317
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

CRISPRi-Mediated Gene Suppression Reveals Putative Reverse Transcriptase Gene PA0715 to Be a Global Regulator of Pseudomonas aeruginosa

ORCID Icon, , , , ORCID Icon, , & show all
Pages 7577-7599 | Received 16 Aug 2022, Accepted 09 Nov 2022, Published online: 22 Dec 2022

References

  • Weiner LM, Webb AK, Limbago B, et al. Antimicrobial-resistant pathogens associated with healthcare-associated infections: summary of data reported to the national healthcare safety network at the centers for disease control and prevention, 2011–2014. Infect Control Hosp Epidemiol. 2016;37(11):1288–1301. doi:10.1017/ice.2016.174
  • Magill SS, O’Leary E, Janelle SJ, et al. Changes in prevalence of health care-associated infections in U.S. hospitals. N Engl J Med. 2018;379(18):1732–1744. doi:10.1056/NEJMoa1801550
  • Moon DC, Mechesso AF, Kang HY, et al. Imipenem resistance mediated by blaOXA-913 gene in Pseudomonas aeruginosa. Antibiotics. 2021;10(10):1188. doi:10.3390/antibiotics10101188
  • Bonomo RA, Szabo D. Mechanisms of multidrug resistance in Acinetobacter species and Pseudomonas aeruginosa. Clin Infect Dis. 2006;43(Suppl 2):S49–56. doi:10.1086/504477
  • D’Elia MA, Pereira MP, Brown ED. Are essential genes really essential? Trends Microbiol. 2009;17(10):433–438. doi:10.1016/j.tim.2009.08.005
  • Rancati G, Moffat J, Typas A, Pavelka N. Emerging and evolving concepts in gene essentiality. Nat Rev. 2018;19(1):34–49. doi:10.1038/nrg.2017.74
  • Brown ED, Wright GD. Antibacterial drug discovery in the resistance era. Nature. 2016;529(7586):336–343. doi:10.1038/nature17042
  • Millman A, Bernheim A, Stokar-Avihail A, et al. Bacterial retrons function in anti-phage defense. Cell. 2020;183(6):1551–1561 e1512. doi:10.1016/j.cell.2020.09.065
  • Erez Z, Steinberger-Levy I, Shamir M, et al. Communication between viruses guides lysis-lysogeny decisions. Nature. 2017;541(7638):488–493. doi:10.1038/nature21049
  • Al-Anany AM, Fatima R, Hynes AP. Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens. Cell Rep. 2021;35(8):109172. doi:10.1016/j.celrep.2021.109172
  • Marraffini LA. CRISPR-Cas immunity in prokaryotes. Nature. 2015;526(7571):55–61. doi:10.1038/nature15386
  • Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157(6):1262–1278. doi:10.1016/j.cell.2014.05.010
  • Arazoe T, Kondo A, Nishida K. Targeted nucleotide editing technologies for microbial metabolic engineering. Biotechnol J. 2018;13(9):e1700596. doi:10.1002/biot.201700596
  • Su T, Liu F, Chang Y, et al. The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining. Synthetic Syst Biotechnol. 2019;4(2):107–112. doi:10.1016/j.synbio.2019.04.001
  • Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–1183. doi:10.1016/j.cell.2013.02.022
  • Zuberi A, Misba L, Khan AU. CRISPR interference (CRISPRi) inhibition of luxS gene expression in E. coli: an approach to inhibit biofilm. Front Cell Infect Microbiol. 2017;7:214. doi:10.3389/fcimb.2017.00214
  • Zuberi A, Ahmad N, Khan AU. CRISPRi induced suppression of fimbriae gene (fimH) of a uropathogenic Escherichia coli: an approach to inhibit microbial biofilms. Front Immunol. 2017;8:1552. doi:10.3389/fimmu.2017.01552
  • Takacs CN, Scott M, Chang Y, et al. A CRISPR interference platform for selective downregulation of gene expression in Borrelia burgdorferi. Appl Environ Microbiol. 2020;87. doi:10.1128/AEM.02519-20
