Genome-wide protein localization prediction strategies for gram negative bacteria

BMC Genomics

Volumn 12, Issue SUPPL. 1, 2011, Pages

  Romine, Margaret F ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; LIPOPROTEIN; PROTEIN LIPOP; PROTEIN TATP; SIGNAL PEPTIDE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL SECRETION SYSTEM; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; GENE TRANSLOCATION; GENETIC ANALYSIS; GRAM NEGATIVE BACTERIUM; NONHUMAN; ORTHOLOGY; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN PROCESSING; SHEWANELLA; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; GENETICS; METABOLISM; METHODOLOGY; PROTEIN TERTIARY STRUCTURE; PROTEIN TRANSPORT; PROTEOMICS;

NEGIBACTERIA; SHEWANELLA;

ARGININE; BACTERIAL PROTEINS; BACTERIAL SECRETION SYSTEMS; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; GRAM-NEGATIVE BACTERIA; LIPOPROTEINS; MODELS, GENETIC; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT; PROTEOMICS; SHEWANELLA;

EID: 79958812659     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S1-S1     Document Type: Article

References (69)

1. Myers CR, Myers JM. Localization of cytochromes to the outer membrane of anaerobically grown Shewanella putrefaciens MR-1. J Bacteriol 1992, 174(11):3429-3438. 206023, 1592800.
2. Driessen AJ, Nouwen N. Protein translocation across the bacterial cytoplasmic membrane. Annu Rev Biochem 2008, 77:643-667. 10.1146/annurev.biochem.77.061606.160747, 18078384.
3. Sargent F. The twin-arginine transport system: moving folded proteins across membranes. Biochem Soc Trans 2007, 35(Pt 5):835-847.
4. Wang F, Li Q, Xiao X. A novel filamentous phage from the deep-sea bacterium Shewanella piezotolerans WP3 is induced at low temperature. J Bacteriol 2007, 189(19):7151-7153. 10.1128/JB.00569-07, 2045225, 17660281.
5. Qiu X, Sundin GW, Wu L, Zhou J, Tiedje JM. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation. J Bacteriol 2005, 187(10):3556-3564. 10.1128/JB.187.10.3556-3564.2005, 1111996, 15866945.
6. Karpinets TV, Obraztsova AY, Wang Y, Schmoyer DD, Kora GH, Park BH, Serres MH, Romine MF, Land ML, Kothe TB, et al. Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes. Funct Integr Genomics 2010, 10(1):97-110. 10.1007/s10142-009-0142-y, 2834769, 19802638.
7. Yeates TO, Crowley CS, Tanaka S. Bacterial microcompartment organelles: protein shell structure and evolution. Annu Rev Biophys 2010, 39:185-205. 10.1146/annurev.biophys.093008.131418, 20192762.
8. Hatfull GF. Bacteriophage genomics. Curr Opin Microbiol 2008, 11(5):447-453. 10.1016/j.mib.2008.09.004, 2706577, 18824125.
9. Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 2010, 38(Database issue):D57-61. 2808911, 19933762.
10. du Plessis DJ, Nouwen N, Driessen AJ. The Sec translocase. Biochim Biophys Acta 2010,
11. Knowles TJ, Scott-Tucker A, Overduin M, Henderson IR. Membrane protein architects: the role of the BAM complex in outer membrane protein assembly. Nat Rev Microbiol 2009, 7(3):206-214. 10.1038/nrmicro2069, 19182809.
12. Narita S, Tokuda H. An ABC transporter mediating the membrane detachment of bacterial lipoproteins depending on their sorting signals. FEBS Lett 2006, 580(4):1164-1170. 10.1016/j.febslet.2005.10.038, 16288742.
13. Young I, Wang I, Roof WD. Phages will out: strategies of host cell lysis. Trends Microbiol 2000, 8(3):120-128. 10.1016/S0966-842X(00)01705-4, 10707065.
14. Desvaux M, Hebraud M, Talon R, Henderson IR. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol 2009, 17(4):139-145. 10.1016/j.tim.2009.01.004, 19299134.
15. Nakashima H, Nishikawa K. Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. J Mol Biol 1994, 238(1):54-61. 10.1006/jmbi.1994.1267, 8145256.
16. Dueholm MS, Petersen SV, Sonderkaer M, Larsen P, Christiansen G, Hein KL, Enghild JJ, Nielsen JL, Nielsen KL, Nielsen PH, et al. Functional amyloid in Pseudomonas. Mol Microbiol 2010,
17. Dautin N, Bernstein HD. Protein secretion in gram-negative bacteria via the autotransporter pathway. Annu Rev Microbiol 2007, 61:89-112. 10.1146/annurev.micro.61.080706.093233, 17506669.
18. Salacha R, Kovacic F, Brochier-Armanet C, Wilhelm S, Tommassen J, Filloux A, Voulhoux R, Bleves S. The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system. Environ Microbiol 2010, 12(6):1498-1512.
19. Hiss JA, Schneider G. Domain organization of long autotransporter signal sequences. Bioinform Biol Insights 2009, 3:189-204. 2805444, 20072671.
