Identification and Functional Analysis of NcRNAs Regulating Intrinsic Polymyxin Resistance in Foodborne

Overview

Journal Microorganisms

Specialty Microbiology

Date 2024 Aug 29

PMID 39203505

Authors

Hongyang Zhang

Tao Wu

Haihua Ruan

Affiliations

Soon will be listed here.

Abstract

Polymyxin, known as the "last line of defense" against bacterial infection, exerts a significant inhibitory effect on a wide range of Gram-negative pathogenic bacteria. The presence of strains, specifically species, displaying intrinsic polymyxin resistance poses significant challenges to current clinical treatment. However, the underlying mechanism responsible for this intrinsic resistance remains unclear. Bacterial non-coding RNAs (ncRNAs) are abundant in genomes and have been demonstrated to have significant regulatory roles in antibiotic resistance across various bacterial species. However, it remains to be determined whether ncRNAs in can regulate intrinsic polymyxin resistance. This study focused on investigating the foodborne strain P3M and its intrinsic polymyxin resistance regulation mediated by ncRNAs. Through a combination of bioinformatics analysis, mutant construction, and phenotypic experimental verification, we successfully identified the ncRNAs involved and their potential target genes. These findings serve as an essential foundation for the precise identification of ncRNAs participating in the intricate regulation process of polymyxin resistance. Additionally, this study offers valuable insights into the efficient screening of bacterial ncRNAs that contribute positively to antibiotic resistance regulation.

References

Lahiry A, Stimple S, Wood D, Lease R . Retargeting a Dual-Acting sRNA for Multiple mRNA Transcript Regulation. ACS Synth Biol. 2017; 6(4):648-658. DOI: 10.1021/acssynbio.6b00261. View

Jagodnik J, Chiaruttini C, Guillier M . Stem-Loop Structures within mRNA Coding Sequences Activate Translation Initiation and Mediate Control by Small Regulatory RNAs. Mol Cell. 2017; 68(1):158-170.e3. DOI: 10.1016/j.molcel.2017.08.015. View

Wertheim H, Van Nguyen K, Hara G, Gelband H, Laxminarayan R, Mouton J . Global survey of polymyxin use: A call for international guidelines. J Glob Antimicrob Resist. 2014; 1(3):131-134. PMC: 3991322. DOI: 10.1016/j.jgar.2013.03.012. View

Baron S, Leulmi Z, Villard C, Olaitan A, Telke A, Rolain J . Inactivation of the arn operon and loss of aminoarabinose on lipopolysaccharide as the cause of susceptibility to colistin in an atypical clinical isolate of proteus vulgaris. Int J Antimicrob Agents. 2017; 51(3):450-457. DOI: 10.1016/j.ijantimicag.2017.11.017. View

Frohlich K, Haneke K, Papenfort K, Vogel J . The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res. 2016; 44(21):10406-10422. PMC: 5137417. DOI: 10.1093/nar/gkw632. View

Kwak J, Choi E, Weisblum B . Transcriptional attenuation control of ermK, a macrolide-lincosamide-streptogramin B resistance determinant from Bacillus licheniformis. J Bacteriol. 1991; 173(15):4725-35. PMC: 208150. DOI: 10.1128/jb.173.15.4725-4735.1991. View

Nation R, Velkov T, Li J . Colistin and polymyxin B: peas in a pod, or chalk and cheese?. Clin Infect Dis. 2014; 59(1):88-94. PMC: 4305129. DOI: 10.1093/cid/ciu213. View

Li M, Zhu J, Lv Z, Qin H, Wang X, Shi H . Recent Advances in RNA-Targeted Cancer Therapy. Chembiochem. 2023; 25(4):e202300633. DOI: 10.1002/cbic.202300633. View

Jiang X, Yang K, Han M, Yuan B, Li J, Gong B . Outer Membranes of Polymyxin-Resistant with Phosphoethanolamine-Modified Lipid A and Lipopolysaccharide Loss Display Different Atomic-Scale Interactions with Polymyxins. ACS Infect Dis. 2020; 6(10):2698-2708. PMC: 7554230. DOI: 10.1021/acsinfecdis.0c00330. View

10.

Jiang S, Liu M, Teng L, Wang W, Hsueh P, Liaw S . Proteus mirabilis pmrI, an RppA-regulated gene necessary for polymyxin B resistance, biofilm formation, and urothelial cell invasion. Antimicrob Agents Chemother. 2010; 54(4):1564-71. PMC: 2849355. DOI: 10.1128/AAC.01219-09. View

11.

Yang Q, Pogue J, Li Z, Nation R, Kaye K, Li J . Agents of Last Resort: An Update on Polymyxin Resistance. Infect Dis Clin North Am. 2020; 34(4):723-750. DOI: 10.1016/j.idc.2020.08.003. View

12.

Andronescu M, Condon A, Hoos H, Mathews D, Murphy K . Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics. 2007; 23(13):i19-28. DOI: 10.1093/bioinformatics/btm223. View

13.

Zhan Y, Deng Z, Yan Y, Zhang H, Lu C, Yang Z . NfiR, a New Regulatory Noncoding RNA (ncRNA), Is Required in Concert with the NfiS ncRNA for Optimal Expression of Nitrogenase Genes in Pseudomonas stutzeri A1501. Appl Environ Microbiol. 2019; 85(14). PMC: 6606865. DOI: 10.1128/AEM.00762-19. View

14.

Zhang H, Zhan Y, Yan Y, Liu Y, Hu G, Wang S . The Pseudomonas stutzeri-Specific Regulatory Noncoding RNA NfiS Targets mRNA Encoding a Catalase Essential for Optimal Oxidative Resistance and Nitrogenase Activity. J Bacteriol. 2019; 201(19). PMC: 6755748. DOI: 10.1128/JB.00334-19. View

15.

Tanwar J, Das S, Fatima Z, Hameed S . Multidrug resistance: an emerging crisis. Interdiscip Perspect Infect Dis. 2014; 2014:541340. PMC: 4124702. DOI: 10.1155/2014/541340. View

16.

Gruber A, Lorenz R, Bernhart S, Neubock R, Hofacker I . The Vienna RNA websuite. Nucleic Acids Res. 2008; 36(Web Server issue):W70-4. PMC: 2447809. DOI: 10.1093/nar/gkn188. View

17.

Huang W, Wilks A . A rapid seamless method for gene knockout in Pseudomonas aeruginosa. BMC Microbiol. 2017; 17(1):199. PMC: 5606073. DOI: 10.1186/s12866-017-1112-5. View

18.

Liu P, Yue C, Liu L, Gao C, Lyu Y, Deng S . The function of small RNA in . PeerJ. 2022; 10:e13738. PMC: 9308961. DOI: 10.7717/peerj.13738. View

19.

Kwiecinska-Pirog J, Skowron K, Bartczak W, Gospodarek-Komkowska E . The Ciprofloxacin Impact on Biofilm Formation by Proteus Mirabilis and P. Vulgaris Strains. Jundishapur J Microbiol. 2016; 9(4):e32656. PMC: 4903162. DOI: 10.5812/jjm.32656. View

20.

Xiaomin S, Yiming L, Yuying Y, Zhangqi S, Yongning W, Shaolin W . Global impact of -positive bacteria on "one health". Crit Rev Microbiol. 2020; 46(5):565-577. DOI: 10.1080/1040841X.2020.1812510. View