A window into lysogeny: revealing temperate phage biology with transcriptomics Open Access

Abstract

Prophages are integrated phage elements that are a pervasive feature of bacterial genomes. The fitness of bacteria is enhanced by prophages that confer beneficial functions such as virulence, stress tolerance or phage resistance, and these functions are encoded by ‘accessory’ or ‘moron’ loci. Whilst the majority of phage-encoded genes are repressed during lysogeny, accessory loci are often highly expressed. However, it is challenging to identify novel prophage accessory loci from DNA sequence data alone. Here, we use bacterial RNA-seq data to examine the transcriptional landscapes of five prophages. We show that transcriptomic data can be used to heuristically enrich for prophage features that are highly expressed within bacterial cells and represent functionally important accessory loci. Using this approach, we identify a novel antisense RNA species in prophage BTP1, STnc6030, which mediates superinfection exclusion of phage BTP1. Bacterial transcriptomic datasets are a powerful tool to explore the molecular biology of temperate phages.

Funding
This study was supported by the:
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH) (Award P2LAP3_158684)
    • Principle Award Recipient: Nicolas Wenner
  • Wellcome Trust (Award 106914/Z/15/Z)
    • Principle Award Recipient: Jay C. D. Hinton
  • H2020 Marie Skłodowska-Curie Actions (Award FP7-PEOPLE-2013-IIF)
    • Principle Award Recipient: Rocío Canals
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2020-02-05
2024-03-28
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References

  1. Ptashne M. A Genetic Switch: Phage Lambda Revisited Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2004
    [Google Scholar]
  2. Barondess JJ, Beckwith J. Bor gene of phage lambda, involved in serum resistance, encodes a widely conserved outer membrane lipoprotein. J Bacteriol 1995; 177:1247–1253 [View Article]
    [Google Scholar]
  3. Chen Y, Golding I, Sawai S, Guo L, Cox EC. Population fitness and the regulation of Escherichia coli genes by bacterial viruses. PLoS Biol 2005; 3:e229 [View Article]
    [Google Scholar]
  4. Liu X, Jiang H, Gu Z, Roberts JW. High-resolution view of bacteriophage lambda gene expression by ribosome profiling. Proc Natl Acad Sci USA 2013; 110:11928–11933 [View Article]
    [Google Scholar]
  5. Osterhout RE, Figueroa IA, Keasling JD, Arkin AP. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol 2007; 7:82 [View Article]
    [Google Scholar]
  6. Vica Pacheco S, García González O, Paniagua Contreras GL. The lom gene of bacteriophage λ is involved in Escherichia coli K12 adhesion to human buccal epithelial cells. FEMS Microbiol Lett 1997; 156:129–132 [View Article]
    [Google Scholar]
  7. Cumby N, Davidson AR, Maxwell KL. The moron comes of age. Bacteriophage 2012; 2:e23146 [View Article]
    [Google Scholar]
  8. Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF et al. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J Mol Biol 2000; 299:27–51 [View Article]
    [Google Scholar]
  9. Casjens SR, Hendrix RW. Bacteriophage lambda: early pioneer and still relevant. Virology 2015; 479-480:310–330 [View Article]
    [Google Scholar]
  10. Veses-Garcia M, Liu X, Rigden DJ, Kenny JG, McCarthy AJ et al. Transcriptomic analysis of Shiga-toxigenic bacteriophage carriage reveals a profound regulatory effect on acid resistance in Escherichia coli . Appl Environ Microbiol 2015; 81:8118–8125 [View Article]
    [Google Scholar]
  11. Brüssow H, Canchaya C, Hardt W-D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 2004; 68:560–602 [View Article]
    [Google Scholar]
  12. Figueroa-Bossi N, Bossi L. Inducible prophages contribute to Salmonella virulence in mice. Mol Microbiol 1999; 33:167–176 [View Article]
    [Google Scholar]
  13. Fortier L-C, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 2013; 4:354–365 [View Article]
    [Google Scholar]
  14. Wahl A, Battesti A, Ansaldi M. Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?. Mol Microbiol 2019; 111:303–316 [View Article]
    [Google Scholar]
  15. Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 2015; 4: [View Article]
    [Google Scholar]
  16. Touchon M, Bernheim A, Rocha EP. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J 2016; 10:2744–2754 [View Article]
    [Google Scholar]
  17. Ashton PM, Owen SV, Kaindama L, Rowe WPM, Lane CR et al. Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa. Genome Med 2017; 9:92 [View Article]
