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Volume 168, Issue 12

Frequency of quorum-sensing mutations in strains isolated from different environments Free

This article is part of the Environmental Sensing and Cell-Cell Communication collection

Abstract

uses quorum sensing (QS) to coordinate the expression of multiple genes necessary for establishing and maintaining infection. It has previously been shown that QS mutations frequently arise in cystic fibrosis (CF) lung infections, however, there has been far less emphasis on determining whether other QS system mutations arise during infection or in other environments. To test this, we utilized 852 publicly available sequenced genomes from the International Consortium Database (IPCD) to study QS mutational signatures. To study isolates by source, we focused on a subset of 654 isolates collected from CF, wounds, and non-infection environmental isolates, where we could clearly identify their source. We also worked with a small collection of isolates to determine the impact of and mutations on isolate phenotypes. We found that mutations are common across all environments and are not specific to infection nor a particular infection type. We also found that the system proteins PqsA, PqsH, PqsL and MexT, a protein of increasing importance to the QS field, are highly variable. Conversely, RsaL, a negative transcriptional regulator of the system, was found to be highly conserved, suggesting selective pressure to repress system activity. Overall, our findings suggest that QS mutations in are common and not limited to the system; however, LasR is unique in the frequency of putative loss-of-function mutations.

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  • Accepted:
  • Published Online:
Keyword(s): cystic fibrosis , LasR , Pseudomonas aeruginosa and quorum sensing
Funding
This study was supported by the:
  • Cystic Fibrosis Foundation (Award DIGGLE20G0)
    • Principle Award Recipient: StephenP Diggle
  • Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Award R01AI153116)
    • Principle Award Recipient: StephenP Diggle
© 2022 The Authors
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2022-12-16
2024-05-04
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References

  1. Diggle SP, Whiteley M. Microbe Profile: Pseudomonas aeruginosa: opportunistic pathogen and lab rat. Microbiology 2021; 167: [View Article]
     [Google Scholar]
  2. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci 2006; 103:8487–8492 [View Article]
     [Google Scholar]
  3. LaFayette SL, Houle D, Beaudoin T, Wojewodka G, Radzioch D et al. Cystic fibrosis–adapted Pseudomonas aeruginosa quorum sensing lasR mutants cause hyperinflammatory responses. Sci Adv 2015; 1:1–15 [View Article]
     [Google Scholar]
  4. Hansen SK, Rau MH, Johansen HK, Ciofu O, Jelsbak L et al. Evolution and diversification of Pseudomonas aeruginosa in the paranasal sinuses of cystic fibrosis children have implications for chronic lung infection. ISME J 2012; 6:31–45 [View Article] [PubMed]
     [Google Scholar]
  5. Ciofu O, Mandsberg LF, Bjarnsholt T, Wassermann T, Høiby N. Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants. Microbiology 2010; 156:1108–1119 [View Article]
     [Google Scholar]
  6. Williams P, Cámara M. Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: a tale of regulatory networks and multifunctional signal molecules. Curr Opin Microbiol 2009; 12:182–191 [View Article] [PubMed]
     [Google Scholar]
  7. Galán-Vásquez E, Luna B, Martínez-Antonio A. The regulatory network of Pseudomonas aeruginosa. Microb Inform Exp 2011; 1:3 [View Article]
     [Google Scholar]
  8. Lee J, Zhang L. The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 2015; 6:26–41 [View Article] [PubMed]
     [Google Scholar]
