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Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria

Abstract

While horizontal gene transfer is prevalent across the biosphere, the regulatory features that enable expression and functionalization of foreign DNA remain poorly understood. Here, we combine high-throughput promoter activity measurements and large-scale genomic analysis of regulatory regions to investigate the cross-compatibility of regulatory elements (REs) in bacteria. Functional characterization of thousands of natural REs in three distinct bacterial species revealed distinct expression patterns according to RE and recipient phylogeny. Host capacity to activate foreign promoters was proportional to their genomic GC content, while many low GC regulatory elements were both broadly active and had more transcription start sites across hosts. The difference in expression capabilities could be explained by the influence of the host GC content on the stringency of the AT-rich canonical σ70 motif necessary for transcription initiation. We further confirm the generalizability of this model and find widespread GC content adaptation of the σ70 motif in a set of 1,545 genomes from all major bacterial phyla. Our analysis identifies a key mechanism by which the strength of the AT-rich σ70 motif relative to a host’s genomic GC content governs the capacity for expression of acquired DNA. These findings shed light on regulatory adaptation in the context of evolving genomic composition.

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Fig. 1: Phylogenetic trends in RE library expression.
Fig. 2: Transcription start site utilization in RE library across hosts.
Fig. 3: Recipient and donor RE GC content govern σ70 motif encoding within regulatory sequences.
Fig. 4: Promiscuity and stringency in transcriptional activation depends on recipient and RE GC compositions.
Fig. 5: The signal for σ70 motif is nearly uniform among 1,545 representative genomes after background GC content correction.

References

  1. 1.

    Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013;29:170–5. https://doi.org/10.1016/j.tig.2012.12.006.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Park C, Zhang J. High expression hampers horizontal gene transfer. Genome Biol Evolut. 2012;4:523–32. https://doi.org/10.1093/gbe/evs030.

    CAS  Article  Google Scholar 

  3. 3.

    Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 2005;3:679–87. https://doi.org/10.1038/nrmicro1204.

    CAS  Article  PubMed  Google Scholar 

  4. 4.

    Rosen, M. J., Davison, M., Bhaya, D. & Fisher, D. S. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science (New York, N.Y.) 2015;348:1019–23. https://doi.org/10.1126/science.aaa4456.

    CAS  Article  Google Scholar 

  5. 5.

    McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH, et al. High frequency of horizontal gene transfer in the oceans. Science. 2010;330:50 https://doi.org/10.1126/science.1192243.

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Doolittle WF. Phylogenetic classification and the universal tree. Science. 1999;284:2124–8. https://doi.org/10.1126/science.284.5423.2124.

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Hehemann J-H, Kelly AG, Pudlo NA, Martens EC, Boraston AB, Davies G. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci USA. 2012;109:19786–91. https://doi.org/10.1073/pnas.1211002109.

    Article  PubMed  Google Scholar 

  8. 8.

    Gomes ALC, Galagan JE, Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. PLoS ONE. 2013;8:e80775 https://doi.org/10.1371/journal.pone.0080775.

    Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Mazel D. Integrons: agents of bacterial evolution. Nat Rev Microbiol. 2006;4:608–20. https://doi.org/10.1038/nrmicro1462.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Heuer H, Schmitt H, Smalla K. Antibiotic resistance gene spread due to manure application on agricultural fields. Curr Opin Microbiol. 2011;14:236–43. https://doi.org/10.1016/j.mib.2011.04.009.

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MOA, Dantas G, et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science. 2012;337:1107–11. https://doi.org/10.1126/science.1220761.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, et al. Population genomics of early events in the ecological differentiation of bacteria. Science. 2012;336:48–51. https://doi.org/10.1126/science.1218198.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Baltrus DA. Exploring the costs of horizontal gene transfer. Trends Ecol Evolut. 2013;28:489–95.

    Article  Google Scholar 

  14. 14.

    San Millan A, Toll-Riera M, Qi Q, MacLean RC. Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa. Nat Commun. 2015;6:6845. https://doi.org/10.1038/ncomms7845.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299–304. https://doi.org/10.1038/35012500.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM. Genome-wide experimental determination of barriers to horizontal gene transfer. Science. 2007;318:1449–52. https://doi.org/10.1126/science.1147112.

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Madan Babu M, Teichmann SA, Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol. 2006;358:614–33. https://doi.org/10.1016/j.jmb.2006.02.019.

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol. 2004;14:283–91. https://doi.org/10.1016/j.sbi.2004.05.004.

