Abstract
Many bacterial pathogens secrete virulence factors, also known as effector proteins, directly into host cells. These effectors suppress pro-inflammatory host signaling while promoting bacterial infection. A particularly interesting subset of effectors post-translationally modify host proteins using novel chemistry that is not otherwise found in the mammalian proteome, which we refer to as ‘orthogonal post-translational modification’ (oPTM). In this Review, we profile oPTM chemistry for effectors that catalyze serine/threonine acetylation, phosphate β-elimination, phosphoribosyl-linked ubiquitination, glutamine deamidation, phosphocholination, cysteine methylation, arginine N-acetylglucosaminylation, and glutamine ADP-ribosylation on host proteins. AMPylation, a PTM that could be considered orthogonal until only recently, is also discussed. We further highlight known cellular targets of oPTMs and their resulting biological consequences. Developing a complete understanding of oPTMs and the host cell processes they hijack will illuminate critical steps in the infection process, which can be harnessed for a variety of therapeutic, diagnostic, and synthetic applications.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Brodsky, I. E. & Medzhitov, R. Targeting of immune signalling networks by bacterial pathogens. Nat. Cell Biol. 11, 521–526 (2009).
Baxt, L. A., Garza-Mayers, A. C. & Goldberg, M. B. Bacterial subversion of host innate immune pathways. Science 340, 697–701 (2013).
Costa, T. R. D. et al. Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat. Rev. Microbiol. 13, 343–359 (2015).
Buchrieser, C. et al. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol. Microbiol. 38, 760–771 (2000).
Hubber, A. & Roy, C. R. Modulation of host cell function by Legionella pneumophila type IV effectors. Annu. Rev. Cell Dev. Biol. 26, 261–283 (2010).
Ribet, D. & Cossart, P. Post-translational modifications in host cells during bacterial infection. FEBS Lett. 584, 2748–2758 (2010).
Collier, R. J. & Cole, H. A. Diphtheria toxin subunit active in vitro. Science 164, 1179–1181 (1969).
Mukherjee, S. et al. Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation. Science 312, 1211–1214 (2006). This article reports the discovery of Ser/Thr acetylation.
Mittal, R., Peak-Chew, S. Y. & McMahon, H. T. Acetylation of MEK2 and I kappa B kinase (IKK) activation loop residues by YopJ inhibits signaling. Proc. Natl. Acad. Sci. USA 103, 18574–18579 (2006).
Ma, K.-W. & Ma, W. YopJ family effectors promote bacterial infection through a unique acetyltransferase activity. Microbiol. Mol. Biol. Rev. 80, 1011–1027 (2016).
Jones, R. M. et al. Salmonella AvrA coordinates suppression of host immune and apoptotic defenses via JNK pathway blockade. Cell Host Microbe 3, 233–244 (2008).
Trosky, J. E. et al. VopA inhibits ATP binding by acetylating the catalytic loop of MAPK kinases. J. Biol. Chem. 282, 34299–34305 (2007).
Orth, K. et al. Disruption of signaling by Yersinia effector YopJ, a ubiquitin-like protein protease. Science 290, 1594–1597 (2000).
Orth, K. et al. Inhibition of the mitogen-activated protein kinase kinase superfamily by a Yersinia effector. Science 285, 1920–1923 (1999).
Meinzer, U. et al. Yersinia pseudotuberculosis effector YopJ subverts the Nod2/RICK/TAK1 pathway and activates caspase-1 to induce intestinal barrier dysfunction. Cell Host Microbe 11, 337–351 (2012).
Paquette, N. et al. Serine/threonine acetylation of TGFβ-activated kinase (TAK1) by Yersinia pestis YopJ inhibits innate immune signaling. Proc. Natl. Acad. Sci. USA 109, 12710–12715 (2012).
Mukherjee, S., Hao, Y. H. & Orth, K. A newly discovered post-translational modification—the acetylation of serine and threonine residues. Trends Biochem. Sci. 32, 210–216 (2007).
Zhang, Z. M. et al. Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family. Nat. Struct. Mol. Biol. 23, 847–852 (2016).
