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A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function

Nature Ecology & Evolution volume 2, pages 1321–1330 (2018)Cite this article

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Abstract

One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing expression of a promiscuous bacterial enzyme. By screening for bacteriophage DNA that rescued an auxotrophic Escherichia coli mutant carrying a deletion of the ilvA gene, we show that bacteriophage-encoded S-adenosylmethionine (SAM) hydrolases reduce SAM levels. Through this perturbation of bacterial metabolism, expression of the promiscuous bacterial enzyme MetB is increased, which in turn complements the absence of IlvA. These results demonstrate how foreign DNA can increase the metabolic capacity of bacteria, not only by transfer of bona fide new genes, but also by bringing cryptic bacterial functions to light via perturbations of cellular physiology.

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Fig. 1: Screening approach and expression profiling.
Fig. 2: SAM hydrolase activity assays.
Fig. 3: Protein and RNA expression of selected metabolic pathways in response to induction of inserts directing ΔilvA prototrophy.
Fig. 4: Mechanism of rescue.
Fig. 5: The proposed rescue mechanism the of ilvA auxotrophic mutant.

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References

  1. Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).

    Article  CAS  Google Scholar 

  2. Leonard, G. & Richards, T. A. Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life. Proc. Natl Acad. Sci. USA 109, 21402–21407 (2012).

    Article  CAS  Google Scholar 

  3. Näsvall, J., Sun, L., Roth, J. R. & Andersson, D. I. Real-time evolution of new genes by innovation, amplification, and divergence. Science 338, 384–387 (2012).

    Article  Google Scholar 

  4. Knowles, D. G. & Aoife, M. Recent de novo origin of human protein-coding genes. Genome Res. 19, 1752–1759 (2009).

    Article  CAS  Google Scholar 

  5. Cai, J., Zhao, R., Jiang, H., & Wang, W. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179, 487–496 (2008).

    Article  CAS  Google Scholar 

  6. Carvunis, A.-R. R. et al. Proto-genes and de novo gene birth. Nature 487, 370–374 (2012).

    Article  CAS  Google Scholar 

  7. Copley, S. D. An evolutionary biochemist’s perspective on promiscuity. Trends Biochem. Sci. 40, 72–78 (2015).

    Article  CAS  Google Scholar 

  8. Patrick, W. M., Quandt, E. M., Swartzlander, D. B. & Matsumura, I. Multicopy suppression underpins metabolic evolvability. Mol. Biol. Evol. 24, 2716–2722 (2007).

    Article  CAS  Google Scholar 

  9. Bergmiller, T., Ackermann, M. & Silander, O. K. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genet. 8, e1002803 (2012).

    Article  CAS  Google Scholar 

  10. D’Ari, R. & Casadesús, J. Underground metabolism. Bioessays 20, 181–186 (1998).

    Article  Google Scholar 

  11. Krahn, T. et al. Intraspecies transfer of the chromosomal Acinetobacter baumannii blaNDM-1 carbapenemase gene. Antimicrob. Agents Chemother. 60, 3032–3040 (2016).

    Article  CAS  Google Scholar 

  12. Penadés, J. R. R., Chen, J., Nuria, Q.-P., Carpena, N. & Novick, R. P. Bacteriophage-mediated spread of bacterial virulence genes. Curr. Opin. Microbiol. 23, 171–178 (2015).

    Article  Google Scholar 

  13. Kitagawa, M. et al. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12, 291–299 (2005).

    Article  CAS  Google Scholar 

  14. Letunic, I., Doerks, T. & Bork, P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 43, D257–D260 (2015).

    Article  CAS  Google Scholar 

  15. Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).

    Article  Google Scholar 

  16. Notredame, C., Higgins, D. & Heringa, J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000).

    Article  CAS  Google Scholar 

  17. LaMonte, B. L. & Hughes, J. A. In vivo hydrolysis of S-adenosylmethionine induces the met regulon of Escherichia coli. Microbiol. Read. Engl. 152, 1451–1459 (2006).

  18. van der Ploeg, J., Eichhorn, E. & Leisinger, T. Sulfonate-sulfur metabolism and its regulation in Escherichia coli. Arch. Microbiol. 176, 1–8 (2001).

    Article  Google Scholar 

  19. Weissbach, H., & Brot, N. Regulation of methionine synthesis in Escherichia coli. Mol. Microbiol. 5, 1593–1597 (1991).

  20. Spoerel, N. & Herrlich, P. Colivirus-T3-coded S-adenosylmethionine hydrolase. Eur. J. Biochem. 95, 227–233 (1979).

    Article  CAS  Google Scholar 

  21. Hughes, J., Brown, L. & Ferro, A. Expression of the cloned coliphage T3 S-adenosylmethionine hydrolase gene inhibits DNA methylation and polyamine biosynthesis in Escherichia coli. J. Bacteriol. 169, 3625–3632 (1987).

    Article  CAS  Google Scholar 

  22. Holbrook, E., Greene, R. & Krueger, J. Purification and properties of cystathionine gamma-synthase from overproducing strains of Escherichia coli. Biochem. 29, 435–442 (1990).

    Article  CAS  Google Scholar 

  23. Mehta, P. K. & Christen, P. in Advances in Enzymology and Related Areas of Molecular Biology 74 (ed. Purich, D. L.) 129–184 (Wiley, New York, 2006).

  24. Eliot, A. C. & Kirsch, J. F. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73, 383–415 (2004).

  25. Born, T. & Blanchard, J. Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Escherichia coli metA-encoded homoserine transsuccinylase. Biochemistry 38, 14416–14423 (1999).

  26. Usuda, Y. & Kurahashi, O. Effects of deregulation of methionine biosynthesis on methionine excretion in Escherichia coli. Appl. Env. Microbiol. 71, 3228–3234 (2005).

