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Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.

Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Yanju Z, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T.

Bioinformatics. 2018 Mar 14. doi: 10.1093/bioinformatics/bty155. [Epub ahead of print]


Correction for Nguyen et al., "Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers".

Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, Schlosser K, Bailey B, Lithgow T, Lazarou M, Luque A, Rohwer F, Blumberg RS, Barr JJ.

MBio. 2018 Jan 2;9(1). pii: e02207-17. doi: 10.1128/mBio.02207-17. No abstract available.


Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.

Wang J, Yang B, An Y, Marquez-Lago T, Leier A, Wilksch J, Hong Q, Zhang Y, Hayashida M, Akutsu T, Webb GI, Strugnell RA, Song J, Lithgow T.

Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx164. [Epub ahead of print]


Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers.

Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, Schlosser K, Bailey B, Lithgow T, Lazarou M, Luque A, Rohwer F, Blumberg RS, Barr JJ.

MBio. 2017 Nov 21;8(6). pii: e01874-17. doi: 10.1128/mBio.01874-17. Erratum in: MBio. 2018 Jan 2;9(1):.


Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

Stubenrauch CJ, Dougan G, Lithgow T, Heinz E.

Open Biol. 2017 Nov;7(11). pii: 170144. doi: 10.1098/rsob.170144.


The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.

Josts I, Stubenrauch CJ, Vadlamani G, Mosbahi K, Walker D, Lithgow T, Grinter R.

Structure. 2017 Dec 5;25(12):1898-1906.e5. doi: 10.1016/j.str.2017.10.002. Epub 2017 Nov 9.


Structure and Membrane Topography of the Vibrio-Type Secretin Complex from the Type 2 Secretion System of Enteropathogenic Escherichia coli.

Hay ID, Belousoff MJ, Dunstan RA, Bamert RS, Lithgow T.

J Bacteriol. 2018 Feb 7;200(5). pii: e00521-17. doi: 10.1128/JB.00521-17. Print 2018 Mar 1.


Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori.

Webb CT, Chandrapala D, Oslan SN, Bamert RS, Grinter RD, Dunstan RA, Gorrell RJ, Song J, Strugnell RA, Lithgow T, Kwok T.

Microbiologyopen. 2017 Dec;6(6). doi: 10.1002/mbo3.513. Epub 2017 Oct 21.


Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, Keane JA, Lithgow T, Ul-Haq I, Dougan G, Strugnell RA, Heinz E.

Emerg Infect Dis. 2017 Nov;23(11):1872-1875. doi: 10.3201/eid2311.170833.


Structural Basis of Type 2 Secretion System Engagement between the Inner and Outer Bacterial Membranes.

Hay ID, Belousoff MJ, Lithgow T.

MBio. 2017 Oct 17;8(5). pii: e01344-17. doi: 10.1128/mBio.01344-17.


The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex.

Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, Tsukazaki T, Narita SI, Akiyama Y.

Mol Microbiol. 2017 Dec;106(5):760-776. doi: 10.1111/mmi.13844. Epub 2017 Oct 17.


POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.

Wang J, Yang B, Revote J, Leier A, Marquez-Lago TT, Webb G, Song J, Chou KC, Lithgow T.

Bioinformatics. 2017 Sep 1;33(17):2756-2758. doi: 10.1093/bioinformatics/btx302.


Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery.

Bamert RS, Lundquist K, Hwang H, Webb CT, Shiota T, Stubenrauch CJ, Belousoff MJ, Goode RJA, Schittenhelm RB, Zimmerman R, Jung M, Gumbart JC, Lithgow T.

Mol Microbiol. 2017 Oct;106(1):142-156. doi: 10.1111/mmi.13757. Epub 2017 Aug 9.


Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB.

Sci Rep. 2017 Jul 18;7(1):5755. doi: 10.1038/s41598-017-06219-7.


Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes.

