메뉴 건너뛰기




Volumn 8, Issue , 2013, Pages

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes

Author keywords

Bacterial; Bioinformatics; Membrane protein; Proteomics; Python

Indexed keywords

BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA;

EID: 84875073951     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-8-9     Document Type: Review
Times cited : (11)

References (31)
  • 1
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • 10.1093/bioinformatics/btq249, 2887053, 20472543
    • Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FSL. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 2010, 26:1608-1615. 10.1093/bioinformatics/btq249, 2887053, 20472543.
    • (2010) Bioinformatics , vol.26 , pp. 1608-1615
    • Yu, N.Y.1    Wagner, J.R.2    Laird, M.R.3    Melli, G.4    Rey, S.5    Lo, R.6    Dao, P.7    Sahinalp, S.C.8    Ester, M.9    Foster, L.J.10    Brinkman, F.S.L.11
  • 2
    • 33746218840 scopus 로고    scopus 로고
    • Prediction of protein subcellular localization
    • 10.1002/prot.21018, 16752418
    • Yu C, Chen Y, Lu C, Hwang J. Prediction of protein subcellular localization. Proteins 2006, 64:643-651. 10.1002/prot.21018, 16752418.
    • (2006) Proteins , vol.64 , pp. 643-651
    • Yu, C.1    Chen, Y.2    Lu, C.3    Hwang, J.4
  • 3
    • 33750980713 scopus 로고    scopus 로고
    • Augur--a computational pipeline for whole genome microbial surface protein prediction and classification
    • 10.1093/bioinformatics/btl466, 16966358
    • Billion A, Ghai R, Chakraborty T, Hain T. Augur--a computational pipeline for whole genome microbial surface protein prediction and classification. Bioinformatics 2006, 22:2819-2820. 10.1093/bioinformatics/btl466, 16966358.
    • (2006) Bioinformatics , vol.22 , pp. 2819-2820
    • Billion, A.1    Ghai, R.2    Chakraborty, T.3    Hain, T.4
  • 4
    • 42549137778 scopus 로고    scopus 로고
    • LocateP: genome-scale subcellular-location predictor for bacterial proteins
    • Zhou M, Boekhorst J, Francke C, Siezen RJ. LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinforma 2008, 9:173.
    • (2008) BMC Bioinforma , vol.9 , pp. 173
    • Zhou, M.1    Boekhorst, J.2    Francke, C.3    Siezen, R.J.4
  • 5
    • 59449088232 scopus 로고    scopus 로고
    • Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria.
    • 10.1002/pmic.200800195, 19053137
    • Barinov A, Loux V, Hammani A, Nicolas P, Langella P, Ehrlich D, Maguin E, Van de Guchte M. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria. Proteomics 2009, 9:61-73. 10.1002/pmic.200800195, 19053137.
    • (2009) Proteomics , vol.9 , pp. 61-73
    • Barinov, A.1    Loux, V.2    Hammani, A.3    Nicolas, P.4    Langella, P.5    Ehrlich, D.6    Maguin, E.7    Van de Guchte, M.8
  • 6
    • 18744403991 scopus 로고    scopus 로고
    • An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
    • 10.1093/bioinformatics/bti303, 15691854
    • Kahsay RY, Gao G, Liao L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics 2005, 21:1853-1858. 10.1093/bioinformatics/bti303, 15691854.
    • (2005) Bioinformatics , vol.21 , pp. 1853-1858
    • Kahsay, R.Y.1    Gao, G.2    Liao, L.3
  • 7
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • 10.1038/nmeth.1701, 21959131
    • Petersen TN, Brunak S, Von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786. 10.1038/nmeth.1701, 21959131.
    • (2011) Nat Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 8
    • 0041341888 scopus 로고    scopus 로고
    • Prediction of lipoprotein signal peptides in Gram-negative bacteria
    • 10.1110/ps.0303703, 2323952, 12876315
    • 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, 12:1652-1662. 10.1110/ps.0303703, 2323952, 12876315.
    • (2003) Protein Sci , vol.12 , pp. 1652-1662
    • Juncker, A.S.1    Willenbrock, H.2    Von Heijne, G.3    Brunak, S.4    Nielsen, H.5    Krogh, A.6
  • 9
    • 84878435051 scopus 로고    scopus 로고
    • HMMER http://hmmer.org.
    • HMMER
  • 10
    • 21844433171 scopus 로고    scopus 로고
    • Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs
    • 10.1128/JB.187.14.4928-4934.2005, 1169495, 15995208
