High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Isolates

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Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA–seq (dRNA–seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA–seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA–seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA–seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level.

Vyšlo v časopise: High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Isolates. PLoS Genet 9(5): e32767. doi:10.1371/journal.pgen.1003495
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003495

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Zdroje

1. WangZ, GersteinM, SnyderM (2009) RNA–Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57–63.

2. CroucherNJ, ThomsonNR (2010) Studying bacterial transcriptomes using RNA–seq. Curr Opin Microbiol 13: 619–624.

3. van VlietAH (2010) Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol Lett 302: 1–7.

4. SharmaCM, HoffmannS, DarfeuilleF, ReignierJ, FindeissS, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250–255.

5. ThomasonMK, StorzG (2010) Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet 44: 167–188.

6. GeorgJ, HessWR (2011) cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 75: 286–300.

7. DastiJI, TareenAM, LugertR, ZautnerAE, GrossU (2010) Campylobacter jejuni: a brief overview on pathogenicity-associated factors and disease-mediating mechanisms. Int J Med Microbiol 300: 205–211.

8. YoungKT, DavisLM, DiritaVJ (2007) Campylobacter jejuni: molecular biology and pathogenesis. Nat Rev Microbiol 5: 665–679.

9. SuerbaumS, LohrengelM, SonnevendA, RubergF, KistM (2001) Allelic diversity and recombination in Campylobacter jejuni. J Bacteriol 183: 2553–2559.

10. DingleKE, CollesFM, WareingDR, UreR, FoxAJ, et al. (2001) Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol 39: 14–23.

11. LinzB, SchusterSC (2007) Genomic diversity in Helicobacter and related organisms. Res Microbiol 158: 737–744.

12. SuerbaumS, JosenhansC (2007) Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat Rev Microbiol 5: 441–452.

13. WassenaarTM, NewellDG (2000) Genotyping of Campylobacter spp. Appl Environ Microbiol 66: 1–9.

14. FoutsDE, MongodinEF, MandrellRE, MillerWG, RaskoDA, et al. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol 3: e15 doi:10.1371/journal.pbio.0030015.

15. ParkerCT, QuinonesB, MillerWG, HornST, MandrellRE (2006) Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J Clin Microbiol 44: 4125–4135.

16. WassenaarTM, BlaserMJ (1999) Pathophysiology of Campylobacter jejuni infections of humans. Microbes Infect 1: 1023–1033.

17. Lara-TejeroM, GalanJE (2000) A bacterial toxin that controls cell cycle progression as a deoxyribonuclease I-like protein. Science 290: 354–357.

18. BaconDJ, AlmRA, HuL, HickeyTE, EwingCP, et al. (2002) DNA sequence and mutational analyses of the pVir plasmid of Campylobacter jejuni 81–176. Infect Immun 70: 6242–6250.

19. HofreuterD, NovikV, GalanJE (2008) Metabolic diversity in Campylobacter jejuni enhances specific tissue colonization. Cell Host Microbe 4: 425–433.

20. ParkhillJ, WrenBW, MungallK, KetleyJM, ChurcherC, et al. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403: 665–668.

21. StorzG, VogelJ, WassarmanKM (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43: 880–891.

22. VogelJ, LuisiBF (2011) Hfq and its constellation of RNA. Nat Rev Microbiol 9: 578–589.

23. ChaoY, VogelJ (2010) The role of Hfq in bacterial pathogens. Curr Opin Microbiol 13: 24–33.

24. ChaudhuriRR, YuL, KanjiA, PerkinsTT, GardnerPP, et al. (2011) Quantitative RNA–seq analysis of the transcriptome of Campylobacter jejuni. Microbiology 157: 2922–2932.

25. HofreuterD, TsaiJ, WatsonRO, NovikV, AltmanB, et al. (2006) Unique features of a highly pathogenic Campylobacter jejuni strain. Infect Immun 74: 4694–4707.

26. BatchelorRA, PearsonBM, FriisLM, GuerryP, WellsJM (2004) Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150: 3507–3517.

27. PearsonBM, GaskinDJ, SegersRP, WellsJM, NuijtenPJ, et al. (2007) The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J Bacteriol 189: 8402–8403.

28. ManningG, DuimB, WassenaarT, WagenaarJA, RidleyA, et al. (2001) Evidence for a genetically stable strain of Campylobacter jejuni. Appl Environ Microbiol 67: 1185–1189.

29. HerbigA, JagerG, BattkeF, NieseltK (2012) GenomeRing: alignment visualization based on SuperGenome coordinates. Bioinformatics 28: i7–15.

30. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36.

31. PetersenL, LarsenTS, UsseryDW, OnSL, KroghA (2003) RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J Mol Biol 326: 1361–1372.

32. MyersJD, KellyDJ (2005) A sulphite respiration system in the chemoheterotrophic human pathogen Campylobacter jejuni. Microbiology 151: 233–242.