  9. Whiteley M, Diggle SP, Greenberg EP. Progress in and promise of bacterial quorum sensing research. Nature 2017; 551:313–320 [View Article] [PubMed]
     [Google Scholar]
  10. Azimi S, Klementiev AD, Whiteley M, Diggle SP. Bacterial quorum sensing during infection. Annu Rev Microbiol 2020; 74:201–219 [View Article]
     [Google Scholar]
  11. Wagner VE, Bushnell D, Passador L, Brooks AI, Iglewski BH. Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment. J Bacteriol 2003; 185:2080–2095 [View Article] [PubMed]
     [Google Scholar]
  12. Schuster M, Lostroh CP, Ogi T, Greenberg EP. Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: A transcriptome analysis. J Bacteriol 2003; 185:2066–2079 [View Article] [PubMed]
     [Google Scholar]
  13. Fuqua WC, Winans SC, Greenberg EP. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 1994; 176:269–275 [View Article] [PubMed]
     [Google Scholar]
  14. Ding F, Oinuma K-I, Smalley NE, Schaefer AL, Hamwy O et al. The Pseudomonas aeruginosa orphan quorum sensing signal receptor QscR regulates global quorum sensing gene expression by activating a single linked operon. mBio 2018; 9:e01274-18 [View Article]
     [Google Scholar]
  15. Schuster M, Greenberg EP. A network of networks: quorum-sensing gene regulation in Pseudomonas aeruginosa. Int J Med Microbiol 2006; 296:73–81 [View Article] [PubMed]
     [Google Scholar]
  16. Rampioni G, Bertani I, Zennaro E, Polticelli F, Venturi V et al. The quorum-sensing negative regulator RsaL of Pseudomonas aeruginosa binds to the lasI promoter. J Bacteriol 2006; 188:815–819 [View Article] [PubMed]
     [Google Scholar]
  17. Rampioni G, Schuster M, Greenberg EP, Zennaro E, Leoni L. Contribution of the RsaL global regulator to Pseudomonas aeruginosa virulence and biofilm formation. FEMS Microbiol Lett 2009; 301:210–217 [View Article] [PubMed]
     [Google Scholar]
  18. Liang H, Deng X, Ji Q, Sun F, Shen T et al. The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression. J Bacteriol 2012; 194:3098–3108 [View Article] [PubMed]
     [Google Scholar]
  19. Juhas M, Wiehlmann L, Huber B, Jordan D, Lauber J et al. Global regulation of quorum sensing and virulence by VqsR in Pseudomonas aeruginosa. Microbiology 2004; 150:831–841 [View Article]
     [Google Scholar]
  20. Gurney J, Azimi S, Brown SP, Diggle SP. Combinatorial quorum sensing in Pseudomonas aeruginosa allows for novel cheating strategies. Microbiology 2020; 166:777–784 [View Article]
     [Google Scholar]
  21. Cornforth DM, Popat R, McNally L, Gurney J, Scott-Phillips TC et al. Combinatorial quorum sensing allows bacteria to resolve their social and physical environment. Proc Natl Acad Sci 2014; 111:4280–4284 [View Article]
     [Google Scholar]
  22. Dubern JF, Diggle SP. Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species. Mol Biosyst 2008; 4:882–888 [View Article] [PubMed]
     [Google Scholar]
  23. Heeb S, Fletcher MP, Chhabra SR, Diggle SP, Williams P et al. Quinolones: from antibiotics to autoinducers. FEMS Microbiol Rev 2011; 35:247–274 [View Article] [PubMed]
     [Google Scholar]
  24. Gambello MJ, Iglewski BH. Cloning and characterization of the Pseudomonas aeruginosa lasR gene, a transcriptional activator of elastase expression. J Bacteriol 1991; 173:3000–3009 [View Article] [PubMed]
     [Google Scholar]
  25. Kostylev M, Kim DY, Smalley NE, Salukhe I, Greenberg EP et al. Evolution of the Pseudomonas aeruginosa quorum-sensing hierarchy. Proc Natl Acad Sci 2019; 116:7027–7032 [View Article]
     [Google Scholar]
  26. Feltner JB, Wolter DJ, Pope CE, Groleau M, Smalley NE et al. LasR variant cystic fibrosis isolates reveal an adaptable quorum. mBio 2016; 7:e01513–16 [View Article]
     [Google Scholar]
  27. Cruz RL, Asfahl KL, Van den Bossche S, Coenye T, Crabbé A et al. RhlR-regulated acyl-homoserine lactone quorum sensing in a cystic fibrosis isolate of Pseudomonas aeruginosa. mBio 2020; 11:e00532-20 [View Article]
