Identification and evolution of dual-topology membrane proteins

Nature Structural and Molecular Biology

Volumn 13, Issue 2, 2006, Pages 112-116

  Rapp, Mikaela ^a   Granseth, Erik ^a   Seppälä, Susanna ^a   Von Heijne, Gunnar ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; ESCHERICHIA COLI; FAMILY; GENE; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CYTOPLASM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MUTATION;

ESCHERICHIA COLI;

EID: 32244436490     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1057     Document Type: Article

References (35)

1. Nilsson, I.M. & von Heijne, G. Fine-tuning the topology of a polytopic membrane protein. Role of positively and negatively charged residues. Cell 62, 1135-1141 (1990).
2. Gafvelin, G. & von Heijne, G. Topological "frustration" in multi-spanning E. coli inner membrane proteins. Cell 77, 401-412 (1994).
3. Ubarretxena-Belandia, I., Baldwin, J.M., Schuldiner, S. & Tate, C.G. Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer. EMBO J. 22, 6175-6181 (2003).
4. Ma, C. & Chang, G. Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli. Proc. Natl. Acad. Sci. USA 101, 2852-2857 (2004).
5. Ninio, S., Elbaz, Y. & Schuldiner, S. The membrane topology of EmrE - a small multidrug transporter from Escherichia coli. FEBS Lett. 562, 193-196 (2004).
6. Daley, D.O. et al. Global topology analysis of the Escherichia coli inner membrane proteome. Science 308, 1321-1323 (2005).
7. Paulsen, I.T. et al. The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs. Mol. Microbiol. 19, 1167-1175 (1996).
8. Sand, O., Gingras, M., Beck, N., Hall, C. & Trun, N. Phenotypic characterization of overexpression or deletion of the Escherichia coli crcA, cspE and crcB genes. Microbiology 149, 2107-2117 (2003).
9. von Heijne, G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J. 5, 3021-3027 (1986).
10. von Heijne, G. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature 341, 456-458 (1989).
11. Whitley, P., Nilsson, I. & von Heijne, G. De novo design of integral membrane proteins. Nat. Struct. Biol. 1, 858-862 (1994).
12. Nishino, K. & Yamaguchi, A. Analysis of a complete library of putative drug transporter genes in Escherichia coli. J. Bacteriol. 183, 5803-5812 (2001).
13. 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, 8540-8544 (1999).
14. Manoil, C. & Beckwith, J. A genetic approach to analyzing membrane protein topology. Science 233, 1403-1408 (1986).
15. Feilmeier, B.J., Iseminger, G., Schroeder, D., Webber, H. & Phillips, G.J. Green fluorescent protein functions as a reporter for protein localization in Escherichia coli. J. Bacteriol. 182, 4068-4076 (2000).
16. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 32, D138-D141 (2004).
17. 2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. J. Biol. Chem. 276, 18905-18907 (2001).
18. Shimizu, T., Mitsuke, H., Noto, K. & Arai, M. Internal gene duplication in the evolution of prokaryotic transmembrane proteins. J. Mol. Biol. 339, 1-15 (2004).
19. Walz, T. et al. The three-dimensional structure of aquaporin-1. Nature 387, 624-627 (1997).
20. Fu, D. et al. Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290, 481-486 (2000).
21. van den Berg, B. et al. X-ray structure of a protein-conducting channel. Nature 427, 36-44 (2004).
22. Dutzler, R., Campbell, E.B., Cadene, M., Chait, B.T. & MacKinnon, R. X-ray structure of a CIC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature 415, 287-294 (2002).
23. - -dependent neurotransmitter transporters. Nature 437, 215-223 (2005).
24. Pornillos, O., Chen, Y.J., Chen, A.P. & Chang, G. X-ray structure of the EmrE multidrug transporter in complex with a substrate. Science 310, 1950-1953 (2005).
25. Rapp, M. et al. Experimentally based topology models for E. coli inner membrane proteins. Protein Sci. 13, 937-945 (2004).
26. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K. & Pease, L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77, 51-59 (1989).
27. Lee, E. & Manoil, C. Mutations eliminating the protein export function of a membrane-spanning sequence. J. Biol. Chem. 269, 28822-28828 (1994).
28. Studier, F.W., Rosenberg, A.H., Dunn, J.J. & Dubendorff, J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60-89 (1990).
29. Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
30. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes. J. Mol. Biol. 305, 567-580 (2001).
31. Melén, K., Krogh, A. & von Heijne, G. Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 327, 735-744 (2003).
32. Granseth, E., Daley, D.O., Rapp, M., Melén, K. & von Heijne, G. Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J. Mol. Biol. 352, 489-494 (2005).
33. Needleman, S.B. & Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 444-453 (1970).
34. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
35. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).