33. BrounsSJJ, JoreMM, LundgrenM, WestraER, SlijkhuisRJH, et al. (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960–964.

34. HaleCR, ZhaoP, OlsonS, DuffMO, GraveleyBR, et al. (2009) RNA–Guided RNA Cleavage by a CRISPR RNA–Cas Protein Complex. Cell 139: 945–956.

35. MarraffiniLA, SontheimerEJ (2008) CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA. Science 322: 1843–1845.

36. DeltchevaE, ChylinskiK, SharmaCM, GonzalesK, ChaoY, et al. (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471: 602–607.

37. MakarovaKS, HaftDH, BarrangouR, BrounsSJ, CharpentierE, et al. (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9: 467–477.

38. JinekM, ChylinskiK, FonfaraI, HauerM, DoudnaJA, et al. (2012) A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science

39. MitschkeJ, GeorgJ, ScholzI, SharmaCM, DienstD, et al. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 108: 2124–2129.

40. AlbrechtM, SharmaCM, ReinhardtR, VogelJ, RudelT (2010) Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res 38: 868–877.

41. JagerD, SharmaCM, ThomsenJ, EhlersC, VogelJ, et al. (2009) Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci U S A 106: 21878–21882.

42. FiliatraultMJ, StodghillPV, MyersCR, BronsteinPA, ButcherBG, et al. (2012) Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS ONE 6: e29335 doi:10.1371/journal.pone.0029335.

43. SchluterJP, ReinkensmeierJ, DaschkeyS, Evguenieva-HackenbergE, JanssenS, et al. (2010) A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 11: 245.

44. WurtzelO, SapraR, ChenF, ZhuY, SimmonsBA, et al. (2010) A single-base resolution map of an archaeal transcriptome. Genome Res 20: 133–141.

45. WurtzelO, SestoN, MellinJR, KarunkerI, EdelheitS, et al. (2012) Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8: 583.

46. SchmidtkeC, FindeissS, SharmaCM, KuhfussJ, HoffmannS, et al. (2012) Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res

47. PolyF, ReadTD, ChenYH, MonteiroMA, SerichantalergsO, et al. (2008) Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies. Infect Immun 76: 5655–5667.

48. FriisC, WassenaarTM, JavedMA, SnipenL, LagesenK, et al. (2010) Genomic characterization of Campylobacter jejuni strain M1. PLoS ONE 5: e12253 doi:10.1371/journal.pone.0012253.

49. GrippE, HlahlaD, DidelotX, KopsF, MaurischatS, et al. (2011) Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics 12: 584.

50. JeromeJP, BellJA, Plovanich-JonesAE, BarrickJE, BrownCT, et al. (2011) Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host. PLoS ONE 6: e16399 doi:10.1371/journal.pone.0016399.

51. GaynorEC, CawthrawS, ManningG, MacKichanJK, FalkowS, et al. (2004) The genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate differ markedly in colonization, gene expression, and virulence-associated phenotypes. J Bacteriol 186: 503–517.

52. PerutzMF (1983) Species adaptation in a protein molecule. Mol Biol Evol 1: 1–28.

53. AlfredsonDA, KorolikV (2007) Antibiotic resistance and resistance mechanisms in Campylobacter jejuni and Campylobacter coli. FEMS Microbiol Lett 277: 123–132.

54. Wilmes-RiesenbergMR, FosterJW, CurtissR3rd (1997) An altered rpoS allele contributes to the avirulence of Salmonella typhimurium LT2. Infect Immun 65: 203–210.

55. HorstmannN, SahasrabhojaneP, SuberB, KumaraswamiM, OlsenRJ, et al. (2011) Distinct single amino acid replacements in the control of virulence regulator protein differentially impact streptococcal pathogenesis. PLoS Pathog 7: e1002311 doi:10.1371/journal.ppat.1002311.

56. Van SteltenA, SimpsonJM, WardTJ, NightingaleKK (2010) Revelation by single-nucleotide polymorphism genotyping that mutations leading to a premature stop codon in inlA are common among Listeria monocytogenes isolates from ready-to-eat foods but not human listeriosis cases. Appl Environ Microbiol 76: 2783–2790.

57. WeissmanSJ, MoseleySL, DykhuizenDE, SokurenkoEV (2003) Enterobacterial adhesins and the case for studying SNPs in bacteria. Trends Microbiol 11: 115–117.

58. ChoiSS, ChiversPT, BergDE (2011) Point mutations in Helicobacter pylori's fur regulatory gene that alter resistance to metronidazole, a prodrug activated by chemical reduction. PLoS ONE 6: e18236 doi:10.1371/journal.pone.0018236.

59. SeshuJ, BoylanJA, HydeJA, SwingleKL, GherardiniFC, et al. (2004) A conservative amino acid change alters the function of BosR, the redox regulator of Borrelia burgdorferi. Mol Microbiol 54: 1352–1363.

