FliZ Is a Global Regulatory Protein Affecting the Expression of Flagellar and Virulence Genes in Individual Bacterial Cells
Heterogeneity in the expression of various bacterial genes has been shown to result in the presence of individuals with different phenotypes within clonal bacterial populations. The genes specifying motility and flagellar functions are coordinately regulated and form a complex regulon, the flagellar regulon. Complex interplay has recently been demonstrated in the regulation of flagellar and virulence gene expression in many bacterial pathogens. We show here that FliZ, a DNA-binding protein, plays a key role in the insect pathogen, Xenorhabdus nematophila, affecting not only hemolysin production and virulence in insects, but efficient swimming motility. RNA-Seq analysis identified FliZ as a global regulatory protein controlling the expression of 278 Xenorhabdus genes either directly or indirectly. FliZ is required for the efficient expression of all flagellar genes, probably through its positive feedback loop, which controls expression of the flhDC operon, the master regulator of the flagellar circuit. FliZ also up- or downregulates the expression of numerous genes encoding non-flagellar proteins potentially involved in key steps of the Xenorhabdus lifecycle. Single-cell analysis revealed the bimodal expression of six identified markers of the FliZ regulon during exponential growth of the bacterial population. In addition, a combination of fluorescence-activated cell sorting and RT-qPCR quantification showed that this bimodality generated a mixed population of cells either expressing (“ON state”) or not expressing (“OFF state”) FliZ-dependent genes. Moreover, studies of a bacterial population exposed to a graded series of FliZ concentrations showed that FliZ functioned as a rheostat, controlling the rate of transition between the “OFF” and “ON” states in individuals. FliZ thus plays a key role in cell fate decisions, by transiently creating individuals with different potentials for motility and host interactions.
Vyšlo v časopise:
FliZ Is a Global Regulatory Protein Affecting the Expression of Flagellar and Virulence Genes in Individual Bacterial Cells. PLoS Genet 9(10): e32767. doi:10.1371/journal.pgen.1003915
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003915
Souhrn
Heterogeneity in the expression of various bacterial genes has been shown to result in the presence of individuals with different phenotypes within clonal bacterial populations. The genes specifying motility and flagellar functions are coordinately regulated and form a complex regulon, the flagellar regulon. Complex interplay has recently been demonstrated in the regulation of flagellar and virulence gene expression in many bacterial pathogens. We show here that FliZ, a DNA-binding protein, plays a key role in the insect pathogen, Xenorhabdus nematophila, affecting not only hemolysin production and virulence in insects, but efficient swimming motility. RNA-Seq analysis identified FliZ as a global regulatory protein controlling the expression of 278 Xenorhabdus genes either directly or indirectly. FliZ is required for the efficient expression of all flagellar genes, probably through its positive feedback loop, which controls expression of the flhDC operon, the master regulator of the flagellar circuit. FliZ also up- or downregulates the expression of numerous genes encoding non-flagellar proteins potentially involved in key steps of the Xenorhabdus lifecycle. Single-cell analysis revealed the bimodal expression of six identified markers of the FliZ regulon during exponential growth of the bacterial population. In addition, a combination of fluorescence-activated cell sorting and RT-qPCR quantification showed that this bimodality generated a mixed population of cells either expressing (“ON state”) or not expressing (“OFF state”) FliZ-dependent genes. Moreover, studies of a bacterial population exposed to a graded series of FliZ concentrations showed that FliZ functioned as a rheostat, controlling the rate of transition between the “OFF” and “ON” states in individuals. FliZ thus plays a key role in cell fate decisions, by transiently creating individuals with different potentials for motility and host interactions.
Zdroje
1. RamosHC, RumboM, SirardJC (2004) Bacterial flagellins: mediators of pathogenicity and host immune responses in mucosa. Trends Microbiol 12: 509–517.
2. MacnabRM (1992) Genetics and biogenesis of bacterial flagella. Annu Rev Genet 26: 131–158.
3. KalirS, McClureJ, PabbarajuK, SouthwardC, RonenM, et al. (2001) Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292: 2080–2083.
