Uncovering the GacS-mediated Role in Evolutionary Progression Through Trajectory Reconstruction in Pseudomonas Aeruginosa

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2024 Mar 13

PMID 38477346

Authors

Bo Jiang

Huifang Qiu

Chenghui Lu

Mingqi Lu

Yuanhao Li

Weijun Dai

Affiliations

Soon will be listed here.

Abstract

The genetic diversities of subpopulations drive the evolution of pathogens and affect their ability to infect hosts and cause diseases. However, most studies to date have focused on the identification and characterization of adaptive mutations in single colonies, which do not accurately reflect the phenotypes of an entire population. Here, to identify the composition of variant subpopulations within a pathogen population, we developed a streamlined approach that combines high-throughput sequencing of the entire population cells with genotyping of single colonies. Using this method, we reconstructed a detailed quorum-sensing (QS) evolutionary trajectory in Pseudomonas aeruginosa. Our results revealed a new adaptive mutation in the gacS gene, which codes for a histidine kinase sensor of a two-component system (TCS), during QS evolution. This mutation reduced QS activity, allowing the variant to sweep throughout the whole population, while still being vulnerable to invasion by the emerging QS master regulator LasR-null mutants. By tracking the evolutionary trajectory, we found that mutations in gacS facilitated QS-rewiring in the LasR-null mutant. This rapid QS revertant caused by inactive GacS was found to be associated with the promotion of ribosome biogenesis and accompanied by a trade-off of reduced bacterial virulence on host cells. In conclusion, our findings highlight the crucial role of the global regulator GacS in modulating the progression of QS evolution and the virulence of the pathogen population.

References

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

Cheng X, Lu M, Qiu H, Li Y, Huang L, Dai W . Spontaneous quorum-sensing hierarchy reprogramming in Pseudomonas aeruginosa laboratory strain PAO1. AMB Express. 2022; 12(1):6. PMC: 8792115. DOI: 10.1186/s13568-022-01344-7. View

Tirumalai M, Rivas M, Tran Q, Fox G . The Peptidyl Transferase Center: a Window to the Past. Microbiol Mol Biol Rev. 2021; 85(4):e0010421. PMC: 8579967. DOI: 10.1128/MMBR.00104-21. View

Reimmann C, Beyeler M, Latifi A, Winteler H, Foglino M, Lazdunski A . The global activator GacA of Pseudomonas aeruginosa PAO positively controls the production of the autoinducer N-butyryl-homoserine lactone and the formation of the virulence factors pyocyanin, cyanide, and lipase. Mol Microbiol. 1997; 24(2):309-19. DOI: 10.1046/j.1365-2958.1997.3291701.x. View

Oshri R, Zrihen K, Shner I, 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(10):2458-2469. PMC: 6154968. DOI: 10.1038/s41396-018-0205-y. View

Bruger E, Waters C . Bacterial Quorum Sensing Stabilizes Cooperation by Optimizing Growth Strategies. Appl Environ Microbiol. 2016; 82(22):6498-6506. PMC: 5086544. DOI: 10.1128/AEM.01945-16. View

Feltner J, Wolter D, Pope C, Groleau M, Smalley N, Greenberg E . LasR Variant Cystic Fibrosis Isolates Reveal an Adaptable Quorum-Sensing Hierarchy in Pseudomonas aeruginosa. mBio. 2016; 7(5). PMC: 5050340. DOI: 10.1128/mBio.01513-16. View

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

Castaneda-Tamez P, Ramirez-Peris J, Perez-Velazquez J, Kuttler C, Jalalimanesh A, Saucedo-Mora M . Pyocyanin Restricts Social Cheating in . Front Microbiol. 2018; 9:1348. PMC: 6030374. DOI: 10.3389/fmicb.2018.01348. View

10.

Ventre I, Goodman A, Vallet-Gely I, Vasseur P, Soscia C, Molin S . Multiple sensors control reciprocal expression of Pseudomonas aeruginosa regulatory RNA and virulence genes. Proc Natl Acad Sci U S A. 2005; 103(1):171-6. PMC: 1324988. DOI: 10.1073/pnas.0507407103. View

11.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

12.

Luong P, Shogan B, Zaborin A, Belogortseva N, Shrout J, Zaborina O . Emergence of the P2 phenotype in Pseudomonas aeruginosa PAO1 strains involves various mutations in mexT or mexF. J Bacteriol. 2013; 196(2):504-13. PMC: 3911258. DOI: 10.1128/JB.01050-13. View

13.

Smith E, Buckley D, Wu Z, Saenphimmachak C, Hoffman L, DArgenio D . Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci U S A. 2006; 103(22):8487-92. PMC: 1482519. DOI: 10.1073/pnas.0602138103. View

14.

Darch S, McNally A, Harrison F, Corander J, Barr H, Paszkiewicz K . Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection. Sci Rep. 2015; 5:7649. PMC: 4289893. DOI: 10.1038/srep07649. View

15.

Lapouge K, Schubert M, Allain F, Haas D . Gac/Rsm signal transduction pathway of gamma-proteobacteria: from RNA recognition to regulation of social behaviour. Mol Microbiol. 2007; 67(2):241-53. DOI: 10.1111/j.1365-2958.2007.06042.x. View

16.

Marden J, Diaz M, Walton W, Gode C, Betts L, Urbanowski M . An unusual CsrA family member operates in series with RsmA to amplify posttranscriptional responses in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2013; 110(37):15055-60. PMC: 3773774. DOI: 10.1073/pnas.1307217110. View

17.

Hoch J, Varughese K . Keeping signals straight in phosphorelay signal transduction. J Bacteriol. 2001; 183(17):4941-9. PMC: 95367. DOI: 10.1128/JB.183.17.4941-4949.2001. View

18.

Sonnleitner E, Schuster M, Sorger-Domenigg T, Greenberg E, Blasi U . Hfq-dependent alterations of the transcriptome profile and effects on quorum sensing in Pseudomonas aeruginosa. Mol Microbiol. 2006; 59(5):1542-58. DOI: 10.1111/j.1365-2958.2006.05032.x. View

19.

Brencic A, Lory S . Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA. Mol Microbiol. 2009; 72(3):612-32. PMC: 5567987. DOI: 10.1111/j.1365-2958.2009.06670.x. View

20.

Wang M, Schaefer A, Dandekar A, Greenberg E . Quorum sensing and policing of Pseudomonas aeruginosa social cheaters. Proc Natl Acad Sci U S A. 2015; 112(7):2187-91. PMC: 4343120. DOI: 10.1073/pnas.1500704112. View