20. Desvaux M, Cooper LM, Filenko NA, Scott-Tucker A, Turner SM, Cole JA, Henderson IR. The unusual extended signal peptide region of the type V secretion system is phylogenetically restricted. FEMS Microbiol Lett 2006, 264(1):22-30. 10.1111/j.1574-6968.2006.00425.x, 17020545.
21. von Heijne G. The signal peptide. J Membr Biol 1990, 115(3):195-201. 10.1007/BF01868635, 2197415.
22. Tuteja R. Type I signal peptidase: an overview. Arch Biochem Biophys 2005, 441(2):107-111. 10.1016/j.abb.2005.07.013, 16126156.
23. Hayashi S, Wu HC. Lipoproteins in bacteria. J Bioenerg Biomembr 1990, 22(3):451-471. 10.1007/BF00763177, 2202727.
24. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340(4):783-795. 10.1016/j.jmb.2004.05.028, 15223320.
25. Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 1998, 6:122-130.
26. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10(1):1-6. 10.1093/protein/10.1.1, 9051728.
27. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 2010, 26(13):1608-1615. 10.1093/bioinformatics/btq249, 2887053, 20472543.
28. Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 2003, 12(8):1652-1662. 10.1110/ps.0303703, 2323952, 12876315.
29. Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A, Lillehaug JR, Eidhammer I, Jensen HB. Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Arch Microbiol 2006, 184(6):362-377. 10.1007/s00203-005-0055-7, 16311759.
30. Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S. Prediction of twin-arginine signal peptides. BMC Bioinformatics 2005, 6:167. 10.1186/1471-2105-6-167, 1182353, 15992409.
31. Palmer T, Sargent F, Berks BC. Export of complex cofactor-containing proteins by the bacterial Tat pathway. Trends Microbiol 2005, 13(4):175-180. 10.1016/j.tim.2005.02.002, 15817387.
32. Gralnick JA, Vali H, Lies DP, Newman DK. Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1. Proc Natl Acad Sci U S A 2006, 103(12):4669-4674. 10.1073/pnas.0505959103, 1450229, 16537430.
33. Saltikov CW, Newman DK. Genetic identification of a respiratory arsenate reductase. Proc Natl Acad Sci U S A 2003, 100(19):10983-10988. 10.1073/pnas.1834303100, 196913, 12939408.
34. Rose RW, Bruser T, Kissinger JC, Pohlschroder M. Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway. Mol Microbiol 2002, 45(4):943-950. 10.1046/j.1365-2958.2002.03090.x, 12180915.
35. Babu MM, Priya ML, Selvan AT, Madera M, Gough J, Aravind L, Sankaran K. A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol 2006, 188(8):2761-2773. 10.1128/JB.188.8.2761-2773.2006, 1446993, 16585737.
36. Shruthi H, Babu MM, Sankaran K. TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes. J Mol Evol 2010, 70(4):359-370. 10.1007/s00239-010-9334-2, 20333370.
37. Rodrigue A, Chanal A, Beck K, Muller M, Wu LF. Co-translocation of a periplasmic enzyme complex by a hitchhiker mechanism through the bacterial tat pathway. J Biol Chem 1999, 274(19):13223-13228. 10.1074/jbc.274.19.13223, 10224080.
38. Rawlings ND. A large and accurate collection of peptidase cleavages in the MEROPS database. Database (Oxford) 2009, bap015. 2790309, 20157488.
39. Dirix G, Monsieurs P, Dombrecht B, Daniels R, Marchal K, Vanderleyden J, Michiels J. Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters. Peptides 2004, 25(9):1425-1440. 10.1016/j.peptides.2003.10.028, 15374646.
40. Romine MF, Carlson TS, Norbeck AD, McCue LA, Lipton MS. Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome. Appl Environ Microbiol 2008, 74(10):3257-3265. 10.1128/AEM.02720-07, 2394961, 18378659.
41. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006, 34(Database issue):D32-36. 1347377, 16381877.
42. Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV. Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res 2010, 38(Database issue):D69-74. 2808893, 19783826.
43. Duncan MW, Aebersold R, Caprioli RM. The pros and cons of peptide-centric proteomics. Nat Biotechnol 2010, 28(7):659-664. 10.1038/nbt0710-659, 20622832.
44. Olsen JV, Ong SE, Mann M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics 2004, 3(6):608-614. 10.1074/mcp.T400003-MCP200, 15034119.
45. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, et al. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 2007, 17(9):1362-1377. 10.1101/gr.6427907, 1950905, 17690205.
46. Frottin F, Martinez A, Peynot P, Mitra S, Holz RC, Giglione C, Meinnel T. The proteomics of N-terminal methionine cleavage. Mol Cell Proteomics 2006, 5(12):2336-2349. 10.1074/mcp.M600225-MCP200, 16963780.
