Citation: Bitter W, Houben ENG, Bottai D, Brodin P, Brown EJ, Cox JS, et al. (2009) Systematic Genetic Nomenclature for Type VII Secretion Systems. PLoS Pathog 5(10): e1000507. https://doi.org/10.1371/journal.ppat.1000507
Editor: Glenn F. Rall, The Fox Chase Cancer Center, United States of America
Published: October 30, 2009
Copyright: © 2009 Bitter et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work has received funding from the European Community's Seventh Framework Programme ([FP7/2007–2013]) under grant agreement n°201762. In addition, the authors acknowledge their individual external funding for T7S/ESX related research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Mycobacteria, such as the etiological agent of human tuberculosis, Mycobacterium tuberculosis, are protected by an impermeable cell envelope composed of an inner cytoplasmic membrane, a peptidoglycan layer, an arabinogalactan layer, and an outer membrane. This second membrane consists of covalently linked, tightly packed long-chain mycolic acids , and non-covalently bound shorter lipids involved in pathogenicity –. To ensure protein transport across this complex cell envelope, mycobacteria use various secretion pathways, such as the SecA1-mediated general secretory pathway ,, an alternative SecA2-operated pathway , a twin-arginine translocation system ,, and a specialized secretion pathway variously named ESAT-6-, SNM-, ESX-, or type VII secretion –. The latter pathway, hereafter referred to as type VII secretion (T7S), has recently become a large and competitive research topic that is closely linked to studies of host–pathogen interactions of M. tuberculosis  and other pathogenic mycobacteria . Molecular details are just beginning to be revealed – showing that T7S systems are complex machineries with multiple components and multiple substrates. Despite their biological importance, there has been a lack of a clear naming policy for the components and substrates of these systems. As there are multiple paralogous T7S systems within the Mycobacteria and orthologous systems in related bacteria, we are concerned that, without a unified nomenclature system, a multitude of redundant and obscure gene names will be used that will inevitably lead to confusion and hinder future progress. In this opinion piece we will therefore propose and introduce a systematic nomenclature with guidelines for name selection of new components that will greatly facilitate communication and understanding in this rapidly developing field of research.
The first T7S-associated protein to be identified was the 6-kD early secreted antigenic target ESAT-6 . This small, highly immunogenic protein lacks a classical N-terminal signal sequence and is present in large amounts in the culture filtrate of M. tuberculosis , but is missing from the closely related attenuated live vaccine Mycobacterium bovis bacille Calmette-Guérin (BCG)  due to the deletion of region of difference 1 (RD1) . ESAT-6 and its protein partner, the 10-kD culture filtrate protein CFP-10 , form a 1∶1 protein complex  that involves hydrophobic interaction ,. Secretion of ESAT-6 and CFP-10 is required for the pathogenicity of M. tuberculosis –. The absence of ESAT-6 secretion is responsible in part for the attenuation of the BCG and Mycobacterium microti vaccines ,,, as well as for the decrease in virulence of the attenuated M. tuberculosis H37Ra strain .
In M. tuberculosis, ESAT-6 and CFP-10 belong to the WXG100 family of 23 small secreted proteins that share a size of approximately 100 amino acids, a helical structure, and a characteristic hairpin bend formed by the conserved Trp-Xaa-Gly (W-X-G) motif . The genes encoding these proteins, many of which represent immunodominant T cell antigens , are called esx genes in M. tuberculosis (esxA-W, Table 1) and are arranged in tandem pairs at 11 genomic loci . In five of these genomic loci (ESX-1–ESX-5), the esx genes are flanked by genes coding for components of secretion machineries involved in the export of the corresponding ESX proteins (Figure 1). These proteins constitute the major building blocks of the T7S systems ,,,,. Four of these regions are also characterized by the presence of genes encoding PE and/or PPE proteins (Figure 1, Table 2), named after their characteristic N-terminal motifs proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) . Apart from genes localized in these core ESX regions, additional genes situated elsewhere on the chromosome may be required for the function of T7S systems. For example, the rv3616c-rv3614c genes are required for secretion of ESAT-6 and CFP-10 by ESX-1 –.