    • Boekhorst J, De Been MWHJ, Kleerebezem M, Siezen RJ. Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. J Bacteriol 2005, 187:4928-4934. 10.1128/JB.187.14.4928-4934.2005, 1169495, 15995208.
    • (2005) J Bacteriol , vol.187 , pp. 4928-4934
    • Boekhorst, J.1    De Been, M.W.H.J.2    Kleerebezem, M.3    Siezen, R.J.4
  • 11
    • 0033404562 scopus 로고    scopus 로고
    • Interaction between the protein InlB of Listeria monocytogenes and lipoteichoic acid: a novel mechanism of protein association at the surface of Gram-positive bacteria
    • 10.1046/j.1365-2958.1999.01652.x, 10594817
    • Jonquieres R, Bierne H, Fiedler F, Gounon P, Cossart P. Interaction between the protein InlB of Listeria monocytogenes and lipoteichoic acid: a novel mechanism of protein association at the surface of Gram-positive bacteria. Mol Microbiol 1999, 34:902-914. 10.1046/j.1365-2958.1999.01652.x, 10594817.
    • (1999) Mol Microbiol , vol.34 , pp. 902-914
    • Jonquieres, R.1    Bierne, H.2    Fiedler, F.3    Gounon, P.4    Cossart, P.5
  • 12
    • 0025779454 scopus 로고
    • Cloning, expression, sequence analysis and biochemical characterization of an autolytic amidase of Bacillus subtilis 168 trpC2
    • 10.1099/00221287-137-8-1987, 1683402
    • Foster SJ. Cloning, expression, sequence analysis and biochemical characterization of an autolytic amidase of Bacillus subtilis 168 trpC2. J Gen Microbiol 1991, 137:1987-1998. 10.1099/00221287-137-8-1987, 1683402.
    • (1991) J Gen Microbiol , vol.137 , pp. 1987-1998
    • Foster, S.J.1
  • 13
    • 0034333342 scopus 로고    scopus 로고
    • Location of repeat elements in glucansucrases of Leuconostoc and Streptococcus species
    • 10.1111/j.1574-6968.2000.tb09358.x, 11040428
    • Janecek T, Svensson B, Russell RRB. Location of repeat elements in glucansucrases of Leuconostoc and Streptococcus species. FEMS Microbiol Lett 2000, 192:53-57. 10.1111/j.1574-6968.2000.tb09358.x, 11040428.
    • (2000) FEMS Microbiol Lett , vol.192 , pp. 53-57
    • Janecek, T.1    Svensson, B.2    Russell, R.R.B.3
  • 14
    • 0034674162 scopus 로고    scopus 로고
    • The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD)
    • 10.1006/jmbi.2000.3778, 10843862
    • Bateman A, Bycroft M. The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). J Mol Biol 2000, 299:1113-1119. 10.1006/jmbi.2000.3778, 10843862.
    • (2000) J Mol Biol , vol.299 , pp. 1113-1119
    • Bateman, A.1    Bycroft, M.2
  • 15
    • 0035077376 scopus 로고    scopus 로고
    • Characterization of a cell surface protein of Clostridium difficile with adhesive properties
    • 10.1128/IAI.69.4.2144-2153.2001, 98141, 11254569
    • Waligora AJ, Hennequin C, Mullany P, Bourlioux P, Collignon A, Karjalainen T. Characterization of a cell surface protein of Clostridium difficile with adhesive properties. Infect Immun 2001, 69:2144-2153. 10.1128/IAI.69.4.2144-2153.2001, 98141, 11254569.
    • (2001) Infect Immun , vol.69 , pp. 2144-2153
    • Waligora, A.J.1    Hennequin, C.2    Mullany, P.3    Bourlioux, P.4    Collignon, A.5    Karjalainen, T.6
  • 16
    • 0034283014 scopus 로고    scopus 로고
    • Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation
    • 10.1093/emboj/19.17.4473, 302060, 10970841
    • Mesnage S, Fontaine T, Mignot T, Delepierre M, Mock M, Fouet A. Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation. EMBO J 2000, 19:4473-4484. 10.1093/emboj/19.17.4473, 302060, 10970841.
    • (2000) EMBO J , vol.19 , pp. 4473-4484
    • Mesnage, S.1    Fontaine, T.2    Mignot, T.3    Delepierre, M.4    Mock, M.5    Fouet, A.6
  • 17
    • 1542472730 scopus 로고    scopus 로고
    • New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system
    • 10.1186/gb-2003-4-12-r81, 329420, 14659018
    • Anantharaman V, Aravind L. New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol 2003, 4:R81. 10.1186/gb-2003-4-12-r81, 329420, 14659018.
    • (2003) Genome Biol , vol.4
    • Anantharaman, V.1    Aravind, L.2
  • 18
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • 10.1006/jmbi.2000.4315, 11152613
    • Krogh A, Larsson B, Von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305:567-580. 10.1006/jmbi.2000.4315, 11152613.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 19
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • 10.1093/bioinformatics/btl677, 17237066