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Artsimovitch I, Svetlov V, Anthony L, Burgess RR, Landick R. RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro. J Bacteriol. 2000;182:6027–35. https://doi.org/10.1128/JB.182.21.6027-6035.2000.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Yus E, Yang J-S, Sogues A, Serrano L. A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants. Nat Commun. 2017;8:368 https://doi.org/10.1038/s41467-017-00239-7.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Vingadassalom D, Kolb A, Mayer C, Rybkine T, Collatz E, Podglajen I. An unusual primary sigma factor in the Bacteroidetes phylum. Mol Microbiol. 2005;56:888–902. https://doi.org/10.1111/j.1365-2958.2005.04590.x.

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, et al. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nat Methods. 2018;15:323–9. https://doi.org/10.1038/nmeth.4633.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Mordaka PM, Heap JT. Stringency of synthetic promoter sequences in clostridium revealed and circumvented by tuning promoter library mutation rates. ACS Synth Biol. 2018;7:672–81. https://doi.org/10.1021/acssynbio.7b00398.

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Jensen PR, Hammer K. The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol. 1998;64:82–7.

    CAS  Article  Google Scholar 

  25. 25.

    Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011;480:241–4. https://doi.org/10.1038/nature10571.

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Liu B, Pop M. ARDB-antibiotic resistance genes database. Nucleic Acids Res. 2009;37:D443–7. https://doi.org/10.1093/nar/gkn656.

    CAS  Article  Google Scholar 

  27. 27.

    Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 2012;40:D641–5. https://doi.org/10.1093/nar/gkr989.

    CAS  Article  PubMed  Google Scholar 

  28. 28.

    Hook-Barnard IG, Hinton DM. Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters. Gene Regul Syst Biol. 2007;1:275–93.

    Google Scholar 

  29. 29.

    Navarre WW, Mcclelland M, Libby SJ, Fang FC. Silencing of xenogeneic DNA by H-NS—facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA; 2007. 1456–71. https://doi.org/10.1101/gad.1543107.evolution.

  30. 30.

    Koo B-M, Rhodius VA, Nonaka G, deHaseth PL, Gross CA. Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes Dev. 2009;23:2426–36. https://doi.org/10.1101/gad.1843709.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Ramirez-Romero MA. The Rhizobium etli sigma70 (SigA) factor recognizes a lax consensus promoter. Nucleic Acids Res. 2006;34:1470–80. https://doi.org/10.1093/nar/gkl023.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Jeong Y, Kim J-N, Kim MW, Bucca G, Cho S, Yoon YJ, et al. The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2). Nat Commun. 2016;7:11605 https://doi.org/10.1038/ncomms11605.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, et al. Global repositioning of transcription start sites in a plant-fermenting bacterium. Nat Commun. 2016;7:13783. https://doi.org/10.1038/ncomms13783.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Urtecho G, Tripp AD, Insigne KD, Kim H, Kosuri S. Systematic dissection of sequence elements controlling σ70 promoters using a genomically encoded multiplexed reporter assay in Escherichia coli. Biochemistry. 2019;58:1539–51. https://doi.org/10.1021/acs.biochem.7b01069.

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Einav T, Phillips R. How the avidity of polymerase binding to the −35/−10 promoter sites affects gene expression. Proc Natl Acad Sci USA. 2019;116:13340–5. https://doi.org/10.1073/pnas.1905615116.

    CAS  Article  PubMed  Google Scholar 

  36. 36.

    Daubin V, Lerat E, Perrière G. The source of laterally transferred genes in bacterial genomes. Genome Biol. 2003;4:R57. https://doi.org/10.1186/gb-2003-4-9-r57.

    Article  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Rocha EPC, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet. 2002;18:291–4. https://doi.org/10.1016/S0168-9525(02)02690-2.

    CAS  Article  PubMed  Google Scholar 

  38. 38.

    Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, et al. Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol. 2017;2:16249 https://doi.org/10.1038/nmicrobiol.2016.249.

    CAS  Article  PubMed  Google Scholar 

  39. 39.

    Perez-Rueda E, Ibarra JA. Distribution of putative xenogeneic silencers in prokaryote genomes. Comput Biol Chem. 2015;58:167–72. https://doi.org/10.1016/J.COMPBIOLCHEM.2015.06.007.

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Flores-Ríos R, Quatrini R, Loyola A. Endogenous and foreign nucleoid-associated proteins of bacteria: occurrence, interactions and effects on mobile genetic elements and Host’s biology. Comput Struct Biotechnol J. 2019;17:746–56. https://doi.org/10.1016/J.CSBJ.2019.06.010.

    Article  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Pfeifer E, Hünnefeld M, Popa O, Frunzke J. Impact of xenogeneic silencing on phage–host interactions. J Mol Biol. 2019. https://doi.org/10.1016/J.JMB.2019.02.011.