Zhang, Z. M. et al. Mechanism of host substrate acetylation by a YopJ family effector. Nat. Plants 3, 17115 (2017).
Monack, D. M., Mecsas, J., Bouley, D. & Falkow, S. Yersinia-induced apoptosis in vivo aids in the establishment of a systemic infection of mice. J. Exp. Med. 188, 2127–2137 (1998).
Du, F. & Galán, J. E. Selective inhibition of type III secretion activated signaling by the Salmonella effector AvrA. PLoS Pathog. 5, e1000595 (2009).
Li, H. et al. The phosphothreonine lyase activity of a bacterial type III effector family. Science 315, 1000–1003 (2007). This article reports the discovery of phosphothreonine lyase activity.
Arbibe, L. et al. An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses. Nat. Immunol. 8, 47–56 (2007).
Gulig, P. A. et al. Molecular analysis of spv virulence genes of the Salmonella virulence plasmids. Mol. Microbiol. 7, 825–830 (1993).
Zhu, Y. et al. Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase. Mol. Cell 28, 899–913 (2007).
Chen, L. et al. Structural basis for the catalytic mechanism of phosphothreonine lyase. Nat. Struct. Mol. Biol. 15, 101–102 (2008).
Ke, Z., Smith, G. K., Zhang, Y. & Guo, H. Molecular mechanism for eliminylation, a newly discovered post-translational modification. J. Am. Chem. Soc. 133, 11103–11105 (2011).
Chambers, K. A., Abularrage, N. S. & Scheck, R. A. Selectivity within a family of bacterial phosphothreonine lyases. Biochemistry 57, 3790–3796 (2018).
Schmutz, C. et al. Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Mol. Cell. Proteomics 12, 2952–2968 (2013).
Lippmann, J. et al. Bacterial internalization, localization, and effectors shape the epithelial immune response during Shigella flexneri Infection. Infect. Immun. 83, 3624–3637 (2015).
Chambers, K. A., Abularrage, N. S., Hill, C. J., Khan, I. H. & Scheck, R. A. A chemical probe for dehydrobutyrine. Angew. Chem. Int. Edn Engl. 59, 7350–7355 (2020).
Peeler, J. C., Schedin-Weiss, S., Soula, M., Kazmi, M. A. & Sakmar, T. P. Isopeptide and ester bond ubiquitination both regulate degradation of the human dopamine receptor 4. J. Biol. Chem. 292, 21623–21630 (2017).
Golnik, R., Lehmann, A., Kloetzel, P. M. & Ebstein, F. Major histocompatibility complex (MHC) class I processing of the NY-ESO-1 antigen is regulated by Rpn10 and Rpn13 proteins and immunoproteasomes following non-lysine ubiquitination. J. Biol. Chem. 291, 8805–8815 (2016).
Bhogaraju, S. et al. Phosphoribosylation of ubiquitin promotes serine ubiquitination and impairs conventional ubiquitination. Cell 167, 1636–1649.e13 (2016). This article, along with ref. 35, reports the discovery of phosphoribose ubiquitin transferase activity.
Kotewicz, K. M. et al. A single Legionella effector catalyzes a multistep ubiquitination pathway to rearrange tubular endoplasmic reticulum for replication. Cell Host Microbe 21, 169–181 (2017). This article, along with ref. 34, reports the discovery of phosphoribose ubiquitin transferase activity.
Qiu, J. et al. Ubiquitination independent of E1 and E2 enzymes by bacterial effectors. Nature 533, 120–124 (2016).
Dong, Y. et al. Structural basis of ubiquitin modification by the Legionella effector SdeA. Nature 557, 674–678 (2018).
Wang, Y. et al. Structural insights into non-canonical ubiquitination catalyzed by SidE. Cell 173, 1231–1243.e16 (2018).
Akturk, A. et al. Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector. Nature 557, 729–733 (2018).
Kalayil, S. et al. Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination. Nature 557, 734–738 (2018).
Qiu, J. et al. A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination. Cell Res. 27, 865–881 (2017).
