27. Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, et al. (2006) Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci USA 103: 8060–8065. 28. Cascales E, Christie PJ (2003) The versatile bacterial Type IV secretion systems. Nature Rev Microbiol 1: 137–149. 29. Filloux A (2004) The underlying mechanisms of type II protein secretion. Biochimica et Biophysica Acta 1694: 163–179. 30. Henderson IR, Navarro-Garcia F, Desvaux M, Fernandez RC, Ala’Aldeen D (2004) Type V secretion pathway: the autotransporter story. Micribiol Mol Biol Rev 68: 692–744. 31. Daugelat S, Kowall J, Mattow J, Bumann D, Winter R, et al. (2003) The RD1proteins of Mycobacterium tuberculosis: expression in Mycobacterium smegmatis and biochemical characterization. Microbes Infect 5: 1082–1095. 32. Schmidt H, Hensel M (2004) Pathogenicity Islands in Bacterial Pathogenesis. Clin Microbiol Rev 17: 14–56. 33. Rajan I, Aravamuthan S, Mande SS (2007) Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics 23: 2672–2677. 34. Liu XQ, Dosanjh D, Varia H, Ewer K, Cockle P, et al. (2004) Evaluation of T- cell responses to novel RD1- and RD2-encoded Mycobacterium tuberculosis gene products for specific detection of human tuberculosis infection. Infect Immun 72: 2574–2581. 35. Geiman DE, Raghunand TR, Agarwal N, Bishai WR (2006) Differential Gene Expression in Response to Antimycobacterial Agents and Other Stress Conditions among Seven Mycobacterium tuberculosis whiB-like genes. Antimicrobial Agents and Chemotherapy 50: 2836–2841. 36. Steyn AJ, Collins DM, Hondalus MK, Jacobs WR, Jr., Kawakami RP, et al. (2002) Mycobacterium tuberculosis WhiB3 interacts with RpoV to affect host survival but is dispensable for in vivo growth. Proc Natl Acad Sci USA 99: 3147–3152. 37. Rhode KH, Abramovitch RV, Russell DG (2007) Mycobacterium tuberculosis Invasion of macrophages: Linking bacterial Gene expression to Environmental Cues. Cell Host Microbe 2: 352–364. 38. 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. 39. 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 ONE 4: e33. doi:10.1371/journal.ppat.0040033. 40. Shrivastava S, Mande SS (2008) Identification and Functional Characterization of Gene Components of Type VI Secretion System in Bacterial Genomes. PLoS ONE 3: e2955. doi: 10.1371/journal. Pone.0002955. 41. Champion PADG, Champion MM, Manzanillo P, Cox JS (2009) ESX-1 secreted virulence factors are recognized by multiple cytosolic AAA ATPases in pathogenic mycobacteria. Mol Microbiol 73: 950–962. 42. Massey TH, Mercogliano CP, Yates J, Sherratt DJ, Lowe J (2006) Double- Stranded DNA Translocation: Structure and Mechanism of Hexameric FtsK. Molecular Cell 23: 457–469. 43. Rich A, Nordheim A, Wanj AH (1984) The chemistry and biology of left handed Z-DNA. Ann Rev Biochem 53: 791–846. Model of Type VII Secretion System 44. Ho PS (1994) The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc Natl Acad Sci USA 91: 9549–9553. 45. Stahl C, Kubetzko S, Kaps I, Seeber S, Engelhardt H, et al. (2001) MspA provides the main hydrophilic pathway through the cell wall of Mycobacterium smegmatis. Mol Microbiol 40: 451–464. 46. Siroy A, Mailaender C, Harder D, Koerber S, Wolschendorf F, et al. (2008) Rv1698 of Mycobacterium tuberculosis represents a new class of channel- forming outer membrane proteins. J Biol Chem 283: 17827–17837. 47. Song H, Sandie R, Wang Y, Andrade-Navarro MA, Niederweis M (2008) Identification of outer membrane proteins of Mycobacterium tuberculosis. Tuber- culosis (Edinb) 88: 526–544. 48. Mah N, Perez-Iratxeta C, Andrade-Navarro MA (2010) Outer membrane pore protein prediction in mycobacteria using genomic comparison. Microbiology 156: 2506–2515. 49. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410. 50. Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, et al. (2002) Prodom: automated clustering of homologous domains. Brief Bioinform 3: 246–251. 51. Marchler-Bauer A, Bryant SH (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32: W327–W331. 52. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33: W116–W120. 53. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. J Mol Biol 305: 567–580. 54. Hofmann K, Stoffel W (1993) TMbase - A database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 374: 166. 55. HirokawaT, Boon-Chieng S, Mitaku S (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14: 378–379. 56. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33: W244–W248. 57. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–795. 58. Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, et al. (1998) NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycocon J 15: 115–130. 59. Dell A, Galadari A, Sastre F, Hitchen P (2010) Similarities and differences in glycosylation mechanisms in prokaryotes and eukaryotes. Int J Microbiol 2010: 148178. doi: 10.1155/2010/148178. 60. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680. 61. Shrivastava S, Reddy CVSK, Mande SS (2010) INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms. J Biosci 35: 351–364. PLoS ONE | www.plosone.org 12 November 2011 | Volume 6 | Issue 11 | e27980