  42. 42.

    Doyle M, Fookes M, Ivens A, Mangan MW, Wain J, Dorman CJ. An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. 2007:315:251–2. https://doi.org/10.1126/science.1137550.

  43. 43.

    Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JCD. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog. 2006;2:e81 https://doi.org/10.1371/journal.ppat.0020081.

    Article  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, Daubin V. GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PLoS Genet. 2015;11:1–20. https://doi.org/10.1371/journal.pgen.1004941.

    CAS  Article  Google Scholar 

  45. 45.

    Hildebrand F, Meyer A, Eyre-walker A. Evidence of selection upon genomic GC-content in bacteria. PLoS Genet. 2010;6 https://doi.org/10.1371/journal.pgen.1001107.

  46. 46.

    Gophna U. The unbearable ease of expression—how avoidance of spurious transcription can shape G+C content in bacterial genomes. FEMS Microbiol Lett. 2018;365. https://doi.org/10.1093/femsle/fny267.

  47. 47.

    Raghavan R, Kelkar YD, Ochman H. A selective force favoring increased G+C content in bacterial genes. Proc Natl Acad Sci USA. 2012;109:14504–7. https://doi.org/10.1073/pnas.1205683109.

    Article  PubMed  Google Scholar 

  48. 48.

    Long H, Sung W, Kucukyildirim S, Williams E, Miller SF, Guo W, et al. Evolutionary determinants of genome-wide nucleotide composition. Nat Ecol Evolut. 2018;2:237–40. https://doi.org/10.1038/s41559-017-0425-y.

    Article  Google Scholar 

  49. 49.

    Yona AH, Alm EJ, Gore J. Random sequences rapidly evolve into de novo promoters. Nat Commun. 2018;9:1530. https://doi.org/10.1038/s41467-018-04026-w.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Cordero OX, Hogeweg P. The consequences of base pair composition biases for regulatory network organization in prokaryotes. Mol Biol Evolut. 2009;26:2171–3. https://doi.org/10.1093/molbev/msp132.

    CAS  Article  Google Scholar 

  51. 51.

    Popa O, Hazkani-covo E, Landan G, Martin W, Dagan T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 2011;21:599–609. https://doi.org/10.1101/gr.115592.110.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Munck C, Sheth RU, Freedberg DE, Wang HH. Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform. Nat Commun. 2020;11:95. https://doi.org/10.1038/s41467-019-14012-5.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–22. https://doi.org/10.1093/nar/gkr1044.

    CAS  Article  PubMed  Google Scholar 

  54. 54.

    Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci USA. 2013;110:14024–9. https://doi.org/10.1073/pnas.1301301110.

    Article  PubMed  Google Scholar 

  55. 55.

    Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8. https://doi.org/10.1093/nar/gkp335.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Mathews DH. RNA secondary structure analysis using RNA structure. Curr Protoc Bioinforma. 2014;46:12.16.11–12.16.25. https://doi.org/10.1002/0471250953.bi1206s46.

    Article  Google Scholar 

  57. 57.

    Gomes AL, Abeel T, Peterson M, Azizi E, Lyubetskaya A, Carvalho L, et al. Decoding ChIP-Seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction. Genome Res. 2014:1686–97. https://doi.org/10.1101/gr.161711.113.

  58. 58.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. https://doi.org/10.1093/bioinformatics/btu153.

    CAS  Article  Google Scholar 

  59. 59.

    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60. https://doi.org/10.1038/nmeth.3176.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43:D261–9. https://doi.org/10.1093/nar/gku1223.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank members of the Wang lab for helpful scientific discussions and feedback. HHW acknowledges funding support from the NIH (1DP5OD009172-02, 1U01GM110714-01A1, 1R01AI132403-01), NSF (MCB‐1453219), Sloan Foundation (FR-2015-65795), DARPA (W911NF-15-2-0065), and ONR (N00014-15-1-2704). NIJ was supported by a NSF Graduate Research Fellowship (DGE-16-44869).

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ALCG, NIJ, and HHW designed the study with help from CSS, MBS, and EJA; ALCG, NIJ, and AY performed the experiments and analyzed the data. AG, NIJ, and HHW wrote the paper with input from all authors.

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Correspondence to Harris H. Wang.

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HHW is a member of the Scientific Advisory Board of SNIPR Biome. The authors declare no other competing financial interests.

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Gomes, A.L.C., Johns, N.I., Yang, A. et al. Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. ISME J 14, 2347–2357 (2020). https://doi.org/10.1038/s41396-020-0696-1

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