메뉴 건너뛰기




Volumn 339, Issue 1, 2004, Pages 1-15

Internal gene duplication in the evolution of prokaryotic transmembrane proteins

Author keywords

diploid type internal repeats; evolutionary pathway; internal gene duplication; n tms, the number of transmembrane segment(s) is n; ORF, open reading frame; TM, transmembrane; TMS, transmembrane segment; transmembrane protein; transmembrane topology

Indexed keywords

MEMBRANE PROTEIN;

EID: 2342578691     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.03.048     Document Type: Article
Times cited : (37)

References (47)
  • 1
    • 0031584266 scopus 로고    scopus 로고
    • Potein evolution viewed through Escherichua coli protein sequences: Introducing the notion of a structural segment of homology, the module
    • Riley M., Labedan B. Potein evolution viewed through Escherichua coli protein sequences: introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268:1997;857-868
    • (1997) J. Mol. Biol. , vol.268 , pp. 857-868
    • Riley, M.1    Labedan, B.2
  • 2
    • 0034674175 scopus 로고    scopus 로고
    • Estimating the number of protein folds and families from complete genome data
    • Wolf Y.I., Grishin N.V., Koonin E.V. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. 299:2000;897-905
    • (2000) J. Mol. Biol. , vol.299 , pp. 897-905
    • Wolf, Y.I.1    Grishin, N.V.2    Koonin, E.V.3
  • 3
    • 0037079014 scopus 로고    scopus 로고
    • The structure of the protein universe and genome evolution
    • Koonin E.V., Wolf Y.I., Karev G.P. The structure of the protein universe and genome evolution. Nature. 420:2002;218-223
    • (2002) Nature , vol.420 , pp. 218-223
    • Koonin, E.V.1    Wolf, Y.I.2    Karev, G.P.3
  • 7
    • 0032424307 scopus 로고    scopus 로고
    • Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements
    • Teichmann S.A., Park J., Chothia C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl Acid. Sci. USA. 9:1998;14658-14663
    • (1998) Proc. Natl Acid. Sci. USA , vol.9 , pp. 14658-14663
    • Teichmann, S.A.1    Park, J.2    Chothia, C.3
  • 8
    • 0031892162 scopus 로고    scopus 로고
    • How many membrane proteins are there?
    • Boyd D., Schierle C., Beckwith J. How many membrane proteins are there? Protein Sci. 7:1998;201-205
    • (1998) Protein Sci. , vol.7 , pp. 201-205
    • Boyd, D.1    Schierle, C.2    Beckwith, J.3
  • 9
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane protein superfolds exist?
    • Jones D.T. Do transmembrane protein superfolds exist? FEBS Letters. 423:1998;281-285
    • (1998) FEBS Letters , vol.423 , pp. 281-285
    • Jones, D.T.1
  • 10
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E., von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7:1998;1029-1038
    • (1998) Protein Sci. , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 11
    • 0032834939 scopus 로고    scopus 로고
    • An hierarchical artificial neural network system for the classification of transmembrane proteins
    • Pasquier C., Hamodrakas S.J. An hierarchical artificial neural network system for the classification of transmembrane proteins. Protein Eng. 12:1999;631-634
    • (1999) Protein Eng. , vol.12 , pp. 631-634
    • Pasquier, C.1    Hamodrakas, S.J.2
  • 12
    • 0033552649 scopus 로고    scopus 로고
    • Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system
    • Mitaku S., Ono M., Hirokawa T., Boon-Chieng S., Sonoyama M. Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. Biophys. Chem. 82:1999;165-171
    • (1999) Biophys. Chem. , vol.82 , pp. 165-171
    • Mitaku, S.1    Ono, M.2    Hirokawa, T.3    Boon-Chieng, S.4    Sonoyama, M.5
  • 13
    • 0034213573 scopus 로고    scopus 로고
    • Do more complex organisms have a greater proportion of membrane proteins in their genomes?
    • Stevens T.J., Arkin I.T. Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins: Struct. Funct. Genet. 39:2000;417-420
    • (2000) Proteins: Struct. Funct. Genet. , vol.39 , pp. 417-420
    • Stevens, T.J.1    Arkin, I.T.2
  • 14
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:2001;567-580
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 15
    • 0034808117 scopus 로고    scopus 로고
