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Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria

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Abstract

Bacterial lipoproteins are a diverse and functionally important group of proteins that are amenable to bioinformatic analyses because of their unique signal peptide features. Here we have used a dataset of sequences of experimentally verified lipoproteins of Gram-positive bacteria to refine our previously described lipoprotein recognition pattern (G+LPP). Sequenced bacterial genomes can be screened for putative lipoproteins using the G+LPP pattern. The sequences identified can then be validated using online tools for lipoprotein sequence identification. We have used our protein sequence datasets to evaluate six online tools for efficacy of lipoprotein sequence identification. Our analyses demonstrate that LipoP (http://www.cbs.dtu.dk/services/LipoP/) performs best individually but that a consensus approach, incorporating outputs from predictors of general signal peptide properties, is most informative.

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References

  • Babu M, Sankaran K (2002) DOLOP—database of bacterial lipoproteins. Bioinformatics 18:641–643. doi:10.1093/bioinformatics/18.4.641

    Article  CAS  Google Scholar 

  • Babu MM, Priya ML, Selvan AT, Madera M, Gough J, Aravind L et al (2006) A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol 188:2761–2773. doi:10.1128/JB.188.8.2761-2773.2006

    Article  CAS  Google Scholar 

  • Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S et al (2005) The universal protein resource (UniProt). Nucleic Acids Res 33:D154–D159. doi:10.1093/nar/gki070

    Article  CAS  Google Scholar 

  • Baumgärtner M, Kärst U, Gerstel B, Loessner M, Wehland J, Jänsch L (2006) Inactivation of Lgt allows systematic characterization of lipoproteins from Listeria monocytogenes. J Bacteriol 189:313–324. doi:10.1128/JB.00976-06

    Article  CAS  Google Scholar 

  • Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795. doi:10.1016/j.jmb.2004.05.028

    Article  CAS  Google Scholar 

  • Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW (2005) Genome update: prediction of secreted proteins in 225 bacterial proteomes. Microbiology 151:1725–1727. doi:10.1099/mic.0.28029-0

    Article  CAS  Google Scholar 

  • Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A et al (2006) Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Arch Microbiol 184:362–377. doi:10.1007/s00203-005-0055-7

    Article  CAS  Google Scholar 

  • Braun V, Wu HC (1994) Lipoproteins: structure function, biosynthesis and model for protein export. N Comp Biochem 27:319–341

    Article  CAS  Google Scholar 

  • De Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E et al (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34:W362-W365. doi:10.1093/nar/gkl124

    Article  CAS  Google Scholar 

  • Fariselli P, Finocchiaro G, Casadio R (2003) SPEPLip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19:2498–2499. doi:10.1093/bioinformatics/btg360

    Article  CAS  Google Scholar 

  • Gardy JL, Brinkman FSL (2006) Methods for predicting bacterial protein subcellular localisation. Nat Rev Microbiol 4:741–751. doi:10.1038/nrmicro1494

    Article  CAS  Google Scholar 

  • Juncker AS, Willenbrock H, von Heijne G, Nielsen H, Brunak S, Krogh A (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12:1652–1662. doi:10.1110/ps.0303703

    Article  CAS  Google Scholar 

  • Käll L, Krogh A, Sonnhammer ELL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338:1027–1036. doi:10.1016/j.jmb.2004.03.016

    Article  CAS  Google Scholar 

  • Klein P, Somorjai RL, Lau PCK (1988) Distinctive properties of signal sequences from bacterial lipoproteins. Protein Eng 2:15–20. doi:10.1093/protein/2.1.15

    Article  CAS  Google Scholar 

  • Nakai K, Horton P (1999) PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization. Trends Biochem Sci 24:34–35. doi:10.1016/S0968-0004(98)01336-X

    Article  CAS  Google Scholar 

  • Nielsen H, Krogh A (1998) Prediction of signal peptides and signal anchors by a hidden Markov model. In: Proceedings of the sixth international conference on intelligent systems for molecular biology (ISMB 6), AAAI Press, Menlo Park, California, pp 122–130

  • Réglier-Poupet H, Frehel C, Dubail I, Beretti JL, Berche P, Charbit A, Raynaud C (2003) Maturation of lipoproteins by type II signal peptidase is required for phagosomal escape of Listeria monocytogenes. J Biol Chem 278:49469–49477

    Article  CAS  Google Scholar 

  • Setubal JC, Reis M, Matsunaga J, Haake DA (2006) Lipoprotein computational prediction in spriochaetal genomes. Microbiology 152:113–121. doi:10.1099/mic.0.28317-0

    Article  CAS  Google Scholar 

  • Sutcliffe IC, Harrington DJ (2002) Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes. Microbiology 148:2065–2077

    CAS  Google Scholar 

  • Sutcliffe IC, Harrington DJ (2004) Lipoproteins of Mycobacterium tuberculosis: an abundant and functionally diverse class of cell envelope components. FEMS Microbiol Rev 28:645–659. doi:10.1016/j.femsre.2004.06.002

    Article  CAS  Google Scholar 

  • Sutcliffe IC, Hutchings MI (2007) Putative lipoproteins identified by bioinformatic genome analysis of Leifsonia xyli subsp. xyli, the causative agent of sugarcane ratoon stunting disease. Mol Plant Pathol 8:121–128. doi:10.1111/j.1364-3703.2006.00377.x

    Article  CAS  Google Scholar 

  • Sutcliffe IC, Russell RRB (1995) Lipoproteins of Gram-positive bacteria. J Bacteriol 177:1123–1128

    CAS  Google Scholar 

  • Sutcliffe IC, Tao L, Ferretti JJ, Russell RRB (1993) MsmE, a lipoprotein involved in sugar transport in Streptococcus mutans. J Bacteriol 175:1853–1855

    CAS  Google Scholar 

  • Taylor PD, Toseland CP, Attwood CK, Flower DR (2006) LIPPRED: a web server for accurate prediction of lipoprotein signal sequences and cleavage sites. Bioinformation 1:176–179

    Google Scholar 

  • Tjalsma H, Zanen G, Venema G, Bron S, van Dijl JM (1999) The potential active site of the lipoprotein-specific (type II) signal peptidase of Bacillus subtilis. J Biol Chem 274:28191–28197. doi:10.1074/jbc.274.40.28191

    Article  CAS  Google Scholar 

  • Von Heijne G (1989) The structure of signal peptides from bacterial lipoproteins. Protein Eng 2:531–534. doi:10.1093/protein/2.7.531

    Article  Google Scholar 

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Acknowledgement

The authors thank Northumbria University for financial support from the ‘Research into Teaching’ programme.

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Authors and Affiliations

  1. Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

    Obaidur Rahman, Stephen P. Cummings & Iain C. Sutcliffe

  2. University of Bradford, West Yorkshire, BD7 1DP, UK

    Dean J. Harrington

  3. Biomolecular and Biomedical Research Centre, School of Applied Science, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

    Iain C. Sutcliffe

Authors
  1. Obaidur Rahman
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  2. Stephen P. Cummings
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  3. Dean J. Harrington
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  4. Iain C. Sutcliffe
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Correspondence to Iain C. Sutcliffe.

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Rahman, O., Cummings, S.P., Harrington, D.J. et al. Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria. World J Microbiol Biotechnol 24, 2377–2382 (2008). https://doi.org/10.1007/s11274-008-9795-2

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  • DOI: https://doi.org/10.1007/s11274-008-9795-2

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