    [Google Scholar]
  18. Mottawea W, Duceppe M-O, Dupras AA, Usongo V, Jeukens J et al. Salmonella enterica prophage sequence profiles reflect genome diversity and can be used for high discrimination subtyping. Front Microbiol 2018; 9:00836 [View Article]
    [Google Scholar]
  19. Owen SV, Perez-Sepulveda BM, Adriaenssens EM. Detection of bacteriophages: sequence-based systems. In Harper DR, Abedon ST, Burrowes BH, McConville ML. eds Bacteriophages: Biology, Technology, Therapy Cham: Springer International Publishing; 2018 pp 1–25
    [Google Scholar]
  20. Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY et al. Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580. PLoS Biol 2019; 17:e3000059 [View Article]
    [Google Scholar]
  21. Hammarlöf DL, Kröger C, Owen SV, Canals R, Lacharme-Lora L et al. Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella . Proc Natl Acad Sci USA 2018; 115:E2614E2623 [View Article]
    [Google Scholar]
  22. Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK et al. An infection-relevant transcriptomic compendium for Salmonella enterica serovar Typhimurium. Cell Host Microbe 2013; 14:683–695 [View Article]
    [Google Scholar]
  23. Wagner GP, Kin K, Lynch VJ. A model based criterion for gene expression calls using RNA-seq data. Theory Biosci 2013; 132:159–164 [View Article]
    [Google Scholar]
  24. Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci 2012; 131:281–285 [View Article]
    [Google Scholar]
  25. Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 2009; 25:2730–2731 [View Article]
    [Google Scholar]
  26. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res 2009; 19:1630–1638 [View Article]
    [Google Scholar]
  27. Bryksin AV, Matsumura I. Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids. Biotechniques 2010; 48:463–465 [View Article]
    [Google Scholar]
  28. Sittka A, Pfeiffer V, Tedin K, Vogel J. The RNA chaperone Hfq is essential for the virulence of Salmonella Typhimurium. Mol Microbiol 2007; 63:193–217 [View Article]
    [Google Scholar]
  29. Rist M, Kertesz MA. Construction of improved plasmid vectors for promoter characterization in Pseudomonas aeruginosa and other Gram-negative bacteria. FEMS Microbiol Lett 1998; 169:179–183 [View Article]
    [Google Scholar]
  30. Green R, Rogers EJ. Transformation of chemically competent E. coli . Meth Enzymol 2013; 529:329–336 [View Article]
    [Google Scholar]
  31. Owen SV, Wenner N, Canals R, Makumi A, Hammarlöf DL et al. Characterization of the prophage repertoire of African Salmonella Typhimurium ST313 reveals high levels of spontaneous induction of novel phage BTP1. Front Microbiol 2017; 8:235 [View Article]
    [Google Scholar]
  32. Kröger C, Dillon SC, Cameron ADS, Papenfort K, Sivasankaran SK et al. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci USA 2012; 109:E1277–E1286 [View Article]
    [Google Scholar]
  33. Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 2009; 19:2279–2287 [View Article]
    [Google Scholar]
  34. Srikumar S, Kröger C, Hébrard M, Colgan A, Owen SV et al. RNA-seq brings new insights to the intra-macrophage transcriptome of Salmonella Typhimurium. PLoS Pathog 2015; 11:e1005262 [View Article]
    [Google Scholar]
  35. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S et al. The primary transcriptome of the major human pathogen Helicobacter pylori . Nature 2010; 464:250–255 [View Article]
    [Google Scholar]
  36. Cenens W, Makumi A, Mebrhatu MT, Lavigne R, Aertsen A. Phage-host interactions during pseudolysogeny: lessons from the Pid/dgo interaction. Bacteriophage 2013; 3:e25029 [View Article]
    [Google Scholar]
  37. Cenens W, Mebrhatu MT, Makumi A, Ceyssens P-J, Lavigne R et al. Expression of a novel P22 ORFan gene reveals the phage carrier state in Salmonella Typhimurium. PLoS Genet 2013; 9:e1003269 [View Article]
    [Google Scholar]
  38. Kintz E, Davies MR, Hammarlöf DL, Canals R, Hinton JCD et al. A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide. Mol Microbiol 2015; 96:263–275 [View Article]
    [Google Scholar]
  39. Davies MR, Broadbent SE, Harris SR, Thomson NR, van der Woude MW. Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity. PLoS Genet 2013; 9:e1003568 [View Article]
    [Google Scholar]
  40. Krinke L, Wulff DL. OOP RNA, produced from multicopy plasmids, inhibits lambda cII gene expression through an RNase III-dependent mechanism. Genes Dev 1987; 1:1005–1013 [View Article]
    [Google Scholar]
  41. Krinke L, Mahoney M, Wulff DL. The role of the OOP antisense RNA in coliphage lambda development. Mol Microbiol 1991; 5:1265–1272 [View Article]