(A) Genetic organization. (B) Model. The abbreviation ecc stands for esx conserved component, whereas esp stands for ESX-1 secretion-associated proteins. The topology of the different proteins in the cytoplasmic membrane shown in (B) refers to the ESX-1 cluster and is based on predictions made using the MEMSAT3 algorithm . Note that the channel drawn in the outer membrane of our model refers to a hypothetical pore, whose existence has not been experimentally demonstrated.
Apart from members of the M. tuberculosis complex, the ESX-1 cluster is also present in a range of mycobacteria, including Mycobacterium kansasii  and Mycobacterium leprae . However, experimental work has mainly focused on the ESX-1 system of Mycobacterium marinum , , –, a fish pathogen that shows high homology in its ESX loci with M. tuberculosis , and the fast grower Mycobacterium smegmatis –. M. marinum has also been used to define a role for the paralogous system ESX-5, which is required for the secretion of PE and PPE proteins ,,. For the remaining ESX-2, ESX-3, and ESX-4 systems, only very limited predictions of their putative functions can be made. ESX-3 transcriptome data suggest that this system is involved in iron/zinc homeostasis ,, which would be consistent with the essential role of ESX-3 in M. tuberculosis . The putative functions of ESX-2 and ESX-4 remain unknown. ESX-4, which harbors a smaller number of genes than other ESX loci (Table 2), appears to represent the most ancestral T7S system in mycobacteria . This hypothesis is based on the observation that ESX-4-like loci are the only ESX clusters that are found in other high GC Gram-positive bacteria, suggesting that the last common ancestor of mycobacteria already harbored an ESX-4 T7S system. Other ESX clusters may have evolved later by gene duplication and gene diversification events. However, the finding that Nocardia farcinica (http://nocardia.nih.go.jp/) contains two T7S systems, one orthologous to ESX-4 and one locus that shows some similarity to all the conserved components of larger T7S systems, suggests that evolution of T7S systems is more complex than previously anticipated. This second T7S locus in N. farcinica even contains two PPE-like genes that were originally thought to be specific for the mycobacteria .
T7S-like systems are also found outside the high GC Gram-positive bacteria, since a number of Firmicutes have WXG100 members . However, the loci containing these WXG100 genes are only weakly similar to the mycobacterial T7S systems: in fact, only the gene encoding the FtsK/SpoIIIE-like protein is present. Therefore, these systems should be called WXG100 systems to differentiate them from true T7S systems. Both Staphylococcus aureus and Bacillus anthracis have an active WXG100 system, and the WXG100 system encoded by S. aureus is important for virulence ,.
Research in the T7S/ESX field is relatively new, but is now rapidly expanding and we therefore would like to propose a systematic nomenclature for all components involved. Until now a small number of genes within the different ESX loci of mycobacteria have been named, but for most genes the original genome annotation numbers are used. These gene numbers vary between different species and even between different strains of the same species, and therefore make comparative studies confusing. Our nomenclature is appropriate for all T7S systems in high GC-Gram-positive species. Extending this nomenclature to the T7S-like systems of Firmicutes is not recommended, since there are only a very few conserved components.
As a starting point for the new nomenclature, we focus on the most studied system, the ESX-1 system of M. tuberculosis, which is the paradigm T7S system. The new nomenclature is given for ESX-1 in M. tuberculosis (Figure 1 and Table 2) and for all ESX systems in various Mycobacteria (Table S1). The proposed rules for the nomenclature are as follows:
- Only genes that have homologues in at least four of the mycobacterial ESX systems will get a general name, whereas the locus-specific genes have a more restricted name reflecting their specificity. The reason for this distinction is that the conserved genes are most likely to represent the core components of the secretion system. Moreover, all of the conserved ESX-1 components have been shown to be essential for ESAT-6/CFP-10 secretion in at least one of the mycobacterial species studied (See below). In contrast, many of the locus-specific genes encode secreted proteins, as has been shown for the ESX-1 system (see below). Furthermore, in M. leprae, an organism with an extreme reductive evolution of its genome, almost all of the non-conserved ESX-1 components are pseudogenes, whereas all of the conserved components seem to be intact .
- The three letter acronym for the conserved components will be ecc, for esx conserved component (Figure 1, Table 2). This abbreviation has not been used for other genes in bacteria.
