Experimentally based topology models for E. coli inner membrane proteins

Protein Science

Volumn 13, Issue 4, 2004, Pages 937-945

  Rapp, Mikaela ^a   Drew, David ^a   Daley, Daniel O ^a   Nilsson, Johan ^a,b   Carvalho, Tiago ^a   Melén, Karin ^a   De Gier, Jan Willem ^a   Von Heijne, Gunnar ^a,b  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Bioinformatics; Fusion protein; GFP; Green fluorescent protein; Membrane proteins; PhoA; Prediction; Topology

Indexed keywords

ALKALINE PHOSPHATASE; ESCHERICHIA COLI INNER MEMBRANE PROTEIN; ESCHERICHIA COLI PROTEIN; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; BIOINFORMATICS; CARBOXY TERMINAL SEQUENCE; CYTOPLASM; ESCHERICHIA COLI; METHODOLOGY; MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; RELIABILITY;

ALKALINE PHOSPHATASE; CELL MEMBRANE; COMPUTATIONAL BIOLOGY; CYCLIN-DEPENDENT KINASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION; GREEN FLUORESCENT PROTEINS; LUMINESCENT PROTEINS; RECOMBINANT FUSION PROTEINS; SOFTWARE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 1842611517     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03553804     Document Type: Article

References (26)

1. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
2. Canfield, V.A. and Levenson, R. 1993. Transmembrane organization of the Na,K-ATPase determined by epitope addition. Biochemistry 32: 13782-13786.
3. Chang, X.B., Hou, Y.X., Jensen, T.J., and Riordan, J.R. 1994. Mapping of cystic fibrosis transmembrane conductance regulator membrane topology by glycosylation site insertion. J. Biol. Chem. 269: 18572-18575.
4. Chen, C.P., Kemytsky, A., and Rost, B. 2002. Transmembrane helix predictions revisited. Protein Sci. 11: 2774-2791.
5. Dalbey, R.E. and Wickner, W. 1986. The role of the polar, carboxyl-terminal domain of Escherichia coli leader peptidase in its translocation across the plasma membrane. J. Biol. Chem. 261: 13844-13849.
6. Derman, A.I. and Beckwith, J. 1995. Escherichia coli alkaline phosphatase localized to the cytoplasm slowly acquires enzymatic activity in cells whose growth has been suspended: A caution for gene fusion studies. J. Bacteriol. 177: 3764-3770.
7. Drew, D., Sjöstrand, D., Nilsson, J., Urbig, T., Chin, C.N., de Gier, J.W., and von Heijne, G. 2002. Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc. Natl. Acad. Sci. 99: 2690-2695.
8. Feilmeier, B.J., Iseminger, G., Schroeder, D., Webber, H., and Phillips, G.J. 2000. Green fluorescent protein functions as a reporter for protein localization in Escherichia coli. J. Bacteriol. 182: 4068-4076.
9. Johnston, S., Lee, J.H., and Ray, D.S. 1985. High-level expression of M13 gene II protein from an inducible polycistronic messenger RNA. Gene 34: 137-145.
10. Kerppola, R.E. and Ames, G.F. 1992. Topology of the hydrophobic membrane-bound components of the histidine periplasmic permease-Comparison with other members of the family. J. Biol. Chem. 267: 2329-2336.
11. Kim, H., Melén, K., and von Heijne, G. 2003. Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and prediction. J. Biol. Chem. 278: 10208-10213.
12. Kimura, T., Ohnuma, M., Sawai, T., and Yamaguchi, A. 1997. Membrane topology of the transposon 10-encoded metal-tetracycline/H+ antiporter as studied by site-directed chemical labeling, J. Biol. Chem. 272: 580-585.
13. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. 2001. Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes. J. Mol. Biol. 305: 567-580.
14. Lee, E. and Manoil, C. 1994. Mutations eliminating the protein export function of a membrane-spanning sequence. J. Biol. Chem. 269: 28822-28828.
15. Locher, K.P., Lee, A.T., and Rees, D.C. 2002. The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism. Science 296: 1091-1098.
16. Manoil, C. 1991. Analysis of membrane protein topology using alkaline phosphatase and β-galactosidase gene fusions. Methods Cell Biol. 34: 61-75.
17. Manoil, C. and Beckwith, J. 1986. A genetic approach to analyzing membrane protein topology. Science 233: 1403-1408.
18. Melén, K., Krogh, A., and von Heijne, G. 2003. Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 327: 735-744.
19. Nilsson, J., Persson, B., and von Heijne, G. 2000. Consensus predictions of membrane protein topology. FEBS Lett. 486: 267-269.
20. Rudd, K. 2000. Ecogene: A genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 28: 60-64.
21. Sääf, A., Johansson, M., Wallin, E., and von Heijne, G. 1999. Divergent evolution of membrane protein topology: The Escherichia coli RnfA and RnfE homologues. Proc. Natl. Acad. Sci. 96: 8540-8544.
22. Tusnady, G.E. and Simon, I. 2001. The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850.
23. Waldo, G.S., Standish, B.M., Berendzen, J., and Terwilliger, T.C. 1999. Rapid protein-folding assay using green fluorescent protein. Nat. Biotechnol. 17: 691-695.
24. Whitley, P., Nilsson, I., and von Heijne, G. 1994. De novo design of integral membrane proteins. Nat. Struct. Biol. 1: 858-862.
25. Wilkinson, B.M., Critchley, A.J., and Stirling, C.J. 1996. Determination of the transmembrane topology of yeast Sec61p, an essential component of the endoplasmic reticulum translocation complex. J. Biol. Chem. 271: 25590-25597.
26. Yankovskaya, V., Horsefield, R., Törnroth, S., Luna-Chavez, C., Miyoshi, H., Léger, C., Byrne, B., Cecchini, G., and Iwata, S. 2003. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299: 700-704.