    [Google Scholar]
  42. Carden SE, Walker GT, Honeycutt J, Lugo K, Pham T et al. Pseudogenization of the secreted effector gene sseI confers rapid systemic dissemination of S. Typhimurium ST313 within migratory dendritic cells. Cell Host Microbe 2017; 21:182–194 [View Article]
    [Google Scholar]
  43. Lemire S, Figueroa-Bossi N, Bossi L. Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genet 2011; 7:e1002149 [View Article]
    [Google Scholar]
  44. Figueroa-Bossi N, Bossi L. Resuscitation of a defective prophage in Salmonella cocultures. J Bacteriol 2004; 186:4038–4041 [View Article]
    [Google Scholar]
  45. Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I et al. Small RNAs encoded within genetic islands of Salmonella Typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 2008; 36:1913–1927 [View Article]
    [Google Scholar]
  46. Stanley TL, Ellermeier CD, Slauch JM. Tissue-sSpecific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar typhimurium survival in Peyer’s patches. J Bacteriol 2000; 182:4406–4413 [View Article]
    [Google Scholar]
  47. Shearwin KE, Brumby AM, Egan JB. The Tum protein of coliphage 186 is an antirepressor. J Biol Chem 1998; 273:5708–5715 [View Article]
    [Google Scholar]
  48. Shearwin KE, Egan JB. Establishment of lysogeny in bacteriophage 186: DNA binding and transcriptional activation by the CII protein. J Biol Chem 2000; 275:29113–29122 [View Article]
    [Google Scholar]
  49. Christie GE, Calendar R. Bacteriophage P2. Bacteriophage 2016; 6:e1145782 [View Article]
    [Google Scholar]
  50. Hinton JCD. The Escherichia coli genome sequence: the end of an era or the start of the FUN?. Mol Microbiol 1997; 26:417–422 [View Article]
    [Google Scholar]
  51. Perez-Sepulveda BM, Hinton JCD. Functional transcriptomics for bacterial gene detectives. Microbiol Spectr 2018; 6:RWR-0033-2018 [View Article]
    [Google Scholar]
  52. Thattai M. Using topology to tame the complex biochemistry of genetic networks. Philos Trans A Math Phys Eng Sci 2013; 371:2011.0548
    [Google Scholar]
  53. Degnan PH, Michalowski CB, Babić AC, Cordes MHJ, Little JW. Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage lambda. Mol Microbiol 2007; 64:232–244 [View Article]
    [Google Scholar]
  54. Herrero-Fresno A, Wallrodt I, Leekitcharoenphon P, Olsen JE, Aarestrup FM et al. The role of the ST313-td gene in virulence of Salmonella Typhimurium ST313. PLoS One 2014; 9:e84566 [View Article]
    [Google Scholar]
  55. Herrero-Fresno A, Espinel IC, Spiegelhauer MR, Guerra PR, Andersen KW et al. The homolog of the gene bstA of the BTP1 phage from Salmonella enterica serovar Typhimurium ST313 is an antivirulence gene in Salmonella enterica serovar Dublin. Infect Immun 2017; 86:e00784-17 [View Article]
    [Google Scholar]
  56. Álvarez-Ordóñez A, Begley M, Prieto M, Messens W, López M et al. Salmonella spp. survival strategies within the host gastrointestinal tract. Microbiology 2011; 157:3268–3281 [View Article]
    [Google Scholar]
  57. Wagner EGH, Altuvia S, Romby P. Antisense RNAs in bacteria and their genetic elements. Adv Genet 2002; 46:361–398 [View Article]
    [Google Scholar]
  58. Thomason MK, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing?. Annu Rev Genet 2010; 44:167–188 [View Article]
    [Google Scholar]
  59. Papenfort K, Said N, Welsink T, Lucchini S, Hinton JCD et al. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 2009; 74:139–158 [View Article]
    [Google Scholar]
  60. Tsao Y-F, Taylor VL, Kala S, Bondy-Denomy J, Khan AN et al. Phage morons play an important role in Pseudomonas aeruginosa phenotypes. J Bacteriol 2018; 200:e00189-18 [View Article]
    [Google Scholar]
  61. Hendrix RW. editor Lambda II (Cold Spring Harbor Monograph series Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1983
    [Google Scholar]
  62. Ehrbar K, Hardt W. Bacteriophage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium. Infect Genet Evol 2005; 5:1–9 [View Article]
    [Google Scholar]
  63. Barquist L, Vogel J. Accelerating discovery and functional analysis of small RNAs with new technologies. Annu Rev Genet 2015; 49:367–394 [View Article]
    [Google Scholar]
  64. Ranade K, Poteete AR. A switch in translation mediated by an antisense RNA. Genes Dev 1993; 7:1498–1507 [View Article]
    [Google Scholar]
  65. Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3:a003798 [View Article]
    [Google Scholar]
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