- The ESAT-6 and CFP-10 encoding genes, esxA and esxB, respectively, and the other esx genes (Table 1) will not be renamed. These gene names are informative, well-accepted, and frequently used in the literature. Furthermore, the esx gene products seem to be secreted proteins and do not seem to be components of the secretion system itself, although their presence is required for the secretion of other substrates. The same reasoning is used for the pe and ppe genes. Four of the five systems harbor pe and ppe genes, but for the moment their functions within the T7S systems remain uncertain. Furthermore, various mycobacterial species contain a large number of genes belonging to the pe and ppe families, and it would be confusing to rename some of them. Finally, the subtilisin-like proteases already have an established and descriptive name in literature, i.e., the mycosins . Therefore, we will not change this name.
- The alphabetic suffix of conserved genes will be based on the gene order in the paradigm ESX-1 system (see Figure 1). This decision is mainly based on the fact that the ESX-1 system is the most studied. The gene order of the different T7S systems is highly variable and it is therefore difficult to propose a logical ordering that would be satisfactory for all systems. The genes of ESX-2/-3/-4 and -5 will therefore be named according to their paralogue in ESX-1 (Table 2 and Table S1), allowing for a direct and relevant comparison. The gene names of each mycobacterial T7S will include a numeral suffix indicating the ESX cluster to which this gene belongs. In order to avoid confusion with numbering of alleles, the ESX cluster number is indicated in subscript. As shown in Figure 1, the first conserved gene of the ESX-1 cluster will be eccA1.
- In some of the T7S clusters, the gene encoding the FtsK/SpoIIIE-like protein is split in two genes. Since these gene products clearly form a functional unit, as has also been shown for the two FtsK/SpoIIIE-like proteins of the ESX-1 system , the split genes will get a lower case alphabetic suffix, i.e., eccCa1 and eccCb1 for the ESX-1 system of M. tuberculosis (Figure 1 and Table 2).
- When working with several different organisms, it can also be useful to indicate the origin of the respective genes. For this we recommend using a two-letter subscript at the end of the gene name. For example, the orthologues of the M. tuberculosis genes eccCa1mt and eccCb1mt would be eccCa1ms and eccCb1ms in M. smegmatis.
- The gene names can be converted into their proteins by capitalization, e.g., EccCa1. Alternatively, once the true function of a protein is known, the name could be changed to indicate this function, as has been done for the secretins of type II and type III secretion systems. If in the future new genes are identified that are essential for the functioning of several T7S systems, these genes could be named similarly using the next alphabetical suffix (eccG, eccH, etc.).
- As discussed above, in addition to the conserved genes, there are also region-specific genes. The role of these genes in ESAT-6/CFP-10 secretion is not entirely clear: some of the encoded proteins seem to be involved in the secretion of T7S substrates in M. marinum, whereas their orthologues show less or no effect on secretion in M. tuberculosis. Recently, it has been shown that a subset of these proteins are in fact also substrates of the ESX-1 system. Thus far, four ESX-1 substrates have been identified in addition to ESAT-6 and CFP-10. These substrates are called EspA , EspB , EspR , and the M. marinum homologue of Rv3864 . The acronym Esp stands for ESX-1 secretion-associated protein. Both rv3864 and espB are located within the ESX-1 cluster, whereas EspA and the secreted regulatory protein EspR are encoded by genes outside the ESX-1 locus. However, the espA gene is part of an operon (rv3616-3614) that has paralogues in the 5′ region of the ESX-1 locus. Therefore, we propose naming all the region-specific genes of the ESX-1 system and the rest of the espA operon esp genes with alphabetical suffixes (see Table 2 and Figure 1). We will follow the espA operon and ESX-1 gene order, with the exception of espB and espR, which are already named. This means that the first gene in the esx-1 operon, whose gene product was recently shown to be secreted protein in M. marinum, will be named espE. One of the new esp genes, espG, is present with low but significant homology in two other ESX systems (ESX-2 and ESX-3) and should therefore also have a numeral suffix (Figure 1, Table 2).
- The nomenclature of esp genes in M. marinum is more complicated, in particular for espA. The genome of M. marinum contains a large gene cluster upstream of the ESX-1 locus, among which are 15 espA-like genes . In addition, there are three more paralogues at other locations in the genome. These genes should all be named espA with a superscript numeral suffix to indicate the exact gene and a subscript “mm” to indicate the species.