  • Zuberi A, Azam MW, Khan AU. CRISPR interference (CRISPRi) mediated suppression of OmpR gene in E. coli: an alternative approach to inhibit biofilm. Curr Microbiol. 2022;79(3):78. doi:10.1007/s00284-021-02760-x
  • Noirot-Gros MF, Forrester S, Malato G, Larsen PE, Noirot P. CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens. Sci Rep. 2019;9(1):15954. doi:10.1038/s41598-019-52400-5
  • Xiang L, Qi F, Jiang L, et al. CRISPR-dCas9-mediated knockdown of prtR, an essential gene in Pseudomonas aeruginosa. Lett Appl Microbiol. 2020;71(4):386–393. doi:10.1111/lam.13337
  • Huang W, Wilks A. A rapid seamless method for gene knockout in Pseudomonas aeruginosa. BMC Microbiol. 2017;17(1):199. doi:10.1186/s12866-017-1112-5
  • Sun Z, Shi J, Liu C, et al. PrtR homeostasis contributes to Pseudomonas aeruginosa pathogenesis and resistance against ciprofloxacin. Infect Immun. 2014;82(4):1638–1647. doi:10.1128/IAI.01388-13
  • Choi KH, Kumar A, Schweizer HP. A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J Microbiol Methods. 2006;64(3):391–397. doi:10.1016/j.mimet.2005.06.001
  • Xu H, Liu C, Li M, et al. In vitro antibacterial experiment of Fuzheng Jiedu Huayu decoction against multidrug-resistant Pseudomonas aeruginosa. Front Pharmacol. 2019;10:1682. doi:10.3389/fphar.2019.01682
  • Zhang Y, Zhao J, Han J, et al. Synergistic activity of imipenem in combination with ceftazidime/avibactam or avibactam against non-MBL-producing extensively drug-resistant Pseudomonas aeruginosa. Microbiol Spectr. 2022;10(2):e0274021. doi:10.1128/spectrum.02740-21
  • Das T, Manefield M. Pyocyanin promotes extracellular DNA release in Pseudomonas aeruginosa. PLoS One. 2012;7(10):e46718. doi:10.1371/journal.pone.0046718
  • Caiazza NC, Shanks RM, O’Toole GA. Rhamnolipids modulate swarming motility patterns of Pseudomonas aeruginosa. J Bacteriol. 2005;187(21):7351–7361. doi:10.1128/JB.187.21.7351-7361.2005
  • Banerjee M, Moulick S, Bhattacharya KK, Parai D, Chattopadhyay S, Mukherjee SK. Attenuation of Pseudomonas aeruginosa quorum sensing, virulence and biofilm formation by extracts of Andrographis paniculata. Microb Pathog. 2017;113:85–93. doi:10.1016/j.micpath.2017.10.023
  • Ozdal M. A new strategy for the efficient production of pyocyanin, a versatile pigment, in Pseudomonas aeruginosa OG1 via toluene addition. 3 Biotech. 2019;9(10):374. doi:10.1007/s13205-019-1907-1
  • Sagar PK, Sharma P, Singh R. Inhibition of quorum sensing regulated virulence factors and biofilm formation by Eucalyptus globulus against multidrug-resistant Pseudomonas aeruginosa. J Pharmacopunct. 2022;25(1):37–45. doi:10.3831/KPI.2022.25.1.37
  • Ramos-Vivas J, Chapartegui-Gonzalez I, Fernandez-Martinez M, et al. Biofilm formation by multidrug resistant Enterobacteriaceae strains isolated from solid organ transplant recipients. Sci Rep. 2019;9(1):8928. doi:10.1038/s41598-019-45060-y
  • Thees AV, Pietrosimone KM, Melchiorre CK, et al. PmtA regulates pyocyanin expression and biofilm formation in Pseudomonas aeruginosa. Front Microbiol. 2021;12:789765. doi:10.3389/fmicb.2021.789765
  • Sesal NC, Kekec O. Inactivation of Escherichia coli and Staphylococcus aureus by ultrasound. J Ultrasound Med. 2014;33(9):1663–1668. doi:10.7863/ultra.33.9.1663
