Type VII secretion systems (T7SSs) have a key role in the secretion of effector proteins in non-pathogenic mycobacteria and pathogenic mycobacteria such as Mycobacterium tuberculosis, the main causative agent of tuberculosis. Tuberculosis-causing mycobacteria, still accounting for 1.4 million deaths annually, rely on paralogous T7SSs to survive in the host and efficiently evade its immune response. Although it is still unknown how effector proteins of T7SSs cross the outer membrane of the diderm mycobacterial cell envelope, recent advances in the structural characterization of these secretion systems have revealed the intricate network of interactions of conserved components in the plasma membrane. This structural information, added to recent advances in the molecular biology and regulation of mycobacterial T7SSs as well as progress in our understanding of their secreted effector proteins, is shedding light on the inner working of the T7SS machinery. In this Review, we highlight the implications of these studies and the derived transport models, which provide new scenarios for targeting the deathly human pathogen M. tuberculosis.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
A microfluidic-based analysis of 3D macrophage migration after stimulation by Mycobacterium, Salmonella and Escherichia
BMC Microbiology Open Access 31 August 2022
BIOspektrum Open Access 28 March 2022
Subscribe to Nature+
Get immediate online access to the entire Nature family of 50+ journals
Subscribe to Journal
Get full journal access for 1 year
only $8.25 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Green, E. R. & Mecsas, J. Bacterial secretion systems: an overview. Microbiol. Spectr. 4, VMBF-0012–VMBF-2015 (2016).
Andersen, P., Andersen, A. B., Sorensen, A. L. & Nagai, S. Recall of long-lived immunity to Mycobacterium tuberculosis infection in mice. J. Immunol. 154, 3359–3372 (1995).
Gerlach, R. G. & Hensel, M. Protein secretion systems and adhesins: the molecular armory of Gram-negative pathogens. Int. J. Med. Microbiol. 297, 401–415 (2007).
Winstanley, C. & Hart, C. A. Type III secretion systems and pathogenicity islands. J. Med. Microbiol. 50, 116–126 (2001).
Costa, T. R. et al. Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat. Rev. Microbiol. 13, 343–359 (2015).
Rapisarda, C., Tassinari, M., Gubellini, F. & Fronzes, R. Using cryo-EM to investigate bacterial secretion systems. Annu. Rev. Microbiol. 72, 231–254 (2018).
Palmer, T., Finney, A. J., Saha, C. K., Atkinson, G. C. & Sargent, F. A holin/peptidoglycan hydrolase-dependent protein secretion system. Mol. Microbiol. 115, 345–355 (2021).
Abby, S. S. et al. Identification of protein secretion systems in bacterial genomes. Sci. Rep. 6, 23080 (2016).
Erhardt, M., Namba, K. & Hughes, K. T. Bacterial nanomachines: the flagellum and type III injectisome. Cold Spring Harb. Perspect. Biol. 2, a000299 (2010).
Ho, B. T., Dong, T. G. & Mekalanos, J. J. A view to a kill: the bacterial type VI secretion system. Cell Host Microbe 15, 9–21 (2014).
Kühlbrandt, W. The resolution revolution. Science 343, 1443–1444 (2014).
Paulson, T. Epidemiology: a mortal foe. Nature 502, S2–S3 (2013).
Berthet, F. X., Rasmussen, P. B., Rosenkrands, I., Andersen, P. & Gicquel, B. A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10). Microbiology 144, 3195–3203 (1998).
Cole, S. T. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544 (1998).
Gey Van Pittius, N. C. et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2, RESEARCH0044 (2001).
Tekaia, F. et al. Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber. Lung Dis. 79, 329–342 (1999).
Bitter, W. et al. Systematic genetic nomenclature for type VII secretion systems. PLoS Pathog. 5, e1000507 (2009).
Harboe, M., Oettinger, T., Wiker, H. G., Rosenkrands, I. & Andersen, P. Evidence for occurrence of the ESAT-6 protein in Mycobacterium tuberculosis and virulent Mycobacterium bovis and for its absence in Mycobacterium bovis BCG. Infect. Immun. 64, 16–22 (1996).
Mahairas, G. G., Sabo, P. J., Hickey, M. J., Singh, D. C. & Stover, C. K. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent. M. bovis. J. Bacteriol. 178, 1274–1282 (1996).
Lewis, K. N. et al. Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette–Guerin attenuation. J. Infect. Dis. 187, 117–123 (2003).
Hsu, T. et al. The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue. Proc. Natl Acad. Sci. USA 100, 12420–12425 (2003).
Pym, A. S., Brodin, P., Brosch, R., Huerre, M. & Cole, S. T. Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol. Microbiol. 46, 709–717 (2002).