- Region-specific genes or genes encoding secreted proteins of the other ESX loci and T7S systems should not be called esp, as this name should be reserved for ESX-1 related genes. If there are important region-specific genes for ESX-2/-3/-4 or -5, a new name has to be introduced.
In order to ensure wide visibility for this new nomenclature it will be included in the most extensively used mycobacterial genome databases. As a first step, selected genome browsers available at the Institut Pasteur (http://genolist.pasteur.fr/) and/or the Ecole Polytechnique Federale de Lausanne (http://tuberculist.epfl.ch/) will adopt these new rules; other databases could follow this example.
In conclusion, we would like to emphasize that the introduction of a uniform gene nomenclature for other secretion systems in Gram-negative bacteria (type II, type III) has facilitated comparative analysis of these systems. We anticipate that the acceptance/implementation of this proposal will provide similar advantages for the T7S systems.
New and old nomenclature of the different conserved components of the T7S systems in selected mycobacteria (M. tuberculosis H37Rv, M. marinum M, M. smegmatis mc2155, M. leprae TN, M. avium paratuberculosis K10). The numeral suffices to indicate the ESX clusters to which the genes belong are omitted. Note that the ESX-2 genes of M. avium paratuberculosis are located in two separate genomic loci. TM, transmembrane domain.
(0.09 MB DOC)
Comparison of the transmembrane topologies and signal sequence predictions of the M. tuberculosis H37Rv Ecc membrane proteins. Amongst the different topology prediction programs that were used (TMHMM Server v. 2.0, MEMSAT3, Philius, SCAMPI, HMMTOP and Phobius) MEMSAT3 gave the correct prediction for the highest number of Ecc membrane proteins. Therefore, only the topology prediction results of TMHMM (used on the TubercuList server) and MEMSAT3 are shown. The clearly incorrect predictions are depicted in gray. TM, transmembrane domain; in, cytoplasmic location; out, periplasmic location; C, C-terminus; N, N-terminus; ss, signal sequence.
(0.07 MB DOC)
We are grateful to our many collaborators and colleagues, who have contributed to the rapid progress in this field.
- 1. Hoffmann C, Leis A, Niederweis M, Plitzko JM, Engelhardt H (2008) Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure. Proc Natl Acad Sci U S A 105: 3963–3967.C. HoffmannA. LeisM. NiederweisJM PlitzkoH. Engelhardt2008Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure.Proc Natl Acad Sci U S A10539633967
- 2. Zuber B, Chami M, Houssin C, Dubochet J, Griffiths G, et al. (2008) Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state. J Bacteriol 190: 5672–5680.B. ZuberM. ChamiC. HoussinJ. DubochetG. Griffiths2008Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state.J Bacteriol19056725680
- 3. Camacho LR, Ensergueix D, Perez E, Gicquel B, Guilhot C (1999) Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis. Mol Microbiol 34: 257–267.LR CamachoD. EnsergueixE. PerezB. GicquelC. Guilhot1999Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis.Mol Microbiol34257267
- 4. Cox JS, Chen B, McNeil M, Jacobs WR Jr (1999) Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice. Nature 402: 79–83.JS CoxB. ChenM. McNeilWR Jacobs Jr1999Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice.Nature4027983
- 5. Trivedi OA, Arora P, Vats A, Ansari MZ, Tickoo R, et al. (2005) Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol Cell 17: 631–643.OA TrivediP. AroraA. VatsMZ AnsariR. Tickoo2005Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid.Mol Cell17631643
- 6. Pugsley AP (1993) The complete general secretory pathway in gram-negative bacteria. Microbiol Rev 57: 50–108.AP Pugsley1993The complete general secretory pathway in gram-negative bacteria.Microbiol Rev5750108
- 7. Wiker HG, Harboe M (1992) The antigen 85 complex: a major secretion product of Mycobacterium tuberculosis. Microbiol Rev 56: 648–661.HG WikerM. Harboe1992The antigen 85 complex: a major secretion product of Mycobacterium tuberculosis.Microbiol Rev56648661