Bi W, Liu H, Dunstan RA, Li B, Torres VVL, Cao J, Chen L, Wilksch JJ, Strugnell RA, Lithgow T, Zhou T.

Front Microbiol. 2017 Jun 30;8:1230. doi: 10.3389/fmicb.2017.01230. eCollection 2017.


Defining Membrane Protein Localization by Isopycnic Density Gradients.

Dunstan RA, Hay ID, Lithgow T.

Methods Mol Biol. 2017;1615:81-86. doi: 10.1007/978-1-4939-7033-9_6.


Super-Resolution Imaging of Protein Secretion Systems and the Cell Surface of Gram-Negative Bacteria.

Gunasinghe SD, Webb CT, Elgass KD, Hay ID, Lithgow T.

Front Cell Infect Microbiol. 2017 May 29;7:220. doi: 10.3389/fcimb.2017.00220. eCollection 2017. Review.


Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome.

Belousoff MJ, Eyal Z, Radjainia M, Ahmed T, Bamert RS, Matzov D, Bashan A, Zimmerman E, Mishra S, Cameron D, Elmlund H, Peleg AY, Bhushan S, Lithgow T, Yonath A.

MBio. 2017 May 9;8(3). pii: e00395-17. doi: 10.1128/mBio.00395-17.


SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems.

An Y, Wang J, Li C, Revote J, Zhang Y, Naderer T, Hayashida M, Akutsu T, Webb GI, Lithgow T, Song J.

Sci Rep. 2017 Jan 23;7:41031. doi: 10.1038/srep41031.


Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.

An Y, Wang J, Li C, Leier A, Marquez-Lago T, Wilksch J, Zhang Y, Webb GI, Song J, Lithgow T.

Brief Bioinform. 2018 Jan 1;19(1):148-161. doi: 10.1093/bib/bbw100.


GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features.

Li F, Li C, Revote J, Zhang Y, Webb GI, Li J, Song J, Lithgow T.

Sci Rep. 2016 Oct 6;6:34595. doi: 10.1038/srep34595.


The modular nature of the β-barrel assembly machinery, illustrated in Borrelia burgdorferi.

Stubenrauch C, Grinter R, Lithgow T.

Mol Microbiol. 2016 Dec;102(5):753-756. doi: 10.1111/mmi.13527. Epub 2016 Sep 30.


Effective assembly of fimbriae in Escherichia coli depends on the translocation assembly module nanomachine.

Stubenrauch C, Belousoff MJ, Hay ID, Shen HH, Lillington J, Tuck KL, Peters KM, Phan MD, Lo AW, Schembri MA, Strugnell RA, Waksman G, Lithgow T.

Nat Microbiol. 2016 May 16;1(7):16064. doi: 10.1038/nmicrobiol.2016.64.


Eliminating Legionella by inhibiting BCL-XL to induce macrophage apoptosis.

Speir M, Lawlor KE, Glaser SP, Abraham G, Chow S, Vogrin A, Schulze KE, Schuelein R, O'Reilly LA, Mason K, Hartland EL, Lithgow T, Strasser A, Lessene G, Huang DC, Vince JE, Naderer T.

Nat Microbiol. 2016 Feb 24;1:15034. doi: 10.1038/nmicrobiol.2015.34.


Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family.

Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW, Strugnell RA, Dougan G, Lithgow T.

Genome Biol Evol. 2016 Jun 13;8(6):1690-705. doi: 10.1093/gbe/evw112.


Antibiotic regimen based on population analysis of residing persister cells eradicates Staphylococcus epidermidis biofilms.

Yang S, Hay ID, Cameron DR, Speir M, Cui B, Su F, Peleg AY, Lithgow T, Deighton MA, Qu Y.

Sci Rep. 2015 Dec 21;5:18578. doi: 10.1038/srep18578.


Identification of BamC on the Surface of E. coli.

Webb CT, Lithgow T.