  • Khusro A, Aarti C, Salem AZM, Buendia Rodriguez G, Rivas-Caceres RR. Antagonistic trait of Staphylococcus succinus strain AAS2 against uropathogens and assessment of its in vitro probiotic characteristics. Microb Pathog. 2018;118:126–132. doi:10.1016/j.micpath.2018.03.022
  • Bello-Lopez JM, Delgado-Balbuena L, Rojas-Huidobro D, Rojo-Medina J. Treatment of platelet concentrates and plasma with riboflavin and UV light: impact in bacterial reduction. Transfusion clinique et biologique. 2018;25(3):197–203. doi:10.1016/j.tracli.2018.03.004
  • Koon MA, Almohammed Ali K, Speaker RM, McGrath JP, Linton EW, Steinhilb ML. Preparation of prokaryotic and eukaryotic organisms using chemical drying for morphological analysis in scanning electron microscopy (SEM). JoVE. 2019;(143). doi:10.3791/58761
  • Zhang L, Zhao SQ, Zhang J, et al. Proteomic analysis of vesicle-producing Pseudomonas aeruginosa PAO1 exposed to X-ray irradiation. Front Microbiol. 2020;11:558233. doi:10.3389/fmicb.2020.558233
  • Hazlett LD, Ekanayaka SA, McClellan SA, Francis R. Glycyrrhizin use for multi-drug resistant Pseudomonas aeruginosa: in vitro and in vivo studies. Invest Ophthalmol Vis Sci. 2019;60(8):2978–2989. doi:10.1167/iovs.19-27200
  • Kim BO, Jang HJ, Chung IY, Bae HW, Kim ES, Cho YH. Nitrate respiration promotes polymyxin B resistance in Pseudomonas aeruginosa. Antioxid Redox Signal. 2021;34(6):442–451. doi:10.1089/ars.2019.7924
  • Seed KD, Dennis JJ. Development of Galleria mellonella as an alternative infection model for the Burkholderia cepacia complex. Infect Immun. 2008;76(3):1267–1275. doi:10.1128/IAI.01249-07
  • Qiu D, Damron FH, Mima T, Schweizer HP, Yu HD. PBAD-based shuttle vectors for functional analysis of toxic and highly regulated genes in Pseudomonas and Burkholderia spp. and other bacteria. Appl Environ Microbiol. 2008;74(23):7422–7426. doi:10.1128/AEM.01369-08
  • Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188–1190. doi:10.1101/gr.849004
  • Harshey RM. Bacterial motility on a surface: many ways to a common goal. Annu Rev Microbiol. 2003;57:249–273. doi:10.1146/annurev.micro.57.030502.091014
  • Blair DF. Flagellar movement driven by proton translocation. FEBS Lett. 2003;545(1):86–95. doi:10.1016/S0014-5793(03)00397-1
  • Merz AJ, So M, Sheetz MP. Pilus retraction powers bacterial twitching motility. Nature. 2000;407(6800):98–102. doi:10.1038/35024105
  • Hassan HM, Fridovich I. Mechanism of the antibiotic action pyocyanine. J Bacteriol. 1980;141(1):156–163. doi:10.1128/jb.141.1.156-163.1980
  • Rada B, Leto TL. Pyocyanin effects on respiratory epithelium: relevance in Pseudomonas aeruginosa airway infections. Trends Microbiol. 2013;21(2):73–81. doi:10.1016/j.tim.2012.10.004
  • Das T, Kutty SK, Tavallaie R, et al. Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation. Sci Rep. 2015;5:8398. doi:10.1038/srep08398
  • Soto GE, Hultgren SJ. Bacterial adhesins: common themes and variations in architecture and assembly. J Bacteriol. 1999;181(4):1059–1071. doi:10.1128/JB.181.4.1059-1071.1999
  • Mulcahy H, Sibley CD, Surette MG, Lewenza S. Drosophila melanogaster as an animal model for the study of Pseudomonas aeruginosa biofilm infections in vivo. PLoS Pathog. 2011;7(10):e1002299. doi:10.1371/journal.ppat.1002299
  • Haller S, Limmer S, Ferrandon D. Assessing Pseudomonas virulence with a nonmammalian host: drosophila melanogaster. Methods Mol Biol. 2014;1149:723–740. doi:10.1007/978-1-4939-0473-0_56
