1887

Abstract

Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.

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2018-08-24
2020-01-26
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References

  1. Darmon E, Leach DR. Bacterial genome instability. Microbiol Mol Biol Rev 2014;78:1–39 [CrossRef][PubMed]
    [Google Scholar]
  2. Vandecraen J, Chandler M, Aertsen A, van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017;43:709–730 [CrossRef][PubMed]
    [Google Scholar]
  3. Bennett PM. Genomic plasticity. In Woodford N, Johnson AP. (editors) Genomics, Proteomics, and Clinical Bacteriology (Methods in Molecular Biology) Totawa, New Jersey: Humana Press; 2004; pp.71–115
    [Google Scholar]
  4. Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 2014;38:865–891 [CrossRef][PubMed]
    [Google Scholar]
  5. Brügger K, Redder P, She Q, Confalonieri F, Zivanovic Y et al. Mobile elements in archaeal genomes. FEMS Microbiol Lett 2002;206:131–141 [CrossRef][PubMed]
    [Google Scholar]
  6. Adams MD, Bishop B, Wright MS. Quantitative assessment of insertion sequence impact on bacterial genome architecture. Microb Genom 2016;2:e000062 [CrossRef][PubMed]
    [Google Scholar]
  7. Newton IL, Bordenstein SR. Correlations between bacterial ecology and mobile DNA. Curr Microbiol 2011;62:198–208 [CrossRef][PubMed]
    [Google Scholar]
  8. Robinson DG, Lee MC, Marx CJ. OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences. Nucleic Acids Res 2012;40:e174 [CrossRef][PubMed]
    [Google Scholar]
  9. Fernández A, Gil E, Cartelle M, Pérez A, Beceiro A et al. Interspecies spread of CTX-M-32 extended-spectrum β-lactamase and the role of the insertion sequence IS1 in down-regulating bla CTX-M gene expression. J Antimicrob Chemother 2007;59:841–847 [CrossRef][PubMed]
    [Google Scholar]
  10. Wright MS, Mountain S, Beeri K, Adams MD. Assessment of insertion sequence mobilization as an adaptive response to oxidative stress in Acinetobacter baumannii using IS-seq. J Bacteriol 2017;199:e00833-16 [CrossRef][PubMed]
    [Google Scholar]
  11. Draper JL, Hansen LM, Bernick DL, Abedrabbo S, Underwood JG et al. Fallacy of the unique genome: sequence diversity within single Helicobacter pylori strains. MBio 2017;8:e02321-16 [CrossRef][PubMed]
    [Google Scholar]
  12. Martusewitsch E, Sensen CW, Schleper C. High spontaneous mutation rate in the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by transposable elements. J Bacteriol 2000;182:2574–2581 [CrossRef][PubMed]
    [Google Scholar]
  13. Redder P, Garrett RA. Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol 2006;188:4198–4206 [CrossRef][PubMed]
    [Google Scholar]
  14. Sapienza C, Rose MR, Doolittle WF. High-frequency genomic rearrangements involving archaebacterial repeat sequence elements. Nature 1982;299:182–185 [CrossRef][PubMed]
    [Google Scholar]
  15. Pfeifer F, Blaseio U, Ghahraman P. Dynamic plasmid populations in Halobacterium halobium. J Bacteriol 1988;170:3718–3724 [CrossRef][PubMed]
    [Google Scholar]
  16. Zerulla K, Soppa J. Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 2014;5:274 [CrossRef][PubMed]
    [Google Scholar]
  17. Jones DL, Baxter BK. DNA repair and photoprotection: mechanisms of overcoming environmental ultraviolet radiation exposure in halophilic archaea. Front Microbiol 2017;8:8 [CrossRef][PubMed]
    [Google Scholar]
  18. Lange C, Zerulla K, Breuert S, Soppa J. Gene conversion results in the equalization of genome copies in the polyploid haloarchaeon Haloferax volcanii. Mol Microbiol 2011;80:666–677 [CrossRef][PubMed]
    [Google Scholar]
  19. Dassarma S. Identification and analysis of the gas vesicle gene cluster on an unstable plasmid of Halobacterium halobium. Experientia 1993;49:482–486 [CrossRef][PubMed]
    [Google Scholar]
  20. Ng WV, Ciufo SA, Smith TM, Bumgarner RE, Baskin D et al. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?. Genome Res 1998;8:1131–1141[PubMed]
    [Google Scholar]
  21. Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P et al. Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics 2008;91:335–346 [CrossRef][PubMed]
    [Google Scholar]
  22. Grohmann D, Werner F. Recent advances in the understanding of archaeal transcription. Curr Opin Microbiol 2011;14:328–334 [CrossRef][PubMed]
    [Google Scholar]
  23. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M et al. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci USA 2000;97:12176–12181 [CrossRef][PubMed]
    [Google Scholar]
  24. Mackwan RR, Carver GT, Drake JW, Grogan DW. An unusual pattern of spontaneous mutations recovered in the halophilic archaeon Haloferax volcanii. Genetics 2007;176:697–702 [CrossRef][PubMed]
    [Google Scholar]
  25. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA et al. Copy number variation: new insights in genome diversity. Genome Res 2006;16:949–961 [CrossRef][PubMed]
    [Google Scholar]
  26. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH et al. Global variation in copy number in the human genome. Nature 2006;444:444–454 [CrossRef][PubMed]
    [Google Scholar]
  27. Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007;23:657–663 [CrossRef][PubMed]
    [Google Scholar]
  28. Dulmage KA, Todor H, Schmid AK. Growth-phase-specific modulation of cell morphology and gene expression by an archaeal histone protein. MBio 2015;6:e00649-15 [CrossRef][PubMed]
    [Google Scholar]