4. BartlettDH, FrantzBB, MatsumuraP (1988) Flagellar transcriptional activators FlbB and FlaI: gene sequences and 5′ consensus sequences of operons under FlbB and FlaI control. J Bacteriol 170: 1575–1581.
5. KutsukakeK (1994) Excretion of the anti-sigma factor through a flagellar substructure couples flagellar gene expression with flagellar assembly in Salmonella typhimurium. Mol Gen Genet 243: 605–612.
6. WangS, FlemingRT, WestbrookEM, MatsumuraP, McKayDB (2006) Structure of the Escherichia coli FlhDC complex, a prokaryotic heteromeric regulator of transcription. J Mol Biol 355: 798–808.
7. LiuX, MatsumuraP (1994) The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons. J Bacteriol 176: 7345–7351.
8. OhnishiK, KutsukakeK, SuzukiH, IinoT (1990) Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium. Mol Gen Genet 221: 139–147.
9. HughesKT, GillenKL, SemonMJ, KarlinseyJE (1993) Sensing structural intermediates in bacterial flagellar assembly by export of a negative regulator. Science 262: 1277–1280.
10. KutsukakeK, IkebeT, YamamotoS (1999) Two novel regulatory genes, fliT and fliZ, in the flagellar regulon of Salmonella. Genes Genet Syst 74: 287–292.
11. YamamotoS, KutsukakeK (2006) FliT acts as an anti-FlhD2C2 factor in the transcriptional control of the flagellar regulon in Salmonella enterica serovar typhimurium. J Bacteriol 188: 6703–6708.
12. SainiS, BrownJD, AldridgePD, RaoCV (2008) FliZ is a posttranslational activator of FlhD4C2-dependent flagellar gene expression. J Bacteriol 190: 4979–4988.
13. LanoisA, JubelinG, GivaudanA (2008) FliZ, a flagellar regulator, is at the crossroads between motility, haemolysin expression and virulence in the insect pathogenic bacterium Xenorhabdus. Mol Microbiol 68: 516–533.
14. PesaventoC, HenggeR (2012) The global repressor FliZ antagonizes gene expression by sigmaS-containing RNA polymerase due to overlapping DNA binding specificity. Nucleic Acids Res 40: 4783–93.
15. WadaT, TanabeY, KutsukakeK (2011) FliZ acts as a repressor of the ydiV gene, which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar typhimurium. J Bacteriol 193: 5191–5198.
16. LucasRL, LostrohCP, DiRussoCC, SpectorMP, WannerBL, et al. (2000) Multiple factors independently regulate hilA and invasion gene expression in Salmonella enterica serovar typhimurium. J Bacteriol 182: 1872–1882.
17. ChubizJE, GolubevaYA, LinD, MillerLD, SlauchJM (2010) FliZ regulates expression of the Salmonella pathogenicity island 1 invasion locus by controlling HilD protein activity in Salmonella enterica serovar typhimurium. J Bacteriol 192: 6261–6270.
18. Nielsen-LeRouxC, GaudriaultS, RamaraoN, LereclusD, GivaudanA (2012) How the insect pathogen bacteria Bacillus thuringiensis and Xenorhabdus/Photorhabdus occupy their hosts. Curr Opin Microbiol 15: 220–231.
19. RichardsGR, Goodrich-BlairH (2009) Masters of conquest and pillage: Xenorhabdus nematophila global regulators control transitions from virulence to nutrient acquisition. Cell Microbiol 11: 1025–1033.
20. ParkD, ForstS (2006) Co-regulation of motility, exoenzyme and antibiotic production by the EnvZ-OmpR-FlhDC-FliA pathway in Xenorhabdus nematophila. Mol Microbiol 61: 1397–1412.