Brodin, P., Rosenkrands, I., Andersen, P., Cole, S. T. & Brosch, R. ESAT-6 proteins: protective antigens and virulence factors? Trends Microbiol. 12, 500–508 (2004).
Stanley, S. A., Raghavan, S., Hwang, W. W. & Cox, J. S. Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc. Natl Acad. Sci. USA 100, 13001–13006 (2003).
Desvaux, M., Hebraud, M., Talon, R. & Henderson, I. R. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol. 17, 139–145 (2009).
Abdallah, A. M. et al. Type VII secretion–mycobacteria show the way. Nat. Rev. Microbiol. 5, 883–891 (2007).
Newton-Foot, M., Warren, R. M., Sampson, S. L., van Helden, P. D. & Gey van Pittius, N. C. The plasmid-mediated evolution of the mycobacterial ESX (Type VII) secretion systems. BMC Evol. Biol. 16, 62 (2016).
Ummels, R. et al. Identification of a novel conjugative plasmid in mycobacteria that requires both type IV and type VII secretion. mBio 5, e01744–14 (2014).
Dumas, E. et al. Mycobacterial pan-genome analysis suggests important role of plasmids in the radiation of type VII secretion systems. Genome Biol. Evol. 8, 387–402 (2016).
Sutcliffe, I. C. New insights into the distribution of WXG100 protein secretion systems. Antonie van Leeuwenhoek 99, 127–131 (2011).
Unnikrishnan, M., Constantinidou, C., Palmer, T. & Pallen, M. J. The enigmatic Esx proteins: looking beyond mycobacteria. Trends Microbiol. 25, 192–204 (2017).
Abdallah, A. M. et al. A specific secretion system mediates PPE41 transport in pathogenic mycobacteria. Mol. Microbiol. 62, 667–679 (2006).
Brodin, P. et al. Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence. Infect. Immun. 74, 88–98 (2006).
Houben, E. N. et al. Composition of the type VII secretion system membrane complex. Mol. Microbiol. 86, 472–484 (2012). This study provides the first biochemical evidence that EccB–EccE form a secretion complex in the mycobacterial cell wall.
Ohol, Y. M. et al. Mycobacterium tuberculosis MycP1 protease plays a dual role in regulation of ESX-1 secretion and virulence. Cell Host Microbe 7, 210–220 (2010).
Siegrist, M. S. et al. Mycobacterial Esx-3 requires multiple components for iron acquisition. mBio 5, e01073–01014 (2014).
Famelis, N. et al. Architecture of the mycobacterial type VII secretion system. Nature 576, 321–325 (2019). This study shows the first high-resolution structure of the ESX-3 core complex in the dimeric state, revealing the protomer architecture, and enabled the generation of the first structural model for T7SS secretion complexes in the inner membrane.
Champion, P. A., Champion, M. M., Manzanillo, P. & Cox, J. S. ESX-1 secreted virulence factors are recognized by multiple cytosolic AAA ATPases in pathogenic mycobacteria. Mol. Microbiol. 73, 950–962 (2009).
Teutschbein, J. et al. A protein linkage map of the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis. Microbiol. Res. 164, 253–259 (2009).
Phan, T. H. et al. EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF. PLoS Pathog. 14, e1007247 (2018).
Crosskey, T. D., Beckham, K. S. H. & Wilmanns, M. The ATPases of the mycobacterial type VII secretion system: structural and mechanistic insights into secretion. Prog. Biophys. Mol. Biol. 152, 25–34 (2020).
Beckham, K. S. H. et al. Structure of the mycobacterial ESX-5 type VII secretion system hexameric pore complex. Preprint at https://www.biorxiv.org/content/10.1101/2020.11.17.387225v1 (2020).
Bunduc, C. M. et al. Structure and dynamics of the ESX-5 type VII secretion system of Mycobacterium tuberculosis. Preprint at https://www.biorxiv.org/content/10.1101/2020.12.02.408906v1 (2020).
Poweleit, N. et al. The structure of the endogenous ESX-3 secretion system. eLife 8, e52983 (2019).
Hoffmann, C., Leis, A., Niederweis, M., Plitzko, J. M. & Engelhardt, H. Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure. Proc. Natl Acad. Sci. USA 105, 3963–3967 (2008).
Daffe, M. & Marrakchi, H. Unraveling the structure of the mycobacterial envelope. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.GPP3-0027-2018 (2019).
Chiaradia, L. et al. Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane. Sci. Rep. 7, 12807 (2017).
Kalscheuer, R. et al. The Mycobacterium tuberculosis capsule: a cell structure with key implications in pathogenesis. Biochem. J. 476, 1995–2016 (2019).
Renshaw, P. S. et al. Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6. EMBO J. 24, 2491–2498 (2005).