  29. Darnell CL, Tonner PD, Gulli JG, Schmidler SC, Schmid AK. Systematic discovery of archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis. mSystems 2017;2:e00032-17 [CrossRef][PubMed]
    [Google Scholar]
  30. Peck RF, Dassarma S, Krebs MP. Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker. Mol Microbiol 2000;35:667–676 [CrossRef][PubMed]
    [Google Scholar]
  31. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015;43:e47 [CrossRef][PubMed]
    [Google Scholar]
  32. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004;5:R80 [CrossRef][PubMed]
    [Google Scholar]
  33. Wolf YI, Makarova KS, Yutin N, Koonin EV. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct 2012;7:46 [CrossRef][PubMed]
    [Google Scholar]
  34. Darnell CL, Schmid AK. Systems biology approaches to defining transcription regulatory networks in halophilic archaea. Methods 2015;86:102–114 [CrossRef][PubMed]
    [Google Scholar]
  35. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995;57:125–133
    [Google Scholar]
  36. Sharma K, Gillum N, Boyd JL, Schmid A. The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon. BMC Genomics 2012;13:351 [CrossRef][PubMed]
    [Google Scholar]
  37. Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C et al. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res 2004;14:1025–1035 [CrossRef][PubMed]
    [Google Scholar]
  38. Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005;21:2067–2075 [CrossRef][PubMed]
    [Google Scholar]
  39. Saeed AI, Sharov V, White J, Li J, Liang W et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003;34:374–378[PubMed]
    [Google Scholar]
  40. Andrews S. 2010; FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/
  41. Krueger F. 2012; TrimGalore! A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files. www.bioinformatics.babraham.ac.uk/projects/trim_galore/
  42. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 2011;17:10 [CrossRef]
    [Google Scholar]
  43. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357–359 [CrossRef][PubMed]
    [Google Scholar]
  44. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25:2078–2079 [CrossRef][PubMed]
    [Google Scholar]
  45. Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–169 [CrossRef][PubMed]
    [Google Scholar]
  46. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 2001;25:402–408 [CrossRef]
    [Google Scholar]
  47. Schmid AK, Pan M, Sharma K, Baliga NS. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res 2011;39:2519–2533 [CrossRef][PubMed]
    [Google Scholar]
  48. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006;34:D32–D36 [CrossRef][PubMed]
    [Google Scholar]
  49. Martinez-Pastor M, Lancaster WA, Tonner PD, Adams MWW, Schmid AK. A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea. Nucleic Acids Res 2017;45:9990–10001 [CrossRef][PubMed]
    [Google Scholar]
  50. Schmid AK, Reiss DJ, Kaur A, Pan M, King N et al. The anatomy of microbial cell state transitions in response to oxygen. Genome Res 2007;17:1399–1413 [CrossRef][PubMed]
    [Google Scholar]
  51. Pfeifer F. Haloarchaea and the formation of gas vesicles. Life 2015;5:385–402 [CrossRef][PubMed]
    [Google Scholar]
  52. Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT et al. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol 2009;5:285 [CrossRef][PubMed]
    [Google Scholar]
  53. Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS. Diurnally entrained anticipatory behavior in archaea. PLoS One 2009;4:e5485 [CrossRef][PubMed]
    [Google Scholar]
  54. Pfeifer F, Blaseio U. Insertion elements and deletion formation in a halophilic archaebacterium. J Bacteriol 1989;171:5135–5140 [CrossRef][PubMed]
    [Google Scholar]
  55. Sapienza C, Doolittle WF. Unusual physical organization of the Halobacterium genome. Nature 1982;295:384–389 [CrossRef][PubMed]
    [Google Scholar]
  56. She Q, Brügger K, Chen L. Archaeal integrative genetic elements and their impact on genome evolution. Res Microbiol 2002;153:325–332 [CrossRef][PubMed]
    [Google Scholar]
  57. Hawkins M, Malla S, Blythe MJ, Nieduszynski CA, Allers T. Accelerated growth in the absence of DNA replication origins. Nature 2013;503:544–547 [CrossRef][PubMed]
    [Google Scholar]
  58. Breuert S, Allers T, Spohn G, Soppa J. Regulated polyploidy in halophilic archaea. PLoS One 2006;1:e92 [CrossRef][PubMed]
    [Google Scholar]
  59. Pfeifer F, Blaseio U. Transposition burst of the ISH27 insertion element family in Halobacterium halobium. Nucleic Acids Res 1990;18:6921–6925 [CrossRef][PubMed]
    [Google Scholar]
  60. Kottemann M, Kish A, Iloanusi C, Bjork S, Diruggiero J. Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation. Extremophiles 2005;9:219–227 [CrossRef][PubMed]
    [Google Scholar]
  61. Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ et al. An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2006;2:47 [CrossRef][PubMed]
    [Google Scholar]
  62. Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr Biol 2012;22:1444–1448 [CrossRef][PubMed]
    [Google Scholar]
  63. Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D et al. Searching for species in haloarchaea. Proc Natl Acad Sci USA 2007;104:14092–14097 [CrossRef][PubMed]
    [Google Scholar]
  64. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES et al. Integrative genomics viewer. Nat Biotechnol 2011;29:24–26 [CrossRef][PubMed]
    [Google Scholar]
  65. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013;14:178–192 [CrossRef][PubMed]
    [Google Scholar]
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