21. VigneuxF, ZumbihlR, JubelinG, RibeiroC, PoncetJ, et al. (2007) The xaxAB genes encoding a new apoptotic toxin from the insect pathogen Xenorhabdus nematophila are present in plant and human pathogens. J Biol Chem 282: 9571–9580.
22. CowlesKN, Goodrich-BlairH (2005) Expression and activity of a Xenorhabdus nematophila haemolysin required for full virulence towards Manduca sexta insects. Cell Microbiol 7: 209–219.
23. JubelinG, PagesS, LanoisA, BoyerMH, GaudriaultS, et al. (2011) Studies of the dynamic expression of the Xenorhabdus FliAZ regulon reveal atypical iron-dependent regulation of the flagellin and haemolysin genes during insect infection. Environ Microbiol 13: 1271–1284.
24. SpudichJL, KoshlandDEJr (1976) Non-genetic individuality: chance in the single cell. Nature 262: 467–471.
25. KorobkovaE, EmonetT, VilarJM, ShimizuTS, CluzelP (2004) From molecular noise to behavioural variability in a single bacterium. Nature 428: 574–578.
26. CummingsLA, WilkersonWD, BergsbakenT, CooksonBT (2006) In vivo, fliC expression by Salmonella enterica serovar Typhimurium is heterogeneous, regulated by ClpX, and anatomically restricted. Mol Microbiol 61: 795–809.
27. FreedNE, SilanderOK, StecherB, BohmA, HardtWD, et al. (2008) A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genet 4: e1000307.
28. SainiS, KoiralaS, FloessE, MearsPJ, ChemlaYR, et al. (2010) FliZ induces a kinetic switch in flagellar gene expression. J Bacteriol 192: 6477–6481.
29. KearnsDB, LosickR (2005) Cell population heterogeneity during growth of Bacillus subtilis. Genes Dev 19: 3083–3094.
30. LanoisA, OgierJ-C, GouzyJ, LarouiC, RouyZ, et al. (2013) Draft genome sequence and annotation of the entomopathogenic bacterium, Xenorhabdus nematophila strain F1. Genome Announcements 1: e00342–00313.
31. ParkD, CiezkiK, van der HoevenR, SinghS, ReimerD, et al. (2009) Genetic analysis of xenocoumacin antibiotic production in the mutualistic bacterium Xenorhabdus nematophila. Mol Microbiol 73: 938–949.
32. GualtieriM, AumelasA, ThalerJO (2009) Identification of a new antimicrobial lysine-rich cyclolipopeptide family from Xenorhabdus nematophila. J Antibiot (Tokyo) 62: 295–302.
33. FuchsSW, ProschakA, JaskollaTW, KarasM, BodeHB (2011) Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila. Org Biomol Chem 9: 3130–3132.
34. ChastonJM, SuenG, TuckerSL, AndersenAW, BhasinA, et al. (2011) The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PLoS One 6: e27909.
35. OgierJC, CalteauA, ForstS, Goodrich-BlairH, RocheD, et al. (2010) Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 11: 568.
36. MorganJA, SergeantM, EllisD, OusleyM, JarrettP (2001) Sequence analysis of insecticidal genes from Xenorhabdus nematophilus PMFI296. Appl Environ Microbiol 67: 2062–2069.
37. PesaventoC, HenggeR (2012) The global repressor FliZ antagonizes gene expression by sigmaS-containing RNA polymerase due to overlapping DNA binding specificity. Nucleic Acids Res 40: 4783–4793.
38. CowlesCE, Goodrich-BlairH (2006) nilR is necessary for co-ordinate repression of Xenorhabdus nematophila mutualism genes. Mol Microbiol 62: 760–771.
39. GivaudanA, LanoisA (2000) flhDC, the flagellar master operon of Xenorhabdus nematophilus: requirement for motility, lipolysis, extracellular hemolysis, and full virulence in insects. J Bacteriol 182: 107–115.
40. IkebeT, IyodaS, KutsukakeK (1999) Structure and expression of the fliA operon of Salmonella typhimurium. Microbiology 145 Pt 6 1389–1396.