Ates, L. S. et al. Essential role of the ESX-5 secretion system in outer membrane permeability of pathogenic mycobacteria. PLoS Genet. 11, e1005190 (2015). Ates et al. provide the first evidence that ESX-5 and PE–PPE proteins are involved in nutrient uptake across the outer membrane of slow-growing mycobacteria.
Abdallah, A. M. et al. The ESX-5 secretion system of Mycobacterium marinum modulates the macrophage response. J. Immunol. 181, 7166–7175 (2008).
Gey van Pittius, N. C. et al. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 6, 95 (2006).
Tufariello, J. M. et al. Separable roles for Mycobacterium tuberculosis ESX-3 effectors in iron acquisition and virulence. Proc. Natl Acad. Sci. USA 113, E348–E357 (2016).
Serafini, A., Boldrin, F., Palu, G. & Manganelli, R. Characterization of a Mycobacterium tuberculosis ESX-3 conditional mutant: essentiality and rescue by iron and zinc. J. Bacteriol. 191, 6340–6344 (2009).
Siegrist, M. S. et al. Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition. Proc. Natl Acad. Sci. USA 106, 18792–18797 (2009).
Mehra, A. et al. Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking. PLoS Pathog. 9, e1003734 (2013).
Portal-Celhay, C. et al. Mycobacterium tuberculosis EsxH inhibits ESCRT-dependent CD4+ T-cell activation. Nat. Microbiol. 2, 16232 (2016).
Mittal, E. et al. Mycobacterium tuberculosis type VII secretion system effectors differentially impact the ESCRT endomembrane damage response. mBio 9, e01765–18 (2018).
Simeone, R. et al. Phagosomal rupture by Mycobacterium tuberculosis results in toxicity and host cell death. PLoS Pathog. 8, e1002507 (2012).
Augenstreich, J. et al. ESX-1 and phthiocerol dimycocerosates of Mycobacterium tuberculosis act in concert to cause phagosomal rupture and host cell apoptosis. Cell. Microbiol. 19, e12726 (2017).
Houben, D. et al. ESX-1-mediated translocation to the cytosol controls virulence of mycobacteria. Cell. Microbiol. 14, 1287–1298 (2012).
Beckwith, K. S. et al. Plasma membrane damage causes NLRP3 activation and pyroptosis during Mycobacterium tuberculosis infection. Nat. Commun. 11, 2270 (2020).
Girard-Misguich, F. et al. [The most ancestral mycobacterial ESX-4 secretion system is essential for intracellular growth of Mycobacterium abscessus within environmental and human phagocytes]. Med. Sci. 34, 795–797 (2018).
Laencina, L. et al. Identification of genes required for Mycobacterium abscessus growth in vivo with a prominent role of the ESX-4 locus. Proc. Natl Acad. Sci. USA 115, E1002–E1011 (2018).
Gray, T. A. et al. Intercellular communication and conjugation are mediated by ESX secretion systems in mycobacteria. Science 354, 347–350 (2016).
Bosserman, R. E. et al. WhiB6 regulation of ESX-1 gene expression is controlled by a negative feedback loop in Mycobacterium marinum. Proc. Natl Acad. Sci. USA 114, E10772–E10781 (2017).
Sanchez, K. G. et al. EspM is a conserved transcription factor that regulates gene expression in response to the ESX-1 system. mBio 11, e02807–e02819 (2020).
Kundu, M. The role of two-component systems in the physiology of Mycobacterium tuberculosis. IUBMB Life 70, 710–717 (2018).
Broset, E., Martin, C. & Gonzalo-Asensio, J. Evolutionary landscape of the Mycobacterium tuberculosis complex from the viewpoint of PhoPR: implications for virulence regulation and application to vaccine development. mBio 6, e01289–01215 (2015).
Frigui, W. et al. Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP. PLoS Pathog. 4, e33 (2008).
Anil Kumar, V. et al. EspR-dependent ESAT-6 protein secretion of Mycobacterium tuberculosis requires the presence of virulence regulator PhoP. J. Biol. Chem. 291, 19018–19030 (2016).
Fortune, S. M. et al. Mutually dependent secretion of proteins required for mycobacterial virulence. Proc. Natl Acad. Sci. USA 102, 10676–10681 (2005).
MacGurn, J. A., Raghavan, S., Stanley, S. A. & Cox, J. S. A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis. Mol. Microbiol. 57, 1653–1663 (2005).
Pang, X. et al. MprAB regulates the espA operon in Mycobacterium tuberculosis and modulates ESX-1 function and host cytokine response. J. Bacteriol. 195, 66–75 (2013).
Kahramanoglou, C. et al. Genomic mapping of cAMP receptor protein (CRP Mt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor. Nucleic Acids Res. 42, 8320–8329 (2014).
Gordon, B. R. et al. Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 107, 5154–5159 (2010).