    • Comparing function and structure between entire proteomes
    • Liu J., Rost B. Comparing function and structure between entire proteomes. Protein Sci. 10:2001;1970-1979
    • (2001) Protein Sci. , vol.10 , pp. 1970-1979
    • Liu, J.1    Rost, B.2
  • 16
    • 0037472764 scopus 로고    scopus 로고
    • Comprehensive analysis of transmembrane topologies in prokaryotic genomes
    • Arai M., Ikeda M., Shimizu T. Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene. 304:2003;77-86
    • (2003) Gene , vol.304 , pp. 77-86
    • Arai, M.1    Ikeda, M.2    Shimizu, T.3
  • 17
    • 0035379645 scopus 로고    scopus 로고
    • 2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies
    • 2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. J. Biol. Chem. 276:2001;18905-18907
    • (2001) J. Biol. Chem. , vol.276 , pp. 18905-18907
    • Sääf, A.1    Baars, L.2    Von Heijne, G.3
  • 18
    • 0030309453 scopus 로고    scopus 로고
    • Phylogenetic approaches to the identification and characterization of protein families and superfamilies
    • Saier M.H. Jr. Phylogenetic approaches to the identification and characterization of protein families and superfamilies. Microb. Comp. Genomics. 1:1996;129-150
    • (1996) Microb. Comp. Genomics , vol.1 , pp. 129-150
    • Saier Jr., M.H.1
  • 19
    • 0033821267 scopus 로고    scopus 로고
    • Vectorial metabolism and the evolution of transport systems
    • Saier M.H. Jr. Vectorial metabolism and the evolution of transport systems. J. Bacteriol. 182:2000;5029-5035
    • (2000) J. Bacteriol. , vol.182 , pp. 5029-5035
    • Saier Jr., M.H.1
  • 20
    • 0037783318 scopus 로고    scopus 로고
    • Tracing pathways of transport protein evolution
    • Saier M.H. Jr. Tracing pathways of transport protein evolution. Mol. Microbiol. 48:2003;1145-1156
    • (2003) Mol. Microbiol. , vol.48 , pp. 1145-1156
    • Saier Jr., M.H.1
  • 23
    • 0027193530 scopus 로고
    • Sequence homology between bacteriorhodopsin and G-protein coupled receptors: Exon shuffling or evolution by duplication?
    • Taylor E.W., Agarwal A. Sequence homology between bacteriorhodopsin and G-protein coupled receptors: exon shuffling or evolution by duplication? FEBS Letters. 325:1993;161-166
    • (1993) FEBS Letters , vol.325 , pp. 161-166
    • Taylor, E.W.1    Agarwal, A.2
  • 24
    • 0035795114 scopus 로고    scopus 로고
    • Homologues of archaeal rhodopsins in plants, animals and fungi: Structural and functional predictions for a putative fungal chaperone protein
    • Zhai Y., Heijne W.H., Smith D.W., Saier M.H. Jr. Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predictions for a putative fungal chaperone protein. Biochim. Biophys. Acta. 1511:2001;206-223
    • (2001) Biochim. Biophys. Acta , vol.1511 , pp. 206-223
    • Zhai, Y.1    Heijne, W.H.2    Smith, D.W.3    Saier Jr., M.H.4
  • 25
    • 0024442722 scopus 로고
    • Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues
    • von Heijne G. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature. 341:1989;456-458
    • (1989) Nature , vol.341 , pp. 456-458
    • Von Heijne, G.1
  • 26
    • 0023676242 scopus 로고
    • Topogenic signals in integral membrane proteins
    • von Heijne G., Gavel Y. Topogenic signals in integral membrane proteins. Eur. J. Biochem. 174:1988;671-678
    • (1988) Eur. J. Biochem. , vol.174 , pp. 671-678
    • Von Heijne, G.1    Gavel, Y.2
  • 27
    • 0027264995 scopus 로고
    • Predicting the topology of eukaryotic membrane proteins
    • Sipos L., von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 213:1993;1333-1340
    • (1993) Eur. J. Biochem. , vol.213 , pp. 1333-1340
    • Sipos, L.1    Von Heijne, G.2
  • 28
    • 0036132818 scopus 로고    scopus 로고
    • Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally- characterized transmembrane topologies
    • Ikeda M., Arai M., Lao D.M., Shimizu T. Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. In Silico Biol. 2:2002;19-33
    • (2002) In Silico Biol. , vol.2 , pp. 19-33
    • Ikeda, M.1    Arai, M.2    Lao, D.M.3    Shimizu, T.4
  • 29
    • 0037249645 scopus 로고    scopus 로고
    • TMPDB: A database of experimentally-characterized transmembrane topologies