Wan, M. et al. Deubiquitination of phosphoribosyl-ubiquitin conjugates by phosphodiesterase-domain-containing Legionella effectors. Proc. Natl. Acad. Sci. USA 116, 23518–23526 (2019).
Shin, D. et al. Regulation of phosphoribosyl-linked serine ubiquitination by deubiquitinases DupA and DupB. Mol. Cell 77, 164–179.e6 (2020).
Bhogaraju, S. et al. Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation. Nature 572, 382–386 (2019).
Black, M. H. et al. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Science 364, 787–792 (2019).
Robinson, N. E. & Robinson, A. B. Use of Merrifield solid phase peptide synthesis in investigations of biological deamidation of peptides and proteins. Biopolymers 90, 297–306 (2008).
Flatau, G. et al. Toxin-induced activation of the G protein p21 Rho by deamidation of glutamine. Nature 387, 729–733 (1997). This article, along with ref. 48, reports the discovery of Gln deamidase activity for CNF family effectors.
Schmidt, G. et al. Gln 63 of Rho is deamidated by Escherichia coli cytotoxic necrotizing factor-1. Nature 387, 725–729 (1997). This article, along with ref. 47, reports the discovery of Gln deamidase activity for CNF family effectors.
Cui, J. et al. Glutamine deamidation and dysfunction of ubiquitin/NEDD8 induced by a bacterial effector family. Science 329, 1215–1218 (2010). This article reports the discovery of Gln deamidase activity for Cif family effectors.
Marchès, O. et al. Enteropathogenic and enterohaemorrhagic Escherichia coli deliver a novel effector called Cif, which blocks cell cycle G2/M transition. Mol. Microbiol. 50, 1553–1567 (2003).
Taieb, F., Nougayrède, J. P., Watrin, C., Samba-Louaka, A. & Oswald, E. Escherichia coli cyclomodulin Cif induces G2 arrest of the host cell cycle without activation of the DNA-damage checkpoint-signalling pathway. Cell. Microbiol. 8, 1910–1921 (2006).
Samba-Louaka, A. et al. Bacterial cyclomodulin Cif blocks the host cell cycle by stabilizing the cyclin-dependent kinase inhibitors p21 and p27. Cell. Microbiol. 10, 2496–2508 (2008).
Yao, Q. et al. A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle. Proc. Natl. Acad. Sci. USA 106, 3716–3721 (2009).
Hsu, Y. et al. Structure of the cyclomodulin Cif from pathogenic Escherichia coli. J. Mol. Biol. 384, 465–477 (2008).
Yu, C. et al. Gln40 deamidation blocks structural reconfiguration and activation of SCF ubiquitin ligase complex by Nedd8. Nat. Commun. 6, 10053 (2015).
Sanada, T. et al. The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response. Nature 483, 623–626 (2012).
Valleau, D. et al. Discovery of ubiquitin deamidases in the pathogenic arsenal of Legionella pneumophila. Cell Rep. 23, 568–583 (2018).
Gan, N. et al. Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. EMBO J. 39, e102806 (2020).
Gan, N., Nakayasu, E. S., Hollenbeck, P. J. & Luo, Z. Q. Legionella pneumophila inhibits immune signalling via MavC-mediated transglutaminase-induced ubiquitination of UBE2N. Nat. Microbiol. 4, 134–143 (2019).
Cruz-Migoni, A. et al. A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A. Science 334, 821–824 (2011).
Hoffmann, C. et al. The Yersinia pseudotuberculosis cytotoxic necrotizing factor (CNFY) selectively activates RhoA. J. Biol. Chem. 279, 16026–16032 (2004).
Zhang, L. et al. Type III effector VopC mediates invasion for Vibrio species. Cell Rep. 1, 453–460 (2012).
Mukherjee, S. et al. Modulation of Rab GTPase function by a protein phosphocholine transferase. Nature 477, 103–106 (2011). This article reports the discovery of phosphocholine transferase activity.
Yarbrough, M. L. et al. AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science 323, 269–272 (2009).