- 8. Braunstein M, Espinosa BJ, Chan J, Belisle JT, Jacobs WR Jr (2003) SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis. Mol Microbiol 48: 453–464.M. BraunsteinBJ EspinosaJ. ChanJT BelisleWR Jacobs Jr2003SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis.Mol Microbiol48453464
- 9. McDonough JA, McCann JR, Tekippe EM, Silverman JS, Rigel NW, Braunstein M (2008) Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins. J Bacteriol 190: 6428–6438.JA McDonoughJR McCannEM TekippeJS SilvermanNW RigelM. Braunstein2008Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins.J Bacteriol19064286438
- 10. Saint-Joanis B, Demangel C, Jackson M, Brodin P, Marsollier L, et al. (2006) Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence. J Bacteriol 188: 6669–6679.B. Saint-JoanisC. DemangelM. JacksonP. BrodinL. Marsollier2006Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence.J Bacteriol18866696679
- 11. Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, et al. (1999) Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber Lung Dis 79: 329–342.F. TekaiaSV GordonT. GarnierR. BroschBG Barrell1999Analysis of the proteome of Mycobacterium tuberculosis in silico.Tuber Lung Dis79329342
- 12. Gey Van Pittius NC, Gamieldien J, Hide W, Brown GD, Siezen RJ, et al. (2001) The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol 2: RESEARCH0044.NC Gey Van PittiusJ. GamieldienW. HideGD BrownRJ Siezen2001The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria.Genome Biol2RESEARCH0044
- 13. Pym AS, Brodin P, Majlessi L, Brosch R, Demangel C, et al. (2003) Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat Med 9: 533–539.AS PymP. BrodinL. MajlessiR. BroschC. Demangel2003Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis.Nat Med9533539
- 14. Stanley SA, Raghavan S, Hwang WW, Cox JS (2003) Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc Natl Acad Sci U S A 100: 13001–13006.SA StanleyS. RaghavanWW HwangJS Cox2003Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system.Proc Natl Acad Sci U S A1001300113006
- 15. Brodin P, Rosenkrands I, Andersen P, Cole ST, Brosch R (2004) ESAT-6 proteins: protective antigens and virulence factors? Trends Microbiol 12: 500–508.P. BrodinI. RosenkrandsP. AndersenST ColeR. Brosch2004ESAT-6 proteins: protective antigens and virulence factors?Trends Microbiol12500508
- 16. Abdallah A, Gey van Pittius N, Champion P, Cox J, Luirink J, et al. (2007) Type VII secretion–mycobacteria show the way. Nat Rev Microbiol 5: 883–891.A. AbdallahN. Gey van PittiusP. ChampionJ. CoxJ. Luirink2007Type VII secretion–mycobacteria show the way.Nat Rev Microbiol5883891
- 17. Simeone R, Bottai D, Brosch R (2009) ESX/type VII secretion systems and their role in host-pathogen interaction. Curr Opin Microbiol 12: 4–10.R. SimeoneD. BottaiR. Brosch2009ESX/type VII secretion systems and their role in host-pathogen interaction.Curr Opin Microbiol12410
- 18. Brodin P, de Jonge MI, Majlessi L, Leclerc C, Nilges M, et al. (2005) Functional analysis of early secreted antigenic target-6, the dominant T-cell antigen of Mycobacterium tuberculosis, reveals key residues involved in secretion, complex formation, virulence, and immunogenicity. J Biol Chem 280: 33953–33959.P. BrodinMI de JongeL. MajlessiC. LeclercM. Nilges2005Functional analysis of early secreted antigenic target-6, the dominant T-cell antigen of Mycobacterium tuberculosis, reveals key residues involved in secretion, complex formation, virulence, and immunogenicity.J Biol Chem2803395333959
- 19. Champion PA, Stanley SA, Champion MM, Brown EJ, Cox JS (2006) C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis. Science 313: 1632–1636.PA ChampionSA StanleyMM ChampionEJ BrownJS Cox2006C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis.Science31316321636
- 20. de Jonge MI, Pehau-Arnaudet G, Fretz MM, Romain F, Bottai D, et al. (2007) 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.MI de JongeG. Pehau-ArnaudetMM FretzF. RomainD. Bottai2007ESAT-6 from Mycobacterium tuberculosis dissociates from its putative chaperone CFP-10 under acidic conditions and exhibits membrane-lysing activity.J Bacteriol18960286034