    • Jones DT. Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 2007, 23:538-544. 10.1093/bioinformatics/btl677, 17237066.
    • (2007) Bioinformatics , vol.23 , pp. 538-544
    • Jones, D.T.1
  • 20
    • 0036038940 scopus 로고    scopus 로고
    • Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway
    • 10.1046/j.1365-2958.2002.03090.x, 12180915
    • Rose RW, Brüser T, Kissinger JC, Pohlschröder M. Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway. Mol Microbiol 2002, 45:943-950. 10.1046/j.1365-2958.2002.03090.x, 12180915.
    • (2002) Mol Microbiol , vol.45 , pp. 943-950
    • Rose, R.W.1    Brüser, T.2    Kissinger, J.C.3    Pohlschröder, M.4
  • 22
    • 0037188471 scopus 로고    scopus 로고
    • Elucidation of the function of lipoprotein-sorting signals that determine membrane localization
    • 10.1073/pnas.112085599, 124241, 12032293
    • Masuda K, Matsuyama S, Tokuda H. Elucidation of the function of lipoprotein-sorting signals that determine membrane localization. Proc Natl Acad Sci U S A 2002, 99:7390-7395. 10.1073/pnas.112085599, 124241, 12032293.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 7390-7395
    • Masuda, K.1    Matsuyama, S.2    Tokuda, H.3
  • 23
    • 3242879514 scopus 로고    scopus 로고
    • BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
    • 10.1093/nar/gkh351, 441489, 15215418
    • Berven FS, Flikka K, Jensen HB, Eidhammer I. BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Nucleic Acids Res 2004, 32:W394-W399. 10.1093/nar/gkh351, 441489, 15215418.
    • (2004) Nucleic Acids Res , vol.32
    • Berven, F.S.1    Flikka, K.2    Jensen, H.B.3    Eidhammer, I.4
  • 24
    • 25444484398 scopus 로고    scopus 로고
    • TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
    • Garrow AG, Agnew A, Westhead DR. TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinforma 2005, 6:56.
    • (2005) BMC Bioinforma , vol.6 , pp. 56
    • Garrow, A.G.1    Agnew, A.2    Westhead, D.R.3
  • 25
    • 43249097732 scopus 로고    scopus 로고
    • TMBETADISC-RBF: discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles
    • Ou Y-YY, Gromiha MMM, Chen S-AA, Suwa M. TMBETADISC-RBF: discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput Biol Chem 2008, 31:227-231.
    • (2008) Comput Biol Chem , vol.31 , pp. 227-231
    • Ou, Y.-Y.Y.1    Gromiha, M.M.M.2    Chen, S.-A.A.3    Suwa, M.4
  • 26
    • 1842688091 scopus 로고    scopus 로고
    • Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins
    • 10.1002/jcc.10386, 14978719
    • Gromiha MM, Ahmad S, Suwa M. Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J Comput Chem 2004, 25:762-767. 10.1002/jcc.10386, 14978719.
    • (2004) J Comput Chem , vol.25 , pp. 762-767
    • Gromiha, M.M.1    Ahmad, S.2    Suwa, M.3
  • 27
    • 13244259253 scopus 로고    scopus 로고
    • Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method
    • Bagos PG, Liakopoulos TD, Hamodrakas SJ. Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinforma 2005, 6:7.
    • (2005) BMC Bioinforma , vol.6 , pp. 7
    • Bagos, P.G.1    Liakopoulos, T.D.2    Hamodrakas, S.J.3
  • 28
    • 48249123880 scopus 로고    scopus 로고
    • Computational biology resources lack persistence and usability
    • 10.1371/journal.pcbi.1000136, 2443418, 18636105
    • Veretnik S, Fink JL, Bourne PE. Computational biology resources lack persistence and usability. PLoS Comput Biol 2008, 4:e1000136. 10.1371/journal.pcbi.1000136, 2443418, 18636105.
    • (2008) PLoS Comput Biol , vol.4
    • Veretnik, S.1    Fink, J.L.2    Bourne, P.E.3
  • 29
    • 36948999784 scopus 로고    scopus 로고
    • A primer on python for life science researchers
    • 10.1371/journal.pcbi.0030199, 2098836, 18052533
    • Bassi S. A primer on python for life science researchers. PLoS Comput Biol 2007, 3:e199. 10.1371/journal.pcbi.0030199, 2098836, 18052533.
    • (2007) PLoS Comput Biol , vol.3
    • Bassi, S.1
  • 30
    • 84878430713 scopus 로고    scopus 로고
    • twill http://twill.idyll.org/.
    • twill
  • 31
    • 84946058784 scopus 로고    scopus 로고
    • BeautifulSoup http://www.crummy.com/software/BeautifulSoup/.
    • BeautifulSoup


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.