Evolution of new protein topologies through multistep gene rearrangements

Nature Genetics

Volumn 38, Issue 2, 2006, Pages 168-174

  Peisajovich, Sergio G ^a   Rockah, Liat ^a   Tawfik, Dan S ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; PROTEIN;

ARTICLE; DIRECTED MOLECULAR EVOLUTION; GENE DUPLICATION; GENE FUSION; GENE REARRANGEMENT; GENETIC LINKAGE; MOLECULAR EVOLUTION; NULL HYPOTHESIS; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; DIRECTED MOLECULAR EVOLUTION; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE REARRANGEMENT; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POINT MUTATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; RECOMBINANT FUSION PROTEINS; SEQUENCE ALIGNMENT; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC);

EID: 31744450975     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1717     Document Type: Article

References (30)

1. Ponting, C.P. & Russell, R.B. Swaposins: circular permutations within genes encoding saposin homologues. Trends Biochem. Sci. 20, 179-180 (1995).
2. Grishin, N.V. Fold change in evolution of protein structures. J. Struct. Biol. 134, 167-185 (2001).
3. Koonin, E.V., Wolf, Y.I. & Karev, G.P. The structure of the protein universe and genome evolution. Nature 420, 218-223 (2002).
4. Aravind, L., Mazumder, R., Vasudevan, S. & Koonin, E.V. Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol. 12, 392-399 (2002).
5. Graf, R. & Schachman, H.K. Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase. Proc. Natl. Acad. Sci. USA 93, 11591-11596 (1996).
6. Cunningham, B.A., Hemperly, J.J., Hopp, T.P. & Edelman, G.E. Favin versus concanavalin A: circularly permuted amino acid sequences. Proc. Natl. Acad. Sci. USA 76, 3218-3222 (1979).
7. Luger, K., Hommel, U., Herold, M., Hofsteenge, J. & Kirschner, K. Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo. Science 243, 206-210 (1989).
8. Jeltsch, A. Circular permutations in the molecular evolution of DNA methyltransferases. J. Mol. Evol. 49, 161-164 (1999).
9. Bujnicki, J.M. Sequence permutations in the molecular evolution of DNA methyltransferases. BMC Evol. Biol. 2, 3 (2002).
10. Richardson, J.S. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167-339 (1981).
11. Martin, J.L. & McMillan, F.M. SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr. Opin. Struct. Biol. 12, 783-793 (2002).
12. Malone, T., Blumenthal, R.M. & Cheng, X. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253, 618-632 (1995).
13. Klimasauskas, S. et al. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases. Nucleic Acids Res. 17, 9823-9832 (1989).
14. Kita, K., Kotani, H., Sugisaki, H. & Takanami, M. The fokl restriction-modification system. I. Organization and nucleotide sequences of the restriction and modification genes. J. Biol. Chem. 264, 5751-5756 (1989).
15. Sugisaki, H., Kita, K. & Takanami, M. The Fokl restriction- modification system. II. Presence of two domains in Fokl methylase responsible for modification of different DNA strands. J. Biol. Chem. 264, 5757-5761 (1989).
16. Leismann, O., Roth, M., Friedrich, T., Wende, W. & Jeltsch, A. The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase M.Fokl is a tandem enzyme of two independent domains with very different kinetic properties. Eur. J. Biochem. 251, 899-906 (1998).
17. Szomolanyi, E., Kiss, A. & Venetianer, P. Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene 10, 219-225 (1980).
18. Ostermeier, M., Shim, J.H. & Benkovic, S.J. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat. Biotechnol. 17, 1205-1209 (1999).
19. Choe, W., Chandrasegaran, S. & Ostermeier, M. Protein fragment complementation in M.Hhal DNA methyltransferase. Biochem. Biophys. Res. Commun. 334, 1233-1240 (2005).
20. Reinisch, K.M., Chen, L., Verdine, G.L. & Lipscomb, W.N. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82, 143-153 (1995).
21. Wagner, A. Robustness, evolvability, and neutrality. FEBS Lett. 579, 1772-1778 (2005).
22. Hennecke, J., Sebbel, P. & Glockshuber, R. Random circular permutation of DsbA reveals segments that are essential for protein folding and stability. J. Mol. Biol. 286, 1197-1215 (1999).
23. Iwakura, M., Nakamura, T., Yamane, C. & Maki, K. Systematic circular permutation of an entire protein reveals essential folding elements. Nat. Struct. Biol. 7, 580-585 (2000).
24. Chothia, C. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105, 1-12 (1976).
25. Jeltsch, A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBioChem 3, 274-293 (2002).
26. Kusano, K., Naito, T., Handa, N. & Kobayashi, I. Restriction- modification systems as genomic parasites in competition for specific sequences. Proc. Natl. Acad. Sci. USA 92, 11095-11099 (1995).
27. Roodveldt, C. & Tawfik, D.S. Directed evolution of phosphotriesterase from Pseudomonas diminuta for heterologous expression in Escherichia coli results in stabilization of the metal-free state. Protein Eng. Des. Sel. (2005).
28. Ostermeier, M., Nixon, A.E., Shim, J.H. & Benkovic, S.J. Combinatorial protein engineering by incremental truncation. Proc. Natl. Acad. Sci. USA 96, 3562-3567 (1999).
29. Tawfik, D.S. & Griffiths, A.D. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol. 16, 652-656 (1998).
30. Fraczkiewicz, R. & Braun, W. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comp. Chem. 19, 319-333 (1998).