     [Google Scholar]
  28. Thomason MK, Voichek M, Dar D, Addis V, Fitzgerald D et al. A rhlI 5’ UTR-derived sRNA regulates RhlR-dependent quorum sensing in Pseudomonas aeruginosa. mBio 2019; 10:e02253-19 [View Article]
     [Google Scholar]
  29. Chen R, Déziel E, Groleau MC, Schaefer AL, Greenberg EP. Social cheating in a Pseudomonas aeruginosa quorum-sensing variant. Proc Natl Acad Sci 2019; 116:7021–7026 [View Article]
     [Google Scholar]
  30. Groleau M-C, Taillefer H, Vincent AT, Constant P, Déziel E. Pseudomonas aeruginosa isolates defective in function of the LasR quorum sensing regulator are frequent in diverse environmental niches. Environ Microbiol 2021; 00:1–14 [View Article]
     [Google Scholar]
  31. Oshri RD, Zrihen KS, Shner I, Omer Bendori S, Eldar A. Selection for increased quorum-sensing cooperation in Pseudomonas aeruginosa through the shut-down of a drug resistance pump. ISME J 2018; 12:2458–2469 [View Article] [PubMed]
     [Google Scholar]
  32. Schweizer HP. Efflux as a mechanism of resistance to antimicrobials in Pseudomonas aeruginosa and related bacteria: unanswered questions. Genet Mol Res 2003; 2:48–62 [PubMed]
     [Google Scholar]
  33. Köhler T, Epp SF, Curty LK, Pechère JC. Characterization of MexT, the regulator of the MexE-MexF-OprN multidrug efflux system of Pseudomonas aeruginosa. J Bacteriol 1999; 181:6300–6305 [View Article] [PubMed]
     [Google Scholar]
  34. Mukherjee S, Moustafa DA, Stergioula V, Smith CD, Goldberg JB et al. The PqsE and RhlR proteins are an autoinducer synthase-receptor pair that control virulence and biofilm development in Pseudomonas aeruginosa. Proc Natl Acad Sci 2018; 115:E9411–E9418 [View Article]
     [Google Scholar]
  35. Farrow JM 3rd, Sund ZM, Ellison ML, Wade DS, Coleman JP et al. PqsE functions independently of PqsR-Pseudomonas quinolone signal and enhances the rhl quorum-sensing system. J Bacteriol 2008; 190:7043–7051 [View Article] [PubMed]
     [Google Scholar]
  36. García-Reyes S, Cocotl-Yañez M, Soto-Aceves MP, González-Valdez A, Servín-González L et al. PqsR-independent quorum-sensing response of Pseudomonas aeruginosa ATCC 9027 outlier-strain reveals new insights on the PqsE effect on RhlR activity. Mol Microbiol 2021; 116:1113–1123 [View Article]
     [Google Scholar]
  37. Freschi L, Vincent AT, Jeukens J, Emond-Rheault J-G, Kukavica-Ibrulj I et al. The Pseudomonas aeruginosa pan-genome provides new insights on its population structure, horizontal gene transfer, and pathogenicity. Genome Biol Evol 2019; 11:109–120 [View Article]
     [Google Scholar]
  38. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci 1992; 89:10915–10919 [View Article]
     [Google Scholar]
  39. Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA et al. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Res 2016; 44:D646–53 [View Article]
     [Google Scholar]
  40. Heberle H, Meirelles GV, da Silva FR, Telles GP, Minghim R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 2015; 16:1–7 [View Article]
     [Google Scholar]
  41. Pagès H, Aboyoun P, Gentleman RDS. n.d. Biostrings: efficient manipulation of biological strings.
  42. Stanton RA, Vlachos N, Halpin AL, Birol I. GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data. Bioinformatics 2022; 38:546–548 [View Article]
     [Google Scholar]
  43. Asfahl KL, Walsh J, Gilbert K, Schuster M. Non-social adaptation defers a tragedy of the commons in Pseudomonas aeruginosa quorum sensing. ISME J 2015; 9:1734–1746 [View Article] [PubMed]
     [Google Scholar]
  44. Smalley NE, Schaefer AL, Asfahl KL, Perez C, Greenberg EP et al. Evolution of the quorum sensing regulon in cooperating populations of Pseudomonas aeruginosa. mBio 2022; 13:1–19 [View Article]
     [Google Scholar]
  45. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  46. Team Rs n.d. RStudio: integrated development environment for R.