- 21. Smith J, Manoranjan J, Pan M, Bohsali A, Xu J, et al. (2008) Evidence for pore formation in host cell membranes by ESX-1-secreted ESAT-6 and its role in Mycobacterium marinum escape from the vacuole. Infect Immun 76: 5478–5487.J. SmithJ. ManoranjanM. PanA. BohsaliJ. Xu2008Evidence for pore formation in host cell membranes by ESX-1-secreted ESAT-6 and its role in Mycobacterium marinum escape from the vacuole.Infect Immun7654785487
- 22. Carlsson F, Joshi SA, Rangell L, Brown EJ (2009) Polar localization of virulence-related Esx-1 secretion in mycobacteria. PLoS Pathog 5: e1000285.F. CarlssonSA JoshiL. RangellEJ Brown2009Polar localization of virulence-related Esx-1 secretion in mycobacteria.PLoS Pathog5e1000285
- 23. Sorensen AL, Nagai S, Houen G, Andersen P, Andersen AB (1995) Purification and characterization of a low-molecular-mass T-cell antigen secreted by Mycobacterium tuberculosis. Infect Immun 63: 1710–1717.AL SorensenS. NagaiG. HouenP. AndersenAB Andersen1995Purification and characterization of a low-molecular-mass T-cell antigen secreted by Mycobacterium tuberculosis.Infect Immun6317101717
- 24. Harboe M, Oettinger T, Wiker HG, Rosenkrands I, Andersen P (1996) 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.M. HarboeT. OettingerHG WikerI. RosenkrandsP. Andersen1996Evidence for occurrence of the ESAT-6 protein in Mycobacterium tuberculosis and virulent Mycobacterium bovis and for its absence in Mycobacterium bovis BCG.Infect Immun641622
- 25. Mahairas GG, Sabo PJ, Hickey MJ, Singh DC, Stover CK (1996) Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol 178: 1274–1282.GG MahairasPJ SaboMJ HickeyDC SinghCK Stover1996Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis.J Bacteriol17812741282
- 26. Berthet FX, Rasmussen PB, Rosenkrands I, Andersen P, Gicquel B (1998) A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10). Microbiology 144: 3195–3203.FX BerthetPB RasmussenI. RosenkrandsP. AndersenB. Gicquel1998A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10).Microbiology14431953203
- 27. Renshaw PS, Panagiotidou P, Whelan A, Gordon SV, Hewinson RG, et al. (2002) Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1∶1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J Biol Chem 277: 21598–21603.PS RenshawP. PanagiotidouA. WhelanSV GordonRG Hewinson2002Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1∶1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence.J Biol Chem2772159821603
- 28. Renshaw PS, Lightbody KL, Veverka V, Muskett FW, Kelly G, et al. (2005) Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6. Embo J 24: 2491–2498.PS RenshawKL LightbodyV. VeverkaFW MuskettG. Kelly2005Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6.Embo J2424912498
- 29. Lewis KN, Liao R, Guinn KM, Hickey MJ, Smith S, et al. (2003) Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guerin attenuation. J Infect Dis 187: 117–123.KN LewisR. LiaoKM GuinnMJ HickeyS. Smith2003Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guerin attenuation.J Infect Dis187117123
- 30. Hsu T, Hingley-Wilson SM, Chen B, Chen M, Dai AZ, et al. (2003) 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 U S A 100: 12420–12425.T. HsuSM Hingley-WilsonB. ChenM. ChenAZ Dai2003The 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 U S A1001242012425
- 31. Guinn KI, Hickey MJ, Mathur SK, Zakel KL, Grotzke JE, et al. (2004) Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis. Mol Microbiol 51: 359–370.KI GuinnMJ HickeySK MathurKL ZakelJE Grotzke2004Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis.Mol Microbiol51359370
- 32. Pym AS, Brodin P, Brosch R, Huerre M, Cole ST (2002) Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol Microbiol 46: 709–717.AS PymP. BrodinR. BroschM. HuerreST Cole2002Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti.Mol Microbiol46709717
