacturing platform
Edward Curry, George Muir, Jixin Qu, Zoltán Kis, Martyn Hulley, Adam Brown
Biotechnology and Bioengineering.2024; 121(6): 1912. CrossRef
- Engineering an Escherichia coli based in vivo mRNA manufacturing platform
- Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6
- Younkyung Choi , Minju Joo , Wooseok Song , Minho Lee , Hana Hyeon , Hyun-Lee Kim , Ji-Hyun Yeom , Kangseok Lee , Eunkyoung Shin
- J. Microbiol. 2022;60(12):1162-1167. Published online November 24, 2022
- DOI: https://doi.org/10.1007/s12275-022-2437-9
- 66 View
- 0 Download
- 2 Web of Science
- 2 Crossref
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Abstract
- Ribosomes composed of genome-encoded heterogeneous rRNAs are implicated in the rapid adaptation of bacterial cells to environmental changes. A previous study showed that ribosomes bearing the most heterogeneous rRNAs expressed from the rrnI operon (I-ribosomes) are implicated in the preferential translation of a subset of mRNAs, including hspA and tpiA, in Vibrio vulnificus CMCP6. In this study, we show that HspA nascent peptides were predominantly bound to I-ribosomes. Specifically, I-ribosomes were enriched more than two-fold in ribosomes that were pulled down by immunoprecipitation of HspA peptides compared with the proportion of I-ribosomes in crude ribosomes and ribosomes pulled down by immunoprecipitation of RNA polymerase subunit ß peptides in the wild-type (WT) and rrnI-completed strains. Other methods that utilized the incorporation of an affinity tag in 23S rRNA or chimeric rRNA tethering 16S and 23S rRNAs, which generated specialized functional ribosomes in Escherichia coli, did not result in functional I-ribosomes in V. vulnificus CMCP6. This study provides direct evidence of the preferential translation of hspA mRNA by I-ribosomes.
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Citations
Citations to this article as recorded by- Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef - Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
Journal of Microbiology.2023; 61(2): 211. CrossRef
- Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
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