    • Ikeda M., Arai M., Shimizu T. TMPDB: a database of experimentally- characterized transmembrane topologies. Nucl. Acids Res. 31:2003;406-409
    • (2003) Nucl. Acids Res. , vol.31 , pp. 406-409
    • Ikeda, M.1    Arai, M.2    Shimizu, T.3
  • 30
    • 0033587738 scopus 로고    scopus 로고
    • Divergent evolution of membrane protein topology: The Escherichia coli RnfA and RnfE homologues
    • Sääf A., Johansson M., Wallin E., von Heijne G. Divergent evolution of membrane protein topology: the Escherichia coli RnfA and RnfE homologues. Proc. Natl Acad. Sci. USA. 96:1999;8540-8544
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 8540-8544
    • Sääf, A.1    Johansson, M.2    Wallin, E.3    Von Heijne, G.4
  • 31
    • 0042880963 scopus 로고    scopus 로고
    • Identification of transmembrane protein functions by binary topology patterns
    • Sugiyama Y., Polulyakh N., Shimizu T. Identification of transmembrane protein functions by binary topology patterns. Protein Eng. 16:2003;479-488
    • (2003) Protein Eng. , vol.16 , pp. 479-488
    • Sugiyama, Y.1    Polulyakh, N.2    Shimizu, T.3
  • 33
    • 0031826040 scopus 로고    scopus 로고
    • SOSUI: Classification and secondary structure prediction system for membrane proteins
    • Hirokawa T., Boon-Chieng S., Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics. 14:1998;378-379
    • (1998) Bioinformatics , vol.14 , pp. 378-379
    • Hirokawa, T.1    Boon-Chieng, S.2    Mitaku, S.3
  • 35
    • 0036947980 scopus 로고    scopus 로고
    • The presence of signal peptide significantly affects transmembrane topology prediction
    • Lao D.M., Arai M., Ikeda M., Shimizu T. The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics. 18:2002;1562-1566
    • (2002) Bioinformatics , vol.18 , pp. 1562-1566
    • Lao, D.M.1    Arai, M.2    Ikeda, M.3    Shimizu, T.4
  • 36
    • 0036936886 scopus 로고    scopus 로고
    • Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction
    • Lao D.M., Okuno T., Shimizu T. Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction. In Silico Biol. 2:2002;485-494
    • (2002) In Silico Biol. , vol.2 , pp. 485-494
    • Lao, D.M.1    Okuno, T.2    Shimizu, T.3
  • 37
    • 0021847027 scopus 로고
    • The detection and classification of membrane-spanning proteins
    • Klein P., Kanehisa M., DeLisi C. The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta. 815:1985;468-476
    • (1985) Biochim. Biophys. Acta , vol.815 , pp. 468-476
    • Klein, P.1    Kanehisa, M.2    Delisi, C.3
  • 38
    • 0028568176 scopus 로고
    • TopPred II: An improved software for membrane protein structure predictions
    • Claros M.G., von Heijne G. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10:1994;685-686
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 685-686
    • Claros, M.G.1    Von Heijne, G.2
  • 39
    • 53249092142 scopus 로고    scopus 로고
    • Prediction of membrane protein topology utilizing multiple sequence alignments
    • Persson B., Argos P. Prediction of membrane protein topology utilizing multiple sequence alignments. J. Protein Chem. 16:1997;453-457
    • (1997) J. Protein Chem. , vol.16 , pp. 453-457
    • Persson, B.1    Argos, P.2
  • 40
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones D.T., Taylor W.R., Thornton J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33:1994;3038-3049
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 42
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
    • Tusnády G.E., Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283:1998;489-506
    • (1998) J. Mol. Biol. , vol.283 , pp. 489-506
    • Tusnády, G.E.1    Simon, I.2
  • 43
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnády G.E., Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:2001;849-850
    • (2001) Bioinformatics , vol.17 , pp. 849-850
    • Tusnády, G.E.1    Simon, I.2
  • 46
    • 0025950944 scopus 로고
    • Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
    • Pearson W.R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics. 11:1991;635-650
    • (1991) Genomics , vol.11 , pp. 635-650
    • Pearson, W.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.