Blasco, B. et al. Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein. PLoS Pathog. 8, e1002621 (2012).
Rosenberg, O. S. et al. EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structure among helix-turn-helix proteins. Proc. Natl Acad. Sci. USA 108, 13450–13455 (2011).
Gonzalo-Asensio, J. et al. Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator. Proc. Natl Acad. Sci. USA 111, 11491–11496 (2014).
Ates, L. S. et al. Unexpected genomic and phenotypic diversity of Mycobacterium africanum lineage 5 affects drug resistance, protein secretion, and immunogenicity. Genome Biol. Evol. 10, 1858–1874 (2018).
Abdallah, A. M. et al. Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator. PLoS ONE 14, e0211003 (2019).
Solans, L. et al. A specific polymorphism in Mycobacterium tuberculosis H37Rv causes differential ESAT-6 expression and identifies WhiB6 as a novel ESX-1 component. Infect. Immun. 82, 3446–3456 (2014).
Serafini, A., Pisu, D., Palu, G., Rodriguez, G. M. & Manganelli, R. The ESX-3 secretion system is necessary for iron and zinc homeostasis in Mycobacterium tuberculosis. PLoS ONE 8, e78351 (2013).
Maciag, A., Piazza, A., Riccardi, G. & Milano, A. Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. BMC Microbiol. 9, 48 (2009).
Rodriguez, G. M., Voskuil, M. I., Gold, B., Schoolnik, G. K. & Smith, I. ideR, an essential gene in Mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 70, 3371–3381 (2002).
Elliott, S. R. & Tischler, A. D. Phosphate starvation: a novel signal that triggers ESX-5 secretion in Mycobacterium tuberculosis. Mol. Microbiol. 100, 510–526 (2016).
Beckham, K. S. et al. Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis. Nat. Microbiol. 2, 17047 (2017). Beckham et al. present the first negative-stain structure of the ESX-5 core complex hexamer (EccB–EccE) and provide evidence for the hexameric organization of T7SS core complexes.
Wagner, J. M. et al. Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. BMC Struct. Biol. 16, 5 (2016).
Zhang, X. L. et al. Core component EccB1 of the Mycobacterium tuberculosis type VII secretion system is a periplasmic ATPase. FASEB J. 29, 4804–4814 (2015).
Rosenberg, O. S. et al. Substrates control multimerization and activation of the multi-domain ATPase motor of type VII secretion. Cell 161, 501–512 (2015). This study shows the first co-structure of the substrate recognition domain with a signal peptide, and shows that oligomerization and allosteric activation are required for activation of the T7SS.
Iyer, L. M., Makarova, K. S., Koonin, E. V. & Aravind, L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res. 32, 5260–5279 (2004).
Puchades, C., Sandate, C. R. & Lander, G. C. The molecular principles governing the activity and functional diversity of AAA+ proteins. Nat. Rev. Mol. Cell Biol. 21, 43–58 (2020).
Wang, S. et al. Structural insights into substrate recognition by the type VII secretion system. Protein Cell 11, 124–137 (2020).
Zoltner, M. et al. EssC: domain structures inform on the elusive translocation channel in the type VII secretion system. Biochem. J. 473, 1941–1952 (2016).
Klein, T. A., Ahmad, S. & Whitney, J. C. Contact-dependent interbacterial antagonism mediated by protein secretion machines. Trends Microbiol. 28, 387–400 (2020).
Taylor, J. C. et al. A type VII secretion system of Streptococcus gallolyticus subsp. gallolyticus contributes to gut colonization and the development of colon tumors. PLoS Pathog. 17, e1009182 (2021).
Ulhuq, F. R. et al. A membrane-depolarizing toxin substrate of the Staphylococcus aureus type VII secretion system mediates intraspecies competition. Proc. Natl Acad. Sci. USA 117, 20836–20847 (2020).
Tassinari, M. et al. Central role and structure of the membrane pseudokinase YukC in the antibacterial Bacillus subtilis type VIIb secretion system. Preprint at https://www.biorxiv.org/content/10.1101/2020.05.09.085852v1 (2020).
Whitney, J. C. et al. A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. eLife 6, e26938 (2017).
Cao, Z., Casabona, M. G., Kneuper, H., Chalmers, J. D. & Palmer, T. The type VII secretion system of Staphylococcus aureus secretes a nuclease toxin that targets competitor bacteria. Nat. Microbiol. 2, 16183 (2016).
Burts, M. L., Williams, W. A., DeBord, K. & Missiakas, D. M. EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections. Proc. Natl Acad. Sci. USA 102, 1169–1174 (2005).
Anderson, M., Aly, K. A., Chen, Y. H. & Missiakas, D. Secretion of atypical protein substrates by the ESAT-6 secretion system of Staphylococcus aureus. Mol. Microbiol. 90, 734–743 (2013).