47. Yoshimoto T, Orawski AT, Simmons WH. Substrate specificity of aminopeptidase P from Escherichia coli: comparison with membrane-bound forms from rat and bovine lung. Arch Biochem Biophys 1994, 311(1):28-34. 10.1006/abbi.1994.1204, 8185318.
48. Kim W, Silby MW, Purvine SO, Nicoll JS, Hixson KK, Monroe M, Nicora CD, Lipton MS, Levy SB. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1. PLoS One 2009, 4(12):e8455. 10.1371/journal.pone.0008455, 2794547, 20041161.
49. Choo KH, Tan TW, Ranganathan S. A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics 2009, 10 Suppl 15:S2. 2788353, 19958512.
50. Gardy JL, Brinkman FS. Methods for predicting bacterial protein subcellular localization. Nat Rev Microbiol 2006, 4(10):741-751. 10.1038/nrmicro1494, 16964270.
51. Robert V, Volokhina EB, Senf F, Bos MP, Van Gelder P, Tommassen J. Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif. PLoS Biol 2006, 4(11):e377. 10.1371/journal.pbio.0040377, 1634882, 17090219.
52. Struyve M, Moons M, Tommassen J. Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. J Mol Biol 1991, 218(1):141-148. 10.1016/0022-2836(91)90880-F, 1848301.
53. Brown RN, Romine MF, Schepmoes AA, Smith RD, Lipton MS. Mapping the subcellular proteome of Shewanella oneidensis MR-1 using sarkosyl-based fractionation and LC-MS/MS protein identification. J Proteome Res 2010, 9(9):4454-4463. 10.1021/pr100215h, 20690604.
54. Filip C, Fletcher G, Wulff JL, Earhart CF. Solubilization of the cytoplasmic membrane of Escherichia coli by the ionic detergent sodium-lauryl sarcosinate. J Bacteriol 1973, 115(3):717-722. 246312, 4580564.
55. Gennity JM, Inouye M. The protein sequence responsible for lipoprotein membrane localization in Escherichia coli exhibits remarkable specificity. J Biol Chem 1991, 266(25):16458-16464.
56. Narita S, Tokuda H. Amino acids at positions 3 and 4 determine the membrane specificity of Pseudomonas aeruginosa lipoproteins. J Biol Chem 2007, 282(18):13372-13378. 10.1074/jbc.M611839200, 17350956.
57. Schulze RJ, Zuckert WR. Borrelia burgdorferi lipoproteins are secreted to the outer surface by default. Mol Microbiol 2006, 59(5):1473-1484. 10.1111/j.1365-2958.2006.05039.x, 16468989.
58. Wiker HG, Wilson MA, Schoolnik GK. Extracytoplasmic proteins of Mycobacterium tuberculosis - mature secreted proteins often start with aspartic acid and proline. Microbiology 2000, 146(Pt 7):1525-1533.
59. Sauvonnet N, Pugsley AP. Identification of two regions of Klebsiella oxytoca pullulanase that together are capable of promoting beta-lactamase secretion by the general secretory pathway. Mol Microbiol 1996, 22(1):1-7. 10.1111/j.1365-2958.1996.tb02650.x, 8899703.
60. Bryksin AV, Tomova A, Godfrey HP, Cabello FC. BmpA is a surface-exposed outer-membrane protein of Borrelia burgdorferi. FEMS Microbiol Lett 2010, 309(1):77-83.
61. Roussel-Jazede V, Jongerius I, Bos MP, Tommassen J, van Ulsen P. NalP-mediated proteolytic release of lactoferrin-binding protein B from the meningococcal cell surface. Infect Immun 2010, 78(7):3083-3089. 10.1128/IAI.01193-09, 2897402, 20421383.
62. Haake DA, Matsunaga J. Leptospira: a spirochaete with a hybrid outer membrane. Mol Microbiol 2010,
63. Shi L, Deng S, Marshall MJ, Wang Z, Kennedy DW, Dohnalkova AC, Mottaz HM, Hill EA, Gorby YA, Beliaev AS, et al. Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcA. J Bacteriol 2008, 190(15):5512-5516. 10.1128/JB.00514-08, 2493258, 18502849.
64. DiChristina TJ, Moore CM, Haller CA. Dissimilatory Fe(III) and Mn(IV) reduction by Shewanella putrefaciens requires ferE, a homolog of the pulE (gspE) type II protein secretion gene. J Bacteriol 2002, 184(1):142-151. 10.1128/JB.184.1.142-151.2002, 134750, 11741854.
65. Smith DR, Chapman MR. Economical evolution: microbes reduce the synthetic cost of extracellular proteins. MBio 2010, 1(2):e00131-e001310. 2932507, 20824102.
66. Delepelaire P. Type I secretion in gram-negative bacteria. Biochim Biophys Acta 2004, 1694(1-3):149-161. 10.1016/j.bbamcr.2004.05.001, 15546664.
67. Samudrala R, Heffron F, McDermott JE. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog 2009, 5(4):e1000375. 10.1371/journal.ppat.1000375, 1266291, 19390620.
68. Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, et al. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc Natl Acad Sci U S A 2009, 106(37):15909-15914. 10.1073/pnas.0902000106, 2747217, 19805231.
69. Lipton MS, Romine MF, Monroe ME, Elias DA, Pasa-Tolic L, Anderson GA, Anderson DJ, Fredrickson J, Hixson KK, Masselon C, et al. AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis. Methods Biochem Anal 2006, 49:113-134.