- 33. Brodin P, Majlessi L, Marsollier L, de Jonge MI, Bottai D, et al. (2006) Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence. Infect Immun 74: 88–98.P. BrodinL. MajlessiL. MarsollierMI de JongeD. Bottai2006Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence.Infect Immun748898
- 34. Frigui W, Bottai D, Majlessi L, Monot M, Josselin E, et al. (2008) Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP. PLoS Pathog 4: e33.W. FriguiD. BottaiL. MajlessiM. MonotE. Josselin2008Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP.PLoS Pathog4e33
- 35. Pallen MJ (2002) The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system? Trends Microbiol 10: 209–212.MJ Pallen2002The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system?Trends Microbiol10209212
- 36. Skjot RL, Oettinger T, Rosenkrands I, Ravn P, Brock I, et al. (2000) Comparative evaluation of low-molecular-mass proteins from Mycobacterium tuberculosis identifies members of the ESAT-6 family as immunodominant T-cell antigens. Infect Immun 68: 214–220.RL SkjotT. OettingerI. RosenkrandsP. RavnI. Brock2000Comparative evaluation of low-molecular-mass proteins from Mycobacterium tuberculosis identifies members of the ESAT-6 family as immunodominant T-cell antigens.Infect Immun68214220
- 37. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537–544.ST ColeR. BroschJ. ParkhillT. GarnierC. Churcher1998Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.Nature393537544
- 38. Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, et al. (2006) 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.NC Gey van PittiusSL SampsonH. LeeY. KimPD van Helden2006Evolution 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 Biol695
- 39. Fortune SM, Jaeger A, Sarracino DA, Chase MR, Sassetti CM, et al. (2005) Mutually dependent secretion of proteins required for mycobacterial virulence. Proc Natl Acad Sci U S A 102: 10676–10681.SM FortuneA. JaegerDA SarracinoMR ChaseCM Sassetti2005Mutually dependent secretion of proteins required for mycobacterial virulence.Proc Natl Acad Sci U S A1021067610681
- 40. MacGurn JA, Raghavan S, Stanley SA, Cox JS (2005) A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis. Mol Microbiol 57: 1653–1663.JA MacGurnS. RaghavanSA StanleyJS Cox2005A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis.Mol Microbiol5716531663
- 41. Raghavan S, Manzanillo P, Chan K, Dovey C, Cox J (2008) Secreted transcription factor controls Mycobacterium tuberculosis virulence. Nature 454: 717–721.S. RaghavanP. ManzanilloK. ChanC. DoveyJ. Cox2008Secreted transcription factor controls Mycobacterium tuberculosis virulence.Nature454717721
- 42. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409: 1007–1011.ST ColeK. EiglmeierJ. ParkhillKD JamesNR Thomson2001Massive gene decay in the leprosy bacillus.Nature40910071011
- 43. Gao LY, Guo S, McLaughlin B, Morisaki H, Engel JN, et al. (2004) A mycobacterial virulence gene cluster extending RD1 is required for cytolysis, bacterial spreading and ESAT-6 secretion. Mol Microbiol 53: 1677–1693.LY GaoS. GuoB. McLaughlinH. MorisakiJN Engel2004A mycobacterial virulence gene cluster extending RD1 is required for cytolysis, bacterial spreading and ESAT-6 secretion.Mol Microbiol5316771693
- 44. Tan T, Lee WL, Alexander DC, Grinstein S, Liu J (2006) The ESAT-6/CFP-10 secretion system of Mycobacterium marinum modulates phagosome maturation. Cell Microbiol 8: 1417–1429.T. TanWL LeeDC AlexanderS. GrinsteinJ. Liu2006The ESAT-6/CFP-10 secretion system of Mycobacterium marinum modulates phagosome maturation.Cell Microbiol814171429
- 45. Xu J, Laine O, Masciocchi M, Manoranjan J, Smith J, et al. (2007) 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.J. XuO. LaineM. MasciocchiJ. ManoranjanJ. Smith2007A unique Mycobacterium ESX-1 protein co-secretes with CFP-10/ESAT-6 and is necessary for inhibiting phagosome maturation.Mol Microbiol66787800
- 46. McLaughlin B, Chon JS, MacGurn JA, Carlsson F, Cheng TL, et al. (2007) A mycobacterium ESX-1-secreted virulence factor with unique requirements for export. PLoS Pathog 3: e105.B. McLaughlinJS ChonJA MacGurnF. CarlssonTL Cheng2007A mycobacterium ESX-1-secreted virulence factor with unique requirements for export.PLoS Pathog3e105