Kneuper, H. et al. Heterogeneity in ess transcriptional organization and variable contribution of the Ess/Type VII protein secretion system to virulence across closely related Staphylocccus aureus strains. Mol. Microbiol. 93, 928–943 (2014).
Casabona, M. G. et al. Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system. Microbiology https://doi.org/10.1099/mic.0.000580 (2017).
Warne, B. et al. The Ess/type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity. BMC Genomics 17, 222 (2016).
Lebeurre, J. et al. Comparative genome analysis of Staphylococcus lugdunensis shows clonal complex-dependent diversity of the putative virulence factor, ess/type VII locus. Front. Microbiol. 10, 2479 (2019).
Zoltner, M., Fyfe, P. K., Palmer, T. & Hunter, W. N. Characterization of Staphylococcus aureus EssB, an integral membrane component of the Type VII secretion system: atomic resolution crystal structure of the cytoplasmic segment. Biochem. J. 449, 469–477 (2013).
Zoltner, M. et al. The architecture of EssB, an integral membrane component of the type VII secretion system. Structure 21, 595–603 (2013).
Klein, T. A. et al. Structure of the extracellular region of the bacterial type VIIb secretion system subunit EsaA. Structure 29, 177–185 e176 (2021).
van den Ent, F. & Lowe, J. Crystal structure of the ubiquitin-like protein YukD from Bacillus subtilis. FEBS Lett. 579, 3837–3841 (2005).
Tanaka, Y. et al. Crystal structure analysis reveals a novel forkhead-associated domain of ESAT-6 secretion system C protein in Staphylococcus aureus. Proteins 69, 659–664 (2007).
Mietrach, N., Damian-Aparicio, D., Mielich-Suss, B., Lopez, D. & Geibel, S. Substrate interaction with the EssC coupling protein of the type VIIb secretion system. J. Bacteriol. 202, e00646–19 (2020).
Jager, F., Zoltner, M., Kneuper, H., Hunter, W. N. & Palmer, T. Membrane interactions and self-association of components of the Ess/Type VII secretion system of Staphylococcus aureus. FEBS Lett. 590, 349–357 (2016).
Jager, F., Kneuper, H. & Palmer, T. EssC is a specificity determinant for Staphylococcus aureus type VII secretion. Microbiology 164, 816–820 (2018).
Dreisbach, A. et al. Profiling the surfacome of Staphylococcus aureus. Proteomics 10, 3082–3096 (2010).
Mietrach, N. et al. The conserved core component EsaA mediates bacterial killing by the type VIIb secretion system. Res. Square https://doi.org/10.21203/rs.3.rs-95626/v1 (2020).
Bunduc, C. M., Ummels, R., Bitter, W. & Houben, E. N. G. Species-specific secretion of ESX-5 type VII substrates is determined by the linker 2 of EccC5. Mol. Microbiol. 114, 66–76 (2020).
de Jonge, M. I. et al. ESAT-6 from Mycobacterium tuberculosis dissociates from its putative chaperone CFP-10 under acidic conditions and exhibits membrane-lysing activity. J. Bacteriol. 189, 6028–6034 (2007).
Okkels, L. M. et al. CFP10 discriminates between nonacetylated and acetylated ESAT-6 of Mycobacterium tuberculosis by differential interaction. Proteomics 4, 2954–2960 (2004).
Brown, G. D. et al. The mycosins of Mycobacterium tuberculosis H37Rv: a family of subtilisin-like serine proteases. Gene 254, 147–155 (2000).
Dave, J. A., Gey van Pittius, N. C., Beyers, A. D., Ehlers, M. R. & Brown, G. D. Mycosin-1, a subtilisin-like serine protease of Mycobacterium tuberculosis, is cell wall-associated and expressed during infection of macrophages. BMC Microbiol. 2, 30 (2002).
McLaughlin, B. et al. A mycobacterium ESX-1-secreted virulence factor with unique requirements for export. PLoS Pathog. 3, e105 (2007).
Xu, J. et al. A unique Mycobacterium ESX-1 protein co-secretes with CFP-10/ESAT-6 and is necessary for inhibiting phagosome maturation. Mol. Microbiol. 66, 787–800 (2007).
van Winden, V. J. et al. Mycosins are required for the stabilization of the ESX-1 and ESX-5 type VII secretion membrane complexes. mBio 7, e01471–16 (2016).
Ekiert, D. C. & Cox, J. S. Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion. Proc. Natl Acad. Sci. USA 111, 14758–14763 (2014). This study presents the first structure of a PE–PPE substrate heterodimer bound to the chaperone EspG and shows that PE–PPE substrates interact specifically with their cognate chaperones.
