Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Liu, Ying ^a,b   Yan, Zhihui ^b   Lu, Xiaoyun ^b   Xiao, Dongguang ^a   Jiang, Huifeng ^b  

^a TIANJIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b Chinese Academy of Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLYL ALCOHOL; BETA CAROTENE; HEMITERPENE; ISOPENTENYL MONOPHOSPHATE KINASE; MUTANT PROTEIN; PROPANOL; PROTEIN KINASE;

ARCHAEON; BIOCATALYSIS; BIOSYNTHESIS; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MUTATION; PHOSPHORYLATION;

ARCHAEA; BETA CAROTENE; BIOCATALYSIS; BIOSYNTHETIC PATHWAYS; EVOLUTION, MOLECULAR; HEMITERPENES; MUTANT PROTEINS; MUTATION; PHOSPHORYLATION; PROPANOLS; PROTEIN KINASES;

EID: 84962863578     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep24117     Document Type: Article

References (48)

1. Bloom, J. D. et al. Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol. 15, 447-452 (2005).
2. Bornscheuer, U. T. et al. Engineering the third wave of biocatalysis. Nature 485, 185-194 (2012).
3. Kiss, G. et al. Computational Enzyme Design. Angew. Chem. Int. Ed. 52, 5700-5725 (2013).
4. Li, X., Zhang, Z., Song, J. Computational enzyme design approaches with significant biological outcomes: progress and challenges. J. Comput. Struct. Biotechnol. 2, e201209007 (2012).
5. Xiao, H., Bao, Z., Zhao, H. High Throughput Screening and Selection Methods for Directed Enzyme Evolution. Ind. Eng. Chem. Res. 54, 4011-4020 (2015).
6. Chica, R. A., Doucet, N., Pelletier, J. N. Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr. Opin. Biotech. 16, 378-384 (2005).
7. Steiner, K., Schwab, H. Recent advances in rational approaches for enzyme engineering. J. Comput. Struct. Biotechnol. 2, 1-12 (2012).
8. Lee, J. W. et al. Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol. 8, 536-546 (2012).
9. Ng, P. C., Henikoff, S. Predicting the Effects of Amino Acid Substitutions on Protein Function. Annu. Rev. Genomics Hum. Genet. 7, 61-80 (2006).
10. Capra, J. A., Singh, M. Predicting functionally important residues from sequence conservation. Bioinformatics 23, 1875-1882 (2007).
11. Halabi, N., Rivoire, O., Leibler, S., Ranganathan, R. Protein sectors: evolutionary units of three-dimensional structure. Cell 138, 774-786 (2009).
12. Lockless, S. W., Ranganathan, R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295-299 (1999).
13. Fares, M. A., McNally, D. CAPS: coevolution analysis using protein sequences. Bioinformatics 22, 2821-2822 (2006).
14. de Juan, D., Pazos, F., Valencia, A. Emerging methods in protein co-evolution. Nat. Rev. Genet. 14, 249-261 (2013).
15. Grana, O. et al. CASP6 assessment of contact prediction. Proteins 61 Suppl 7, 214-224 (2005).
16. Russ, W. P. et al. Natural-like function in artificial WW domains. Nature 437, 579-583 (2005).
17. Socolich, M. et al. Evolutionary information for specifying a protein fold. Nature 437, 512-518 (2005).
18. Suel, G. M., Lockless, S. W., Wall, M. A., Ranganathan, R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10, 59-69 (2003).
19. Lee, J. et al. Surface sites for engineering allosteric control in proteins. Science 322, 438-442 (2008).
20. Reynolds, K. A., McLaughlin, R. N., Ranganathan, R. Hot spots for allosteric regulation on protein surfaces. Cell 147, 1564-1575 (2011).
21. Hernanz-Falcon, P. et al. Identification of amino acid residues crucial for chemokine receptor dimerization. Nat. Immunol. 5, 216-223 (2004).
22. Ribes-Zamora, A., Mihalek, I., Lichtarge, O., Bertuch, A. A. Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions. Nat. Struct. Mol. Biol. 14, 301-307 (2007).
23. Smit, A., Mushegian, A. Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway. Genome Res. 10, 1468-1484 (2000).
24. Grochowski, L. L., Xu, H., White, R. H. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J.Bacteriol. 188, 3192-3198 (2006).
25. Chen, M., Poulter, C. D. Characterization of thermophilic archaeal isopentenyl phosphate kinases. Biochemistry 49, 207-217 (2010).
26. Dellas, N., Noel, J. P. Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates. ACS Chem. Biol. 5, 589-601 (2010).
27. Mabanglo, M. F. et al. X-ray structures of isopentenyl phosphate kinase. ACS Chem. Biol. 5, 517-527 (2010).
28. Mabanglo, M. F., Serohijos, A. W., Poulter, C. D. The Streptomyces-produced antibiotic fosfomycin is a promiscuous substrate for archaeal isopentenyl phosphate kinase. Biochemistry 51, 917-925 (2012).
29. Lange, B. M., Croteau, R. Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: isopentenyl monophosphate kinase catalyzes the terminal enzymatic step. Proc. Natl. Acad. Sci. USA 96, 13714-13719 (1999).
30. Mcginty, D., Jones, L., Letizia, C. S., Api, A. M. Fragrance material review on 3-methyl-2-buten-1-ol. Food Chem. Toxicol. 48, S64-S69 (2010).
31. Durbecq, V. et al. Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase. J. EMBO. 7, 3-7 (2001).
32. Adam, H. In Methods of enzymatic analysis Vol. 2 (ed. Bergmeyer, H. U.) 573-577 (Academic Press, 1965).
33. Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42, D231-D239 (2014).
34. Johnson, L. S., Eddy, S. R., Portugaly, E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11, 431 (2010).
35. King, J. L., Jukes, T. H. Non-Darwinian evolution. Science 164, 788-798 (1969).
36. Dyer, K. F. The Quiet Revolution: A New Synthesis of Biological Knowledge. J.Biol. Educ. 5, 15-24 (1971).
37. Rohmer, M. The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. Nat. Prod. Rep. 16, 565-574 (1999).
38. Lange, B. M., Rujan, T., Martin, W., Croteau, R. Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. Proc. Natl. Acad. Sci. USA 97, 13172-13177 (2000).
39. Kuzuyama, T., Seto, H. Diversity of the biosynthesis of the isoprene units. Nat. Prod.Rep. 20, 171-183 (2003).
40. Boucher, Y., Kamekura, M., Doolittle, W. F. Origins and evolution of isoprenoid lipid biosynthesis in archaea. Mol. Microbiol. 52, 515-527 (2004).
41. Zhao, J. et al. Engineering central metabolic modules of Escherichia coli for improving beta-carotene production. Metab. Eng. 17, 42-50 (2013).
42. Reiling, K. K. et al. Mono and diterpene production in Escherichia coli. Biotechnol. Bioeng. 87, 200-212 (2004).
43. Nam, H. K. et al. Increase in the production of ?-carotene in recombinant Escherichia coli cultured in a chemically defined medium supplemented with amino acids. Biotechnol. Lett. 35, 265-271 (2013).
44. Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J.Comput.Chem. 30, 2785-2791 (2009).
45. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
46. Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
47. Capella-Gutierrez, S., Silla-Martinez, J. M., Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973 (2009).
48. Yuan, L. Z., Rouviere, P. E., Larossa, R. A., Suh, W. Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli. Metab. Eng. 8, 79-90 (2006).