- 47. Davis JM, Ramakrishnan L (2009) The role of the granuloma in expansion and dissemination of early tuberculous infection. Cell 136: 37–49.JM DavisL. Ramakrishnan2009The role of the granuloma in expansion and dissemination of early tuberculous infection.Cell1363749
- 48. Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, et al. (2008) Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res 18: 729–741.TP StinearT. SeemannPF HarrisonGA JenkinJK Davies2008Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.Genome Res18729741
- 49. Flint JL, Kowalski JC, Karnati PK, Derbyshire KM (2004) The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis. Proc Natl Acad Sci U S A 101: 12598–12603.JL FlintJC KowalskiPK KarnatiKM Derbyshire2004The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis.Proc Natl Acad Sci U S A1011259812603
- 50. Converse SE, Cox JS (2005) A protein secretion pathway critical for Mycobacterium tuberculosis virulence is conserved and functional in Mycobacterium smegmatis. J Bacteriol 187: 1238–1245.SE ConverseJS Cox2005A protein secretion pathway critical for Mycobacterium tuberculosis virulence is conserved and functional in Mycobacterium smegmatis.J Bacteriol18712381245
- 51. Coros A, Callahan B, Battaglioli E, Derbyshire KM (2008) The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis. Mol Microbiol 69: 794–808.A. CorosB. CallahanE. BattaglioliKM Derbyshire2008The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis.Mol Microbiol69794808
- 52. Abdallah AM, Verboom T, Hannes F, Safi M, Strong M, et al. (2006) A specific secretion system mediates PPE41 transport in pathogenic mycobacteria. Mol Microbiol 62: 667–679.AM AbdallahT. VerboomF. HannesM. SafiM. Strong2006A specific secretion system mediates PPE41 transport in pathogenic mycobacteria.Mol Microbiol62667679
- 53. Abdallah AM, Savage ND, van Zon M, Wilson L, Vandenbroucke-Grauls CM, et al. (2008) The ESX-5 secretion system of Mycobacterium marinum modulates the macrophage response. J Immunol 181: 7166–7175.AM AbdallahND SavageM. van ZonL. WilsonCM Vandenbroucke-Grauls2008The ESX-5 secretion system of Mycobacterium marinum modulates the macrophage response.J Immunol18171667175
- 54. Rodriguez GM, Voskuil MI, Gold B, Schoolnik GK, Smith I (2002) 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.GM RodriguezMI VoskuilB. GoldGK SchoolnikI. Smith2002ideR, An essential gene in Mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response.Infect Immun7033713381
- 55. Maciag A, Dainese E, Rodriguez GM, Milano A, Provvedi R, et al. (2007) Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J Bacteriol 189: 730–740.A. MaciagE. DaineseGM RodriguezA. MilanoR. Provvedi2007Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon.J Bacteriol189730740
- 56. Sassetti CM, Boyd DH, Rubin EJ (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48: 77–84.CM SassettiDH BoydEJ Rubin2003Genes required for mycobacterial growth defined by high density mutagenesis.Mol Microbiol487784
- 57. Burts ML, Williams WA, Debord K, Missiakas DM (2005) 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 U S A 102: 1169–1174.ML BurtsWA WilliamsK. DebordDM Missiakas2005EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections.Proc Natl Acad Sci U S A10211691174
- 58. Garufi G, Butler E, Missiakas D (2008) ESAT-6-like protein secretion in Bacillus anthracis. J Bacteriol 190: 7004–7011.G. GarufiE. ButlerD. Missiakas2008ESAT-6-like protein secretion in Bacillus anthracis.J Bacteriol19070047011
- 59. Brown GD, Dave JA, Gey van Pittius NC, Stevens L, Ehlers MR, et al. (2000) The mycosins of Mycobacterium tuberculosis H37Rv: a family of subtilisin-like serine proteases. Gene 254: 147–155.GD BrownJA DaveNC Gey van PittiusL. StevensMR Ehlers2000The mycosins of Mycobacterium tuberculosis H37Rv: a family of subtilisin-like serine proteases.Gene254147155
- 60. Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23: 538–544.DT Jones2007Improving the accuracy of transmembrane protein topology prediction using evolutionary information.Bioinformatics23538544