Korotkova, N. et al. Structure of the Mycobacterium tuberculosis type VII secretion system chaperone EspG5 in complex with PE25-PPE41 dimer. Mol. Microbiol. 94, 367–382 (2014).
Phan, T. H., Ummels, R., Bitter, W. & Houben, E. N. Identification of a substrate domain that determines system specificity in mycobacterial type VII secretion systems. Sci. Rep. 7, 42704 (2017). Together with the study of Ekiert and Cox (2014), this study establishes that EspG determines the system specificity of PE–PPE substrates.
Damen, M. P. M. et al. Modification of a PE/PPE substrate pair reroutes an Esx substrate pair from the mycobacterial ESX-1 type VII secretion system to the ESX-5 system. J. Biol. Chem. 295, 5960–5969 (2020).
Williamson, Z. A., Chaton, C. T., Ciocca, W. A., Korotkova, N. & Korotkov, K. V. PE5-PPE4-EspG3 heterotrimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems. J. Biol. Chem. 295, 12706–12715 (2020).
Wagner, J. M., Evans, T. J. & Korotkov, K. V. Crystal structure of the N-terminal domain of EccA(1) ATPase from the ESX-1 secretion system of Mycobacterium tuberculosis. Proteins 82, 159–163 (2014).
Wang, Q. et al. PE/PPE proteins mediate nutrient transport across the outer membrane of Mycobacterium tuberculosis. Science 367, 1147–1151 (2020). Wang et al. provide the first detailed study of porins formed by PE–PPE proteins in the mycobacterial cell envelope.
Lou, Y., Rybniker, J., Sala, C. & Cole, S. T. EspC forms a filamentous structure in the cell envelope of Mycobacterium tuberculosis and impacts ESX-1 secretion. Mol. Microbiol. 103, 26–38 (2017).
Solomonson, M. et al. Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism. Structure 23, 571–583 (2015).
Gijsbers, A. et al. Priming mycobacterial ESX-secreted protein B to form a channel-like structure. Preprint at https://www.biorxiv.org/content/10.1101/2021.01.02.425093v1.full (2021).
Piton, J., Pojer, F., Wakatsuki, S., Gati, C. & Cole, S. T. High resolution CryoEM structure of the ring-shaped virulence factor EspB from Mycobacterium tuberculosis. J. Struct. Biol. 4, 100029 (2020).
Chen, J. M. et al. Mycobacterium tuberculosis EspB binds phospholipids and mediates EsxA-independent virulence. Mol. Microbiol. 89, 1154–1166 (2013).
Punjani, A. & Fleet, D. J. 3D variability analysis: resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM images. J. Struct. Biol. 213, 107702 (2021).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Groschel, M. I., Sayes, F., Simeone, R., Majlessi, L. & Brosch, R. ESX secretion systems: mycobacterial evolution to counter host immunity. Nat. Rev. Microbiol. 14, 677–691 (2016).
Khan, H. S. et al. Identification of scavenger receptor B1 as the airway microfold cell receptor for Mycobacterium tuberculosis. eLife 9, e52551 (2020).
Stamm, L. M. et al. Mycobacterium marinum escapes from phagosomes and is propelled by actin-based motility. J. Exp. Med. 198, 1361–1368 (2003).
van der Wel, N. et al. M. tuberculosis and M. leprae translocate from the phagolysosome to the cytosol in myeloid cells. Cell 129, 1287–1298 (2007).
Simeone, R. et al. Cytosolic access of Mycobacterium tuberculosis: critical impact of phagosomal acidification control and demonstration of occurrence in vivo. PLoS Pathog. 11, e1004650 (2015).
Conrad, W. H. et al. Mycobacterial ESX-1 secretion system mediates host cell lysis through bacterium contact-dependent gross membrane disruptions. Proc. Natl Acad. Sci. USA 114, 1371–1376 (2017).
Lienard, J. et al. The Mycobacterium marinum ESX-1 system mediates phagosomal permeabilization and type I interferon production via separable mechanisms. Proc. Natl Acad. Sci. USA 117, 1160–1166 (2020).
Quigley, J. et al. The cell wall lipid PDIM contributes to phagosomal escape and host cell exit of Mycobacterium tuberculosis. mBio 8, e00148–17 (2017).
Skowyra, M. L., Schlesinger, P. H., Naismith, T. V. & Hanson, P. I. Triggered recruitment of ESCRT machinery promotes endolysosomal repair. Science 360, eaar5078 (2018).
Stanley, S. A., Johndrow, J. E., Manzanillo, P. & Cox, J. S. The type I IFN response to infection with Mycobacterium tuberculosis requires ESX-1-mediated secretion and contributes to pathogenesis. J. Immunol. 178, 3143–3152 (2007).