60. VegaY, DickneiteC, RipioMT, BockmannR, Gonzalez-ZornB, et al. (1998) Functional similarities between the Listeria monocytogenes virulence regulator PrfA and cyclic AMP receptor protein: the PrfA* (Gly145Ser) mutation increases binding affinity for target DNA. J Bacteriol 180: 6655–6660.

61. PapenfortK, PodkaminskiD, HintonJC, VogelJ (2012) The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A 109: E757–764.

62. MandelMJ, WollenbergMS, StabbEV, VisickKL, RubyEG (2009) A single regulatory gene is sufficient to alter bacterial host range. Nature 458: 215–218.

63. SomvanshiVS, SloupRE, CrawfordJM, MartinAR, HeidtAJ, et al. (2012) A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. Science 337: 88–93.

64. LiangX, HallJW, YangJ, YanM, DollK, et al. (2011) Identification of single nucleotide polymorphisms associated with hyperproduction of alpha-toxin in Staphylococcus aureus. PLoS ONE 6: e18428 doi:10.1371/journal.pone.0018428.

65. OkudaJ, NishibuchiM (1998) Manifestation of the Kanagawa phenomenon, the virulence-associated phenotype, of Vibrio parahaemolyticus depends on a particular single base change in the promoter of the thermostable direct haemolysin gene. Mol Microbiol 30: 499–511.

66. TareenAM, DastiJI, ZautnerAE, GrossU, LugertR (2011) Sulphite : cytochrome c oxidoreductase deficiency in Campylobacter jejuni reduces motility, host cell adherence and invasion. Microbiology 157: 1776–1785.

67. CarpenterBM, GanczH, Gonzalez-NievesRP, WestAL, WhitmireJM, et al. (2009) A single nucleotide change affects fur-dependent regulation of sodB in H. pylori. PLoS ONE 4: e5369 doi:10.1371/journal.pone.0005369.

68. Yoder-HimesDR, ChainPS, ZhuY, WurtzelO, RubinEM, et al. (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 106: 3976–3981.

69. BernickDL, DennisPP, LuiLM, LoweTM (2012) Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species. Front Microbiol 3: 231.

70. DiChiaraJM, Contreras-MartinezLM, LivnyJ, SmithD, McDonoughKA, et al. (2010) Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. Nucleic Acids Res 38: 4067–4078.

71. PichonC, FeldenB (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci U S A 102: 14249–14254.

72. KimD, HongJS, QiuY, NagarajanH, SeoJH, et al. (2012) Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling. PLoS Genet 8: e1002867 doi:10.1371/journal.pgen.1002867.

73. PapenfortK, VogelJ (2010) Regulatory RNA in bacterial pathogens. Cell Host Microbe 8: 116–127.

74. BeiselCL, StorzG (2010) Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiol Rev 34: 866–882.

75. ChaoY, PapenfortK, ReinhardtR, SharmaCM, VogelJ (2012) An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs. EMBO J 31: 4005–4019.

76. SchoulsLM, ReulenS, DuimB, WagenaarJA, WillemsRJ, et al. (2003) Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol 41: 15–26.

77. LouwenR, Horst-KreftD, de BoerAG, van der GraafL, de KnegtG, et al. (2012) A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barre syndrome. Eur J Clin Microbiol Infect Dis

78. MaliP, YangL, EsveltKM, AachJ, GuellM, et al. (2013) RNA–Guided Human Genome Engineering via Cas9. Science

79. CongL, RanFA, CoxD, LinS, BarrettoR, et al. (2013) Multiplex Genome Engineering Using CRISPR/Cas Systems. Science

80. BlombergP, WagnerEG, NordstromK (1990) Control of replication of plasmid R1: the duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J 9: 2331–2340.

81. BerezikovE, ThuemmlerF, van LaakeLW, KondovaI, BontropR, et al. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38: 1375–1377.

82. EdgarR, DomrachevM, LashAE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207–210.

83. DarlingAC, MauB, BlattnerFR, PernaNT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394–1403.

84. BaileyTL, BodenM, BuskeFA, FrithM, GrantCE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208.

85. KapplerU, BennettB, RethmeierJ, SchwarzG, DeutzmannR, et al. (2000) Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J Biol Chem 275: 13202–13212.

86. CamachoC, CoulourisG, AvagyanV, MaN, PapadopoulosJ, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.

87. MakarovaKS, WolfYI, KooninEV (2013) Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res doi: 10.1093/nar/gkt157.

88. Barrero-TobonAM, HendrixsonDR (2012) Identification and analysis of flagellar coexpressed determinants (Feds) of Campylobacter jejuni involved in colonization. Mol Microbiol 84: 352–369.

89. WostenMM, WagenaarJA, van PuttenJP (2004) The FlgS/FlgR two-component signal transduction system regulates the fla regulon in Campylobacter jejuni. J Biol Chem 279: 16214–16222.