  • Cheng J, Ding L, Xia A, et al. Hydrogen production using amino acids obtained by protein degradation in waste biomass by combined dark- and photo-fermentation. Bioresour Technol. 2015;179:13–19. doi:10.1016/j.biortech.2014.11.109
  • Fichtner M, Voigt K, Schuster S. The tip and hidden part of the iceberg: proteinogenic and non-proteinogenic aliphatic amino acids. Biochim Biophys Acta. 2017;1861(1 Pt A):3258–3269. doi:10.1016/j.bbagen.2016.08.008
  • Wagenmakers AJ. Protein and amino acid metabolism in human muscle. Adv Exp Med Biol. 1998;441:307–319. doi:10.1007/978-1-4899-1928-1_28
  • Fukao T, Lopaschuk GD, Mitchell GA. Pathways and control of ketone body metabolism: on the fringe of lipid biochemistry. Prostaglandins Leukot Essent Fatty Acids. 2004;70(3):243–251. doi:10.1016/j.plefa.2003.11.001
  • Longo R, Peri C, Cricri D, et al. Ketogenic diet: a new light shining on old but gold biochemistry. Nutrients. 2019;11(10):2497. doi:10.3390/nu11102497
  • Cabeen MT, Jacobs-Wagner C. Bacterial cell shape. Nat Rev. 2005;3(8):601–610. doi:10.1038/nrmicro1205
  • Egan AJF, Errington J, Vollmer W. Regulation of peptidoglycan synthesis and remodelling. Nat Rev. 2020;18(8):446–460. doi:10.1038/s41579-020-0366-3
  • Mueller EA, Levin PA. Bacterial cell wall quality control during environmental stress. mBio. 2020;11(5). doi:10.1128/mBio.02456-20
  • Van Laar TA, Esani S, Birges TJ, Hazen B, Thomas JM, Rawat M. Pseudomonas aeruginosa Gsha mutant is defective in biofilm formation, swarming, and pyocyanin production. mSphere. 2018;3(2). doi:10.1128/mSphere.00155-18
  • Zeng B, Wang C, Zhang P, Guo Z, Chen L, Duan K. Heat shock protein DnaJ in Pseudomonas aeruginosa affects biofilm formation via pyocyanin production. Microorganisms. 2020;8(3):395. doi:10.3390/microorganisms8030395
  • Das T, Kutty SK, Kumar N, Manefield M. Pyocyanin facilitates extracellular DNA binding to Pseudomonas aeruginosa influencing cell surface properties and aggregation. PLoS One. 2013;8(3):e58299. doi:10.1371/journal.pone.0058299
  • McDermott C, Chess-Williams R, Grant GD, et al. Effects of Pseudomonas aeruginosa virulence factor pyocyanin on human urothelial cell function and viability. J Urol. 2012;187(3):1087–1093. doi:10.1016/j.juro.2011.10.129
  • Larian N, Ensor M, Thatcher SE, et al. Pseudomonas aeruginosa-derived pyocyanin reduces adipocyte differentiation, body weight, and fat mass as mechanisms contributing to septic cachexia. Food Chem Toxicol. 2019;130:219–230. doi:10.1016/j.fct.2019.05.012
  • Sharma D, Misba L, Khan AU. Antibiotics versus biofilm: an emerging battleground in microbial communities. Antimicrob Resist Infect Control. 2019;8:76. doi:10.1186/s13756-019-0533-3
  • Vaez H, Safaei HG, Faghri J. The emergence of multidrug-resistant clone ST664 Pseudomonas aeruginosa in a referral burn hospital, Isfahan, Iran. Burns Trauma. 2017;5:27. doi:10.1186/s41038-017-0092-x
  • Jin Y, Yang H, Qiao M, Jin S. MexT regulates the type III secretion system through MexS and PtrC in Pseudomonas aeruginosa. J Bacteriol. 2011;193(2):399–410. doi:10.1128/JB.01079-10
  • Huang G, Shen X, Gong Y, et al. Antibacterial properties of Acinetobacter baumannii phage Abp1 endolysin (PlyAB1). BMC Infect Dis. 2014;14:681. doi:10.1186/s12879-014-0681-2