Methods Mol Biol. 2015;1329:215-25. doi: 10.1007/978-1-4939-2871-2_17.


The β-Barrel Assembly Machinery Complex.

Leyton DL, Belousoff MJ, Lithgow T.

Methods Mol Biol. 2015;1329:1-16. doi: 10.1007/978-1-4939-2871-2_1. Review.


Molecular architecture of the active mitochondrial protein gate.

Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T.

Science. 2015 Sep 25;349(6255):1544-8. doi: 10.1126/science.aac6428.


Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40.

Kuszak AJ, Jacobs D, Gurnev PA, Shiota T, Louis JM, Lithgow T, Bezrukov SM, Rostovtseva TK, Buchanan SK.

J Biol Chem. 2015 Oct 23;290(43):26204-17. doi: 10.1074/jbc.M115.642173. Epub 2015 Sep 2.


Conserved features in TamA enable interaction with TamB to drive the activity of the translocation and assembly module.

Selkrig J, Belousoff MJ, Headey SJ, Heinz E, Shiota T, Shen HH, Beckham SA, Bamert RS, Phan MD, Schembri MA, Wilce MC, Scanlon MJ, Strugnell RA, Lithgow T.

Sci Rep. 2015 Aug 5;5:12905. doi: 10.1038/srep12905.


Evolution of the Translocation and Assembly Module (TAM).

Heinz E, Selkrig J, Belousoff MJ, Lithgow T.

Genome Biol Evol. 2015 May 20;7(6):1628-43. doi: 10.1093/gbe/evv097.


Assembly of the secretion pores GspD, Wza and CsgG into bacterial outer membranes does not require the Omp85 proteins BamA or TamA.

Dunstan RA, Hay ID, Wilksch JJ, Schittenhelm RB, Purcell AW, Clark J, Costin A, Ramm G, Strugnell RA, Lithgow T.

Mol Microbiol. 2015 Aug;97(4):616-29. doi: 10.1111/mmi.13055. Epub 2015 Jun 6.


Positive autoregulation of mrkHI by the cyclic di-GMP-dependent MrkH protein in the biofilm regulatory circuit of Klebsiella pneumoniae.

Tan JW, Wilksch JJ, Hocking DM, Wang N, Srikhanta YN, Tauschek M, Lithgow T, Robins-Browne RM, Yang J, Strugnell RA.

J Bacteriol. 2015 May;197(9):1659-67. doi: 10.1128/JB.02615-14. Epub 2015 Mar 2.


Mitochondrial biogenesis: cell-cycle-dependent investment in making mitochondria.

Shiota T, Traven A, Lithgow T.

Curr Biol. 2015 Jan 19;25(2):R78-80. doi: 10.1016/j.cub.2014.12.006.


Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion.

Drobnak I, Braselmann E, Chaney JL, Leyton DL, Bernstein HD, Lithgow T, Luirink J, Nataro JP, Clark PL.

Mol Microbiol. 2015 Jan;95(1):1-16. doi: 10.1111/mmi.12838. Epub 2014 Nov 24. Review.


Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes.

Shen HH, Leyton DL, Shiota T, Belousoff MJ, Noinaj N, Lu J, Holt SA, Tan K, Selkrig J, Webb CT, Buchanan SK, Martin LL, Lithgow T.

Nat Commun. 2014 Oct 24;5:5078. doi: 10.1038/ncomms6078.


A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution.

Heinz E, Lithgow T.

Front Microbiol. 2014 Jul 21;5:370. doi: 10.3389/fmicb.2014.00370. eCollection 2014.


A mortise-tenon joint in the transmembrane domain modulates autotransporter assembly into bacterial outer membranes.

Leyton DL, Johnson MD, Thapa R, Huysmans GH, Dunstan RA, Celik N, Shen HH, Loo D, Belousoff MJ, Purcell AW, Henderson IR, Beddoe T, Rossjohn J, Martin LL, Strugnell RA, Lithgow T.