Collins, A. C. et al. Cyclic GMP-AMP synthase is an innate immune DNA sensor for Mycobacterium tuberculosis. Cell Host Microbe 17, 820–828 (2015).
Watson, R. O., Manzanillo, P. S. & Cox, J. S. Extracellular M. tuberculosis DNA targets bacteria for autophagy by activating the host DNA-sensing pathway. Cell 150, 803–815 (2012).
Wassermann, R. et al. Mycobacterium tuberculosis differentially activates cGAS- and inflammasome-dependent intracellular immune responses through ESX-1. Cell Host Microbe 17, 799–810 (2015).
Aguilo, J. I. et al. ESX-1-induced apoptosis is involved in cell-to-cell spread of Mycobacterium tuberculosis. Cell. Microbiol. 15, 1994–2005 (2013).
Volkman, H. E. et al. Tuberculous granuloma induction via interaction of a bacterial secreted protein with host epithelium. Science 327, 466–469 (2010).
Kapoor, N. et al. Human granuloma in vitro model, for TB dormancy and resuscitation. PLoS ONE 8, e53657 (2013).
Davis, J. M. & Ramakrishnan, L. The role of the granuloma in expansion and dissemination of early tuberculous infection. Cell 136, 37–49 (2009).
Stoop, E. J. et al. Zebrafish embryo screen for mycobacterial genes involved in the initiation of granuloma formation reveals a newly identified ESX-1 component. Dis. Model. Mech. 4, 526–536 (2011).
Zhang, L. et al. Comprehensive analysis of iron utilization by Mycobacterium tuberculosis. PLoS Pathog. 16, e1008337 (2020).
Chao, A., Sieminski, P. J., Owens, C. P. & Goulding, C. W. Iron acquisition in Mycobacterium tuberculosis. Chem. Rev. 119, 1193–1220 (2019).
Santucci, P. et al. Dissecting the membrane lipid binding properties and lipase activity of Mycobacterium tuberculosis LipY domains. FEBS J. 286, 3164–3181 (2019).
Boritsch, E. C. et al. Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria. Proc. Natl Acad. Sci. USA 113, 9876–9881 (2016).
Flint, J. L., Kowalski, J. C., Karnati, P. K. & Derbyshire, K. M. The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis. Proc. Natl Acad. Sci. USA 101, 12598–12603 (2004).
Gray, T. A., Krywy, J. A., Harold, J., Palumbo, M. J. & Derbyshire, K. M. Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus. PLoS Biol. 11, e1001602 (2013).
Clark, R. R. et al. Direct cell-cell contact activates SigM to express the ESX-4 secretion system in Mycobacterium smegmatis. Proc. Natl Acad. Sci. USA 115, E6595–E6603 (2018).
Coros, A., Callahan, B., Battaglioli, E. & Derbyshire, K. M. The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis. Mol. Microbiol. 69, 794–808 (2008).
Gray, T. A. & Derbyshire, K. M. Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT. Mol. Microbiol. 108, 601–613 (2018).
van Winden, V. J. C., Damen, M. P. M., Ummels, R., Bitter, W. & Houben, E. N. G. Protease domain and transmembrane domain of the type VII secretion mycosin protease determine system-specific functioning in mycobacteria. J. Biol. Chem. 294, 4806–4814 (2019).
Sani, M. et al. Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins. PLoS Pathog. 6, e1000794 (2010).
Garces, A. et al. EspA acts as a critical mediator of ESX1-dependent virulence in Mycobacterium tuberculosis by affecting bacterial cell wall integrity. PLoS Pathog. 6, e1000957 (2010).
Ates, L. S. et al. The ESX-5 system of pathogenic mycobacteria is involved in capsule integrity and virulence through its substrate PPE10. PLoS Pathog. 12, e1005696 (2016).
Akpe San Roman, S. et al. A heterodimer of EsxA and EsxB is involved in sporulation and is secreted by a type VII secretion system in Streptomyces coelicolor. Microbiology 156, 1719–1729 (2010).
Chatterjee, A., Willett, J. L. E., Dunny, G. M. & Duerkop, B. A. Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PLoS Genet. 17, e1009204 (2021).
Chatterjee, A. et al. Parallel genomics uncover novel enterococcal-bacteriophage interactions. mBio https://doi.org/10.1128/mBio.03120-19 (2020).
Lopez, M. S. et al. Host-derived fatty acids activate type VII secretion in Staphylococcus aureus. Proc. Natl Acad. Sci. USA 114, 11223–11228 (2017).
Psonis, J. J. & Thanassi, D. G. Therapeutic approaches targeting the assembly and function of chaperone-usher Pili. EcoSal Plus https://doi.org/10.1128/ecosalplus.ESP-0033-2018 (2019).