41. TanabeY, WadaT, OnoK, AboT, KutsukakeK (2011) The transcript from the sigma(28)-dependent promoter is translationally inert in the expression of the sigma(28)-encoding gene fliA in the fliAZ operon of Salmonella enterica serovar Typhimurium. J Bacteriol 193: 6132–6141.
42. VeeningJW, SmitsWK, KuipersOP (2008) Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol 62: 193–210.
43. ChalanconG, RavaraniCN, BalajiS, Martinez-AriasA, AravindL, et al. (2012) Interplay between gene expression noise and regulatory network architecture. Trends Genet 28: 221–232.
44. GolubevaYA, SadikAY, EllermeierJR, SlauchJM (2012) Integrating global regulatory input into the Salmonella pathogenicity island 1 type III secretion system. Genetics 190: 79–90.
45. IyodaS, KamidoiT, HiroseK, KutsukakeK, WatanabeH (2001) A flagellar gene fliZ regulates the expression of invasion genes and virulence phenotype in Salmonella enterica serovar Typhimurium. Microb Pathog 30: 81–90.
46. SainiS, SlauchJM, AldridgePD, RaoCV (2010) Role of cross talk in regulating the dynamic expression of the flagellar Salmonella pathogenicity island 1 and type 1 fimbrial genes. J Bacteriol 192: 5767–5777.
47. MassaoudMK, MarokhaziJ, FodorA, VenekeiI (2010) Proteolytic enzyme production by strains of the insect pathogen Xenorhabdus and characterization of an early-log-phase-secreted protease as a potential virulence factor. Appl Environ Microbiol 76: 6901–6909.
48. RichardsGR, Goodrich-BlairH (2010) Examination of Xenorhabdus nematophila lipases in pathogenic and mutualistic host interactions reveals a role for xlpA in nematode progeny production. Appl Environ Microbiol 76: 221–229.
49. WaterfieldNR, BowenDJ, FetherstonJD, PerryRD, ffrench-ConstantRH (2001) The tc genes of Photorhabdus: a growing family. Trends Microbiol 9: 185–191.
50. RichardsGR, HerbertEE, ParkY, Goodrich-BlairH (2008) Xenorhabdus nematophila lrhA is necessary for motility, lipase activity, toxin expression, and virulence in Manduca sexta insects. J Bacteriol 190: 4870–4879.
51. VivasEI, Goodrich-BlairH (2001) Xenorhabdus nematophilus as a model for host-bacterium interactions: rpoS is necessary for mutualism with nematodes. J Bacteriol 183: 4687–4693.
52. PesaventoC, BeckerG, SommerfeldtN, PosslingA, TschowriN, et al. (2008) Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev 22: 2434–2446.
53. SomvanshiVS, SloupRE, CrawfordJM, MartinAR, HeidtAJ, et al. (2012) A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. Science 337: 88–93.
54. BoemareN, ThalerJ-O, LanoisA (1997) Simple bacteriological tests for phenotypic characterization of Xenorhabdus and Photorhabdus phase variants. Symbiosis 22: 167–175.
55. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al.. (1993) Current Protocols in Molecular Biology. Sons JW, editor. New York.
56. VallenetD, BeldaE, CalteauA, CruveillerS, EngelenS, et al. (2013) MicroScope–an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41: D636–647.
57. NingZ, CoxAJ, MullikinJC (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11: 1725–1729.
58. AndersS, HuberW (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
59. PfafflMW, HorganGW, DempfleL (2002) Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30: e36.
60. GivaudanA, BaghdiguianS, LanoisA, BoemareN (1995) Swarming and swimming changes concomitant with phase variation in Xenorhabdus nematophilus. Appl Environ Microbiol 61: 1408–1413.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2013 Číslo 10
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Dominant Mutations in Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway
- Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer
- The Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters
- A Mutation in the Gene in Labrador Retrievers with Hereditary Nasal Parakeratosis (HNPK) Provides Insights into the Epigenetics of Keratinocyte Differentiation