Coevolutionary analysis enabled rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production

Applied and Environmental Microbiology

Volumn 77, Issue 13, 2011, Pages 4352-4360

  Chen, Zhen ^a   Meyer, Weiqian ^a   Rappert, Sugima ^a   Sun, Jibin ^a,b   Zeng, An Ping ^a  

^a HAMBURG UNIVERSITY OF TECHNOLOGY   (Germany)

^b Chinese Academy of Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERIC ENZYMES; ALLOSTERIC INHIBITION; ALLOSTERY; ASPARTATES; ASPARTOKINASE; BIO-PRODUCTION; CO-EVOLUTIONARY; CORYNEBACTERIUM GLUTAMICUM; COUPLING ANALYSIS; FED-BATCH FERMENTATION; FEEDBACK INHIBITION; HOMOLOGOUS RECOMBINATION; INTERACTION NETWORKS; KEY ENZYMES; L-LYSINE; LYSINE PRODUCTION; MICROBIAL STRAIN; PROTEIN SEQUENCES; RANDOM MUTATION; REGULATORY DOMAIN; WILD TYPES;

AMINO ACIDS; BINDING SITES; DEREGULATION; ENZYME ACTIVITY; FERMENTATION; PLANTS (BOTANY);

ENZYME INHIBITION;

ASPARTATE KINASE; LYSINE; MUTANT PROTEIN;

AMINO ACID; BACTERIUM; BIOCHEMISTRY; BIOREACTOR; BIOTECHNOLOGY; CHEMICAL BINDING; COEVOLUTION; ENZYME ACTIVITY; FERMENTATION; INDUSTRIAL PRODUCTION; INHIBITION; MICROBIAL ACTIVITY; MUTATION; PROTEIN;

ALLOSTERISM; AMINO ACID SUBSTITUTION; ARTICLE; BIOSYNTHESIS; CHEMICAL STRUCTURE; CORYNEBACTERIUM GLUTAMICUM; GENE EXPRESSION REGULATION; GENETIC RECOMBINATION; GENETICS; METABOLISM; MISSENSE MUTATION; SITE DIRECTED MUTAGENESIS;

ALLOSTERIC REGULATION; AMINO ACID SUBSTITUTION; ASPARTATE KINASE; CORYNEBACTERIUM GLUTAMICUM; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; LYSINE; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; MUTANT PROTEINS; MUTATION, MISSENSE; RECOMBINATION, GENETIC;

CORYNEBACTERIUM GLUTAMICUM;

EID: 79960094055     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02912-10     Document Type: Article

References (31)

1. Agarwal, P. K., S. R. Billeter, P. T. Rajagopalan, S. J. Benkovic, and S. Hammes-Schiffer. 2002. Network of coupled promoting motions in enzyme catalysis. Proc. Natl. Acad. Sci. U. S. A. 99:2794-2799.
2. Black, S., and N. G. Wright. 1954. β-Aspartate kinase and β-aspartyl phosphate. J. Biol. Chem. 213:27-38.
3. Capra, J. A., and M. Singh. 2007. Predicting functionally important residues from sequence conservation. Bioinformatics 23:1875-1882.
4. Chen, Z., M. Wilmanns, and A. P. Zeng. 2010. Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development. Trends Biotechnol. 28:534-542.
5. Chen, Z., S. Rappert, J. Sun, and A. P. Zeng. 2011. Integrating molecular dynamics simulation and co-evolutionary analysis for reliable prediction and deregulation of aspartokinase for amino acid production. J. Biotechnol. [Epub ahead of print.] doi:10.1016/j.jbiotec.2011.05.005.
6. Chipman, D. M., and B. Shaanan. 2001. The ACT domain family. Curr. Opin. Struct. Biol. 11:694-700.
7. Doolittle, R. F. 1996. Computer methods for macromolecular sequence analysis, volume 266. Academic Press, San Diego, CA.
8. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
9. Eggeling, L., and M. Bott. 2005. Handbook of Corynebacterium glutamicum. CRC Press, Boca Raton, FL.
10. Estabrook, R. A., et al. 2005. Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis. Proc. Natl. Acad. Sci. U. S. A. 102:994-999.
11. Grant, G. A. 2006. The ACT domain: a small molecule binding domain and its role as a common regulatory element. J. Biol. Chem. 281:33825-33829.
12. Halabi, N., O. Rivoire, S. Leibler, and R. Ranganathan. 2009. Protein sectors: evolutionary units of three-dimensional structure. Cell 138:774-786.
13. Hatley, M. E., S. W. Lockless, S. K. Gibson, A. G. Gilman, and R. Ranganathan. 2003. Allosteric determinants in guanine nucleotide-binding proteins. Proc. Natl. Acad. Sci. U. S. A. 100:14445-14450.
14. Hsieh, C. L., K. P. Hsiung, and J. C. Su. 1995. Determination of lysine with ninhydrin-ferric reagent. Anal. Biochem. 224:187-189.
15. Ikeda, M., J. Ohnishi, M. Hayashi, and S. Mitsuhashi. 2006. A genomebased approach to create a minimally mutated Corynebacterium glutamicum strain for efficient L-lysine production. J. Ind. Microbiol. Biotechnol. 33:610- 615.
16. Kalinowski, J., B. Bachmann, G. Thierbach, and A. Pühler. 1990. Aspartokinase genes lysC alpha and lysC beta overlap and are adjacent to the aspartate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum. Mol. Gen. Genet. 224:317-324.
17. Kikuchi, Y., H. Kojima, and T. Tanaka. 1999. Mutational analysis of the feedback sites of lysine-sensitive aspartokinase of Escherichia coli. FEMS Microbiol. Lett. 173:211-215.
18. Kotaka, M., J. Ren, M. Lockyer, A. R. Hawkins, and D. K. Stammers. 2006. Structures of R- and T-state Escherichia coli aspartokinase III. Mechanisms of the allosteric transition and inhibition by lysine. J. Biol. Chem. 281:31544- 31552.
19. Lockless, S. W., and R. Ranganathan. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286:295-299.
20. Miyata, Y. O., H. Kojima, and K. Sano. 2001. Mutation analysis of the feedback inhibition site of aspartokinase III of Escherichia coli K-12 and its use in L