  47. Martin DW, Schurr MJ, Mudd MH, Govan JR, Holloway BW et al. Mechanism of conversion to mucoidy in Pseudomonas aeruginosa infecting cystic fibrosis patients. Proc Natl Acad Sci 1993; 90:8377–8381 [View Article]
     [Google Scholar]
  48. Deretic V, Martin DW, Schurr MJ, Mudd MH, Hibler NS et al. Conversion to mucoidy in Pseudomonas aeruginosa. Biotechnology 1993; 11:1133–1136 [View Article]
     [Google Scholar]
  49. Weir TL, Stull VJ, Badri D, Trunck LA, Schweizer HP et al. Global gene expression profiles suggest an important role for nutrient acquisition in early pathogenesis in a plant model of Pseudomonas aeruginosa infection. Appl Environ Microbiol 2008; 74:5784–5791 [View Article] [PubMed]
     [Google Scholar]
  50. Dumas J-L, van Delden C, Perron K, Köhler T. Analysis of antibiotic resistance gene expression in Pseudomonas aeruginosa by quantitative real-time-PCR. FEMS Microbiol Lett 2006; 254:217–225 [View Article] [PubMed]
     [Google Scholar]
  51. D’Argenio DA, Wu M, Hoffman LR, Kulasekara HD, Déziel E et al. Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol Microbiol 2007; 64:512–533 [View Article] [PubMed]
     [Google Scholar]
  52. D’Argenio DA, Calfee MW, Rainey PB, Pesci EC. Autolysis and autoaggregation in Pseudomonas aeruginosa colony morphology mutants. J Bacteriol 2002; 184:6481–6489 [View Article] [PubMed]
     [Google Scholar]
  53. Déziel E, Lépine F, Milot S, He J, Mindrinos MN et al. Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication. Proc Natl Acad Sci 2004; 101:1339–1344 [View Article]
     [Google Scholar]
  54. Hazan R, Que YA, Maura D, Strobel B, Majcherczyk PA et al. Auto poisoning of the respiratory chain by a quorum-sensing-regulated molecule favors biofilm formation and antibiotic tolerance. Curr Biol 2016; 26:195–206 [View Article]
     [Google Scholar]
  55. Groleau M-C, Taillefer H, Vincent AT, Constant P, Déziel E. Pseudomonas aeruginosa isolates defective in function of the LasR quorum sensing regulator are frequent in diverse environmental niches. Microbiology [View Article]
     [Google Scholar]
  56. de Kievit T, Seed PC, Nezezon J, Passador L, Iglewski BH. RsaL, a novel repressor of virulence gene expression in Pseudomonas aeruginosa. J Bacteriol 1999; 181:2175–2184 [View Article] [PubMed]
     [Google Scholar]
  57. Rampioni G, Schuster M, Greenberg EP, Bertani I, Grasso M et al. RsaL provides quorum sensing homeostasis and functions as a global regulator of gene expression in Pseudomonas aeruginosa. Mol Microbiol 2007; 66:1557–1565 [View Article] [PubMed]
     [Google Scholar]
  58. Mould DL, Botelho NJ, Hogan DA. Intraspecies signaling between common variants of Pseudomonas aeruginosa increases production of quorum-sensing-controlled virulence factors. mBio 2020; 11:1–16 [View Article]
     [Google Scholar]
  59. Rumbaugh KP, Diggle SP, Watters CM, Ross-Gillespie A, Griffin AS et al. Quorum sensing and the social evolution of bacterial virulence. Curr Biol 2009; 19:341–345 [View Article] [PubMed]
     [Google Scholar]
  60. Azimi S, Roberts AEL, Peng S, Weitz JS, McNally A et al. Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations. ISME J 2020; 14:1929–1942 [View Article] [PubMed]
     [Google Scholar]
  61. Eldar A. Social conflict drives the evolutionary divergence of quorum sensing. Proc Natl Acad Sci 2011; 108:13635–13640 [View Article]
     [Google Scholar]
  62. LoVullo ED, Schweizer HP. Pseudomonas aeruginosa mexT is an indicator of PAO1 strain integrity. J Med Microbiol 2020; 69:139–145 [View Article] [PubMed]
     [Google Scholar]
  63. Sandoz KM, Mitzimberg SM, Schuster M. Social cheating in Pseudomonas aeruginosa quorum sensing. Proc Natl Acad Sci 2007; 104:15876–15881 [View Article]
     [Google Scholar]
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Frequency of quorum-sensing mutations in Pseudomonas aeruginosa strains isolated from different environments
Microbiology 168, 001265 (2022); https://doi.org/10.1099/mic.0.001265
/content/journal/micro/10.1099/mic.0.001265
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