Fasciano, A. C., Shaban, L. & Mecsas, J. Promises and challenges of the type three secretion system injectisome as an antivirulence target. EcoSal Plus https://doi.org/10.1128/ecosalplus.ESP-0032-2018 (2019).
Bitter, W. & Kuijl, C. Targeting bacterial virulence: the coming out of type VII secretion inhibitors. Cell Host Microbe 16, 430–432 (2014).
Rybniker, J. et al. Anticytolytic screen identifies inhibitors of mycobacterial virulence protein secretion. Cell Host Microbe 16, 538–548 (2014).
Massey, T. H., Mercogliano, C. P., Yates, J., Sherratt, D. J. & Löwe, J. Double-stranded DNA translocation: structure and mechanism of hexameric FtsK. Mol. Cell 23, 457–469 (2006).
Daleke, M. H. et al. General secretion signal for the mycobacterial type VII secretion pathway. Proc. Natl Acad. Sci. USA 109, 11342–11347 (2012). This study identifies the amino acid sequence YXXXD/E as a general type VII secretion signal.
Poulsen, C., Panjikar, S., Holton, S. J., Wilmanns, M. & Song, Y. H. WXG100 protein superfamily consists of three subfamilies and exhibits an alpha-helical C-terminal conserved residue pattern. PLoS ONE 9, e89313 (2014).
Sysoeva, T. A., Zepeda-Rivera, M. A., Huppert, L. A. & Burton, B. M. Dimer recognition and secretion by the ESX secretion system in Bacillus subtilis. Proc. Natl Acad. Sci. USA 111, 7653–7658 (2014).
Korotkova, N. et al. Structure of EspB, a secreted substrate of the ESX-1 secretion system of Mycobacterium tuberculosis. J. Struct. Biol. 191, 236–244 (2015).
Pallen, M. J. The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system? Trends Microbiol. 10, 209–212 (2002).
Champion, P. A., Stanley, S. A., Champion, M. M., Brown, E. J. & Cox, J. S. C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis. Science 313, 1632–1636 (2006). This study shows that the C terminus of WXG100 contains a signal peptide crucial for the interactions of these proteins with the C-terminal segment of the EssC coupling protein.
Ates, L. S. New insights into the mycobacterial PE and PPE proteins provide a framework for future research. Mol. Microbiol. 113, 4–21 (2020).
Meng, L. et al. PPE38 protein of mycobacterium tuberculosis inhibits macrophage MHC class I expression and dampens CD8(+) T cell responses. Front. Cell Infect. Microbiol. 7, 68 (2017).
Brennan, M. J. The enigmatic PE/PPE multigene family of mycobacteria and tuberculosis vaccination. Infect. Immun. 85, e00969–16 (2017).
This work was funded by the Elite Network of Bavaria (N-BM-2013-246 to S.G.), bayresq.net (S.G.), grant SAF2017-82632-P to O.L. from the Spanish Ministry of Science, Innovation and Universities (MCIU/AEI), co-funded by the European Regional Development Fund, the support of the Spanish National Institute of Health Carlos III provided to CNIO, and grants Y2018/BIO4747 and P2018/NMT4443 from the Autonomous Region of Madrid and co-funded by the European Social Fund and the European Regional Development Fund to the activities of the group directed by O.L.
The authors declare no competing interests.
Peer review information
Nature Reviews Microbiology thanks J. Cox and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- Arabinogalactan layer
An essential constituent of the mycobacterial cell wall. Peptidoglycan is covalently attached to the heteropolysaccharide arabinogalactan, which is in turn linked to the mycolic acid layer.
The mycobacterial capsule is the outermost layer of the bacterial cell and consists mainly of a glycogen-like α-glucan with lower amounts of arabinomannan and mannan, proteins and lipids. This layer mediates key interactions with host cells during initial stages of infection and favours bacterial survival.
A term to describe the presence of an inner membrane and an outer membrane in the cell envelope such as in Gram-negative bacteria and mycobacteria.
- 3D variability analysis
A tool to analyse the heterogeneity in single-particle cryogenic electron microscopy data sets revealing the different 3D conformations that appear in the sample. It can be used to characterize the conformational space and the amount of flexibility present in a molecule.
Type of programmed cell death different from apoptosis and necroptosis that promotes lytic cell death, causing the release of the cellular content and inducing inflammatory responses in the organism.
About this article
Cite this article
Rivera-Calzada, A., Famelis, N., Llorca, O. et al. Type VII secretion systems: structure, functions and transport models. Nat Rev Microbiol 19, 567–584 (2021). https://doi.org/10.1038/s41579-021-00560-5
This article is cited by
A microfluidic-based analysis of 3D macrophage migration after stimulation by Mycobacterium, Salmonella and Escherichia
BMC Microbiology (2022)
Nature Reviews Microbiology (2022)