  27. Mordukhova, E. A., Lee, H.-S. S. & Pan, J.-G. G. Improved thermostability and acetic acid tolerance of Escherichia coli via directed evolution of homoserine o-succinyltransferase. Appl. Env. Microbiol. 74, 7660–7668 (2008).

    Article  CAS  Google Scholar 

  28. Laber, B. et al. Mechanisms of interaction of Escherichia coli threonine synthase with substrates and inhibitors. Biochemistry 33, 3413–3423 (1994).

    Article  CAS  Google Scholar 

  29. Soo, V. W., Paulina, H.-M. & Patrick, W. M. Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc. Natl Acad. Sci. USA 108, 1484–1489 (2011).

    Article  CAS  Google Scholar 

  30. Kim, J., Kershner, J. P., Novikov, Y., Shoemaker, R. K. & Copley, S. D. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5’-phosphate synthesis. Mol. Syst. Biol. 6, 436 (2010).

    Article  CAS  Google Scholar 

  31. Downs, D. M. Understanding microbial metabolism. Annu Rev. Microbiol. 60, 533–559 (2006).

    Article  CAS  Google Scholar 

  32. Palmer, L. D., Paxhia, M. D. & Downs, D. M. Induction of the sugar-phosphate stress response allows Saccharomyces cerevisiae 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate synthase to function in Salmonella enterica. J. Bacteriol. 197, 3554–3562 (2015).

    Article  CAS  Google Scholar 

  33. Notebaart, R. A. et al. Network-level architecture and the evolutionary potential of underground metabolism. Proc. Natl Acad. Sci. USA 111, 11762–11767 (2014).

    Article  CAS  Google Scholar 

  34. Sévin, D. C., Fuhrer, T., Zamboni, N. & Sauer, U. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat. Methods 14, 187–194 (2017).

  35. Canchaya, C., Fournous, G. & Brüssow, H. The impact of prophages on bacterial chromosomes. Mol. Microbiol. 53, 9–18 (2004).

    Article  CAS  Google Scholar 

  36. Youle, M., Haynes, M. & Rohwer, F. in Viruses: Essential Agents of Life (ed. Witzany, G.) 61–81 (Springer, Dordrecht, 2012).

  37. Studier, F. & Movva, N. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J. Virol. 19, 136–145 (1976).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Bazurto, J. V., Farley, K. R. & Downs, D. M. An unexpected route to an essential cofactor: Escherichia coli relies on threonine for thiamine biosynthesis. mBio 7, e01840-15 (2016).

  39. John, S. G. et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Env. Microbiol. Rep. 3, 195–202 (2011).

    Article  Google Scholar 

  40. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).

    Article  Google Scholar 

  41. Cherepanov, P. & Wackernagel, W. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 158, 9–14 (1995).

    Article  CAS  Google Scholar 

  42. Zheng, L., Baumann, U. & Reymond, J.-L. L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32, e115 (2004).

    Article  Google Scholar 

  43. Datsenko, K. & Wanner, B. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).

    Article  CAS  Google Scholar 

  44. Knopp, M. & Andersson, D. I. Amelioration of the fitness costs of antibiotic resistance due to reduced outer membrane permeability by upregulation of alternative porins. Mol. Biol. Evol. 32, 3252–3263 (2015).

    CAS  PubMed  Google Scholar 

  45. Wiśniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359–362 (2009).

    Article  Google Scholar 

  46. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).

    Article  CAS  Google Scholar 

  47. Vizcaíno, J. A. et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44, D447–D456 (2016).

    Article  Google Scholar 

  48. Szklarczyk, D. et al. STRINGv10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447–D452 (2015).

    Article  CAS  Google Scholar 

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Acknowledgements

Enriched viral DNA from the CF6C, CF7LLP and Por1LT samples were graciously provided by F. L. Rohwer and S. D. Quistad. We acknowledge the assistance of S. Bertilsson in phage purification. The Proteomics Core Facility at the University of Gothenburg is grateful to IngaBritt och Arne Lundbergs Forskningsstiftelse for donating the Orbitrap Fusion Tribrid MS instrument. This work was supported by grants from the Swedish Research Council and the Knut and Alice Wallenberg foundation (to M.S. and D.I.A.).

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Author notes

  1. Jon Jerlström Hultqvist

    Present address: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

Authors and Affiliations

  1. Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

    Jon Jerlström Hultqvist, Omar Warsi, Michael Knopp & Dan I. Andersson

  2. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Annika Söderholm, Ulrich Eckhard & Maria Selmer

  3. Proteomics Core Facility at Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden

    Egor Vorontsov

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Contributions

J.J.H, O.W., A.S., M.S. and D.I.A. designed the experiments. J.J.H., O.W., M.K., A.S. and M.S. carried out the experiments. U.E. analysed activity data. J.J.H, O.W., M.S. and D.I.A. wrote the manuscript with input from all authors. E.V. carried out the proteomic analysis.

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Correspondence to Jon Jerlström Hultqvist, Maria Selmer or Dan I. Andersson.

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Supplementary information

Supplementary Information

Supplementary Figures 1–8; Legends for Supplementary Tables 1–4; Supplementary References

Reporting Summary

Dataset 1

Supplementary Table 1: Data and lists of hits in screen

Dataset 2

Supplementary Table 2: HHpred searches with inserts sequences directing ΔilvA prototrophy

Dataset 3

Supplementary Table 3: Hierarchical clustering of TMT and RNA-seq data

Dataset 4

Supplementary Table 4: Strains and primers list

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Jerlström Hultqvist, J., Warsi, O., Söderholm, A. et al. A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function. Nat Ecol Evol 2, 1321–1330 (2018). https://doi.org/10.1038/s41559-018-0568-5

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