Worby, C. A. et al. The fic domain: regulation of cell signaling by adenylylation. Mol. Cell 34, 93–103 (2009).
Campanacci, V., Mukherjee, S., Roy, C. R. & Cherfils, J. Structure of the Legionella effector AnkX reveals the mechanism of phosphocholine transfer by the FIC domain. EMBO J. 32, 1469–1477 (2013).
Engel, P. et al. Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Nature 482, 107–110 (2012).
Sreelatha, A. et al. Protein AMPylation by an evolutionarily conserved pseudokinase. Cell 175, 809–821.e819 (2018).
Gavriljuk, K. et al. Unraveling the phosphocholination mechanism of the Legionella pneumophila enzyme AnkX. Biochemistry 55, 4375–4385 (2016).
Goody, P. R. et al. Reversible phosphocholination of Rab proteins by Legionella pneumophila effector proteins. EMBO J. 31, 1774–1784 (2012).
Yao, Q. et al. Structure and specificity of the bacterial cysteine methyltransferase effector NleE suggests a novel substrate in human DNA repair pathway. PLoS Pathog. 10, e1004522 (2014).
Zhang, L. et al. Cysteine methylation disrupts ubiquitin-chain sensing in NF-κB activation. Nature 481, 204–208 (2011). This article reports the discovery of cysteine methylation.
Zhang, Y., Mühlen, S., Oates, C. V., Pearson, J. S. & Hartland, E. L. Identification of a distinct substrate-binding domain in the bacterial cysteine methyltransferase effectors NleE and OspZ. J. Biol. Chem. 291, 20149–20162 (2016).
Ding, J. et al. Structural and functional insights into host death domains inactivation by the bacterial arginine GlcNAcyltransferase effector. Mol Cell 74, 922–935.e926 (2019).
Li, S. et al. Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains. Nature 501, 242–246 (2013). This article, along with ref. 76, reports the discovery of arginine GlcNAcylation.
Pearson, J. S. et al. A type III effector antagonizes death receptor signalling during bacterial gut infection. Nature 501, 247–251 (2013). This article, along with ref. 75, reports the discovery of arginine GlcNAcylation.
Newson, J. P. M. et al. Salmonella effectors SseK1 and SseK3 target death domain proteins in the TNF and TRAIL signaling pathways. Mol. Cell. Proteomics 18, 1138–1156 (2019).
Xu, Y. et al. A bacterial effector reveals the V-ATPase-ATG16L1 axis that initiates xenophagy. Cell 178, 552–566.e520 (2019). This article reports the discovery of glutamine ADP-ribosylation.
Lim, D. V., Simpson, J. M., Kearns, E. A. & Kramer, M. F. Current and developing technologies for monitoring agents of bioterrorism and biowarfare. Clin. Microbiol. Rev. 18, 583–607 (2005).
Enninga, J., Mounier, J., Sansonetti, P. & Tran Van Nhieu, G. Secretion of type III effectors into host cells in real time. Nat. Methods 2, 959–965 (2005).
Isberg, R. R., O’Connor, T. J. & Heidtman, M. The Legionella pneumophila replication vacuole: making a cosy niche inside host cells. Nat. Rev. Microbiol. 7, 13–24 (2009).
Mitchell, A., Wei, P. & Lim, W. A. Oscillatory stress stimulation uncovers an Achilles’ heel of the yeast MAPK signaling network. Science 350, 1379–1383 (2015).
Zhao, J. et al. Bioorthogonal engineering of bacterial effectors for spatial-temporal modulation of cell signaling. ACS Cent. Sci. 5, 145–152 (2019).
Wei, P. et al. Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells. Nature 488, 384–388 (2012).
Ochtrop, P., Ernst, S., Itzen, A. & Hedberg, C. Exploring the substrate scope of the bacterial phosphocholine transferase AnkX for versatile protein functionalization. ChemBioChem 20, 2336–2340 (2019).
Heller, K. et al. Covalent protein labeling by enzymatic phosphocholination. Angew. Chem. Int. Edn Engl. 54, 10327–10330 (2015).
