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- Pioneering strategies for overcoming bacterial drug resistance (2026)
- Advancing microbial engineering through synthetic biology (2025)
- Host-associated microbiome (2024)
- Bacterial regulatory mechanisms for the control of complex cellular mechanisms (2023)
- Two years into COVID-19 pandemic: Where are we? (2022)
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- Design guide for synthetic small regulatory RNAs for high-efficiency gene knockdown in bacteria
- Jun Ren, Yubin Kim, Hyun Jung Nam, Hyang-Mi Lee, Dokyun Na
- Received March 26, 2026 Accepted April 29, 2026 Published online July 6, 2026
- DOI: https://doi.org/10.71150/jm.2603026 [Epub ahead of print]
- 118 View
- 9 Download
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Abstract
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Supplementary Material -
Small regulatory RNAs (sRNAs) are short noncoding RNAs that can fine-control the expression of target genes in trans at the post-transcriptional level in prokaryotes. Since there is a big challenge in constructing gene-knockout libraries, synthetic sRNAs have attracted considerable interest in synthetic biology and metabolic engineering, as they enable targeted gene knockdown without requiring chromosomal modifications. However, the development of high-efficiency synthetic sRNAs remains a demanding task that requires careful consideration of multiple design factors. Here, we provide a detailed protocol for the design and construction of synthetic sRNAs, detailing key design principles and critical optimization factors, including scaffold selection, target mRNA binding affinity, target mRNA secondary structure, and Hfq expression levels. This strategy can be broadly applied across E. coli and other bacterial hosts to modulate gene expression, thereby supporting versatile applications in synthetic biology and metabolic engineering.
- 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
- 10,747 View
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- 10 Web of Science
- 11 Crossref
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Abstract
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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.
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Citations
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- Current insights into the application of bacterial small RNAs in combating multidrug-resistant pathogens
Zeleke Ayenew, Tadesse Eguale, Abebaw Bitew, Eshetu Gadisa, Aklilu Feleke Haile
Scientific African.2026; 31: e03212. CrossRef - From Host-Derived Pressures to the Environmental Anti-Antimicrobial Peptides Resistome: Mechanisms, Reservoirs and Implications for Therapeutic Peptide Design
Yi Lu, Baomei Zhang, Zishuo Wang, Yidi He, Hezi Ge, Hongyue Ma, Pengfei Cui
Marine Drugs.2026; 24(2): 76. CrossRef - Omics Applification of Microalgae-Bacteria Consortium Wonders in Nutrients and Antibiotics Removal from Wastewater
Adamudu Alexander Ogwuche, Ebrima S. Jabbi, Sorie Kalie Bangura, Iyobosa Eheneden, Muhammed Bako
European Journal of Ecology, Biology and Agriculture.2026; 3(2): 53. CrossRef - Pathotype-specific antimicrobial resistance in diarrheagenic Escherichia coli: gene variants, resistance mechanisms, and evolution of treatment strategies
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Frontiers in Microbiology.2026;[Epub] CrossRef - Bacterial secondary metabolites as resistance-modifying adjuvants: microbial origins, molecular mechanisms, and translational relevance
Victor Uchenna Chigozie, Charles Okechukwu Esimone
Frontiers in Microbiology.2026;[Epub] CrossRef - Tackling antibiotic resistance in ESKAPE pathogens through the lens of bacterial small RNAs
Sijia Liu, Xiaorui Song, Kefeng Cui, Hongrui Zhu, Yuchun Liu, Rui Jia, Zhidan Yu, Huiqing Sun, Mingchao Li, Zengyuan Yu, Lifeng Li
Microbial Pathogenesis.2026; 215: 108487. CrossRef - Antechokinetics, the kinetics of antimicrobial resistance molecules
Fernando Baquero, Rafael Cantón, João Alves Gama, Jerónimo Rodríguez-Beltrán
Frontiers in Pharmacology.2026;[Epub] CrossRef - Small regulatory RNAs modulate lactococcal susceptibility to cell wall-targeting antimicrobials
Milda Mickutė, Kotryna Kvederavičiūtė, Janina Ličytė, Renatas Krasauskas, Sigita Grigaitytė, Oskaras Safinas, Danguolė Žiogienė, Naglis Mykolas Pakštys, Loreta Stankevičiūtė, Algirdas Kaupinis, Mindaugas Valius, Pascal Courtin, Marie-Pierre Chapot-Chartie
Nucleic Acids Research.2026;[Epub] CrossRef - Assay-Based High Throughput Screening of Diverse Libraries Identifies Selective Inhibitors of Staphylococcus aureus Ribonuclease P
Swapnil S. Joshi, Loc T. Huynh, Nidhi Kalia, Gabriel Eaton-Landau, Aaron Aponick, Anna M. Pyle, Michael E. Harris
ACS Chemical Biology.2026; 21(5): 972. CrossRef - Biofilm, resistance, and quorum sensing: The triple threat in bacterial pathogenesis
Mohammad Nazrul Islam Bhuiyan
The Microbe.2025; 9: 100578. CrossRef - Biofilm maturation in carbapenem-resistant Pseudomonas aeruginosa is regulated by the sRNA PA213 and its corresponding encoded small protein
Yongli Song, Jie Li, Yating Zhang, Lingge Su, Shuang Qin, Chunyan Wu, Guibo Song
International Journal of Antimicrobial Agents.2025; 66(6): 107625. CrossRef
- Current insights into the application of bacterial small RNAs in combating multidrug-resistant pathogens
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