Nat Commun. 2014 Jun 26;5:4239. doi: 10.1038/ncomms5239.


Efficient construction of unmarked recombinant mycobacteria using an improved system.

Yang F, Tan Y, Liu J, Liu T, Wang B, Cao Y, Qu Y, Lithgow T, Tan S, Zhang T.

J Microbiol Methods. 2014 Aug;103:29-36. doi: 10.1016/j.mimet.2014.05.007. Epub 2014 May 27.


Transcriptional activation of the mrkA promoter of the Klebsiella pneumoniae type 3 fimbrial operon by the c-di-GMP-dependent MrkH protein.

Yang J, Wilksch JJ, Tan JW, Hocking DM, Webb CT, Lithgow T, Robins-Browne RM, Strugnell RA.

PLoS One. 2013 Nov 14;8(11):e79038. doi: 10.1371/journal.pone.0079038. eCollection 2013.


Emerging rules for effective antimicrobial coatings.

Salwiczek M, Qu Y, Gardiner J, Strugnell RA, Lithgow T, McLean KM, Thissen H.

Trends Biotechnol. 2014 Feb;32(2):82-90. doi: 10.1016/j.tibtech.2013.09.008. Epub 2013 Oct 28. Review.


Assembly of β-barrel proteins into bacterial outer membranes.

Selkrig J, Leyton DL, Webb CT, Lithgow T.

Biochim Biophys Acta. 2014 Aug;1843(8):1542-50. doi: 10.1016/j.bbamcr.2013.10.009. Epub 2013 Oct 14. Review.


Structural insight into the biogenesis of β-barrel membrane proteins.

Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, Buchanan SK.

Nature. 2013 Sep 19;501(7467):385-90. doi: 10.1038/nature12521. Epub 2013 Sep 1.


Seaside transportation--from structure to function of translocation machines.

Lithgow T, Waksman G.

EMBO Rep. 2013 Jul;14(7):585-7. doi: 10.1038/embor.2013.79. Epub 2013 Jun 14.


Self-assembly of ciprofloxacin and a tripeptide into an antimicrobial nanostructured hydrogel.

Marchesan S, Qu Y, Waddington LJ, Easton CD, Glattauer V, Lithgow TJ, McLean KM, Forsythe JS, Hartley PG.

Biomaterials. 2013 May;34(14):3678-87. doi: 10.1016/j.biomaterials.2013.01.096. Epub 2013 Feb 17.


Reconstitution of membrane proteins into model membranes: seeking better ways to retain protein activities.

Shen HH, Lithgow T, Martin L.

Int J Mol Sci. 2013 Jan 14;14(1):1589-607. doi: 10.3390/ijms14011589. Review.


Assembly of the type II secretion system such as found in Vibrio cholerae depends on the novel Pilotin AspS.

Dunstan RA, Heinz E, Wijeyewickrema LC, Pike RN, Purcell AW, Evans TJ, Praszkier J, Robins-Browne RM, Strugnell RA, Korotkov KV, Lithgow T.

PLoS Pathog. 2013 Jan;9(1):e1003117. doi: 10.1371/journal.ppat.1003117. Epub 2013 Jan 10.


A model system for mitochondrial biogenesis reveals evolutionary rewiring of protein import and membrane assembly pathways.

Hewitt VL, Heinz E, Shingu-Vazquez M, Qu Y, Jelicic B, Lo TL, Beilharz TH, Dumsday G, Gabriel K, Traven A, Lithgow T.

Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):E3358-66. doi: 10.1073/pnas.1206345109. Epub 2012 Nov 14.


Evolution of the β-barrel assembly machinery.

Webb CT, Heinz E, Lithgow T.

Trends Microbiol. 2012 Dec;20(12):612-20. doi: 10.1016/j.tim.2012.08.006. Epub 2012 Sep 6. Review.


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