Baker, S. J., Payne, D. J., Rappuoli, R. & De Gregorio, E. Technologies to address antimicrobial resistance. Proc. Natl. Acad. Sci. USA 115, 12887–12895 (2018).
Allen, R. C., Popat, R., Diggle, S. P. & Brown, S. P. Targeting virulence: can we make evolution-proof drugs? Nat. Rev. Microbiol. 12, 300–308 (2014).
Dickey, S. W., Cheung, G. Y. C. & Otto, M. Different drugs for bad bugs: antivirulence strategies in the age of antibiotic resistance. Nat. Rev. Drug Discov. 16, 457–471 (2017).
Lakemeyer, M., Zhao, W., Mandl, F. A., Hammann, P. & Sieber, S. A. Thinking outside the box-novel antibacterials to tackle the resistance crisis. Angew. Chem. Int. Edn Engl. 57, 14440–14475 (2018).
McShan, A. C. & De Guzman, R. N. The bacterial type III secretion system as a target for developing new antibiotics. Chem. Biol. Drug Des. 85, 30–42 (2015).
Kauppi, A. M., Nordfelth, R., Uvell, H., Wolf-Watz, H. & Elofsson, M. Targeting bacterial virulence: inhibitors of type III secretion in Yersinia. Chem. Biol. 10, 241–249 (2003).
Slepenkin, A., Chu, H., Elofsson, M., Keyser, P. & Peterson, E. M. Protection of mice from a Chlamydia trachomatis vaginal infection using a Salicylidene acylhydrazide, a potential microbicide. J. Infect. Dis. 204, 1313–1320 (2011).
Lewallen, D. M. et al. Inhibiting AMPylation: a novel screen to identify the first small molecule inhibitors of protein AMPylation. ACS Chem. Biol. 9, 433–442 (2014).
Salomon, D. & Orth, K. What pathogens have taught us about posttranslational modifications. Cell Host Microbe 14, 269–279 (2013).
Kingdon, H. S., Shapiro, B. M. & Stadtman, E. R. Regulation of glutamine synthetase. 8. ATP: glutamine synthetase adenylyltransferase, an enzyme that catalyzes alterations in the regulatory properties of glutamine synthetase. Proc. Natl. Acad. Sci. USA 58, 1703–1710 (1967).
Müller, M. P. et al. The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b. Science 329, 946–949 (2010).
Ham, H. et al. Unfolded protein response-regulated Drosophila Fic (dFic) protein reversibly AMPylates BiP chaperone during endoplasmic reticulum homeostasis. J. Biol. Chem. 289, 36059–36069 (2014).
Sanyal, A. et al. A novel link between Fic (filamentation induced by cAMP)-mediated adenylylation/AMPylation and the unfolded protein response. J. Biol. Chem. 290, 8482–8499 (2015).
Broncel, M., Serwa, R. A., Bunney, T. D., Katan, M. & Tate, E. W. Global profiling of Huntingtin-associated protein E (HYPE)-mediated AMPylation through a chemical proteomic approach. Mol. Cell. Proteomics 15, 715–725 (2016).
Grammel, M., Luong, P., Orth, K. & Hang, H. C. A chemical reporter for protein AMPylation. J. Am. Chem. Soc. 133, 17103–17105 (2011).
Kielkowski, P. et al. FICD activity and AMPylation remodelling modulate human neurogenesis. Nat. Commun. 11, 517 (2020).
Acknowledgements
This work was supported in part by a Tufts Collaborates Award to R.A.S. The authors gratefully acknowledge K. Allen, D. Walt, and J. Kritzer for helpful feedback regarding the preparation of this manuscript.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Chambers, K.A., Scheck, R.A. Bacterial virulence mediated by orthogonal post-translational modification. Nat Chem Biol 16, 1043–1051 (2020). https://doi.org/10.1038/s41589-020-0638-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41589-020-0638-2
This article is cited by
-
TmcA functions as a lysine 2-hydroxyisobutyryltransferase to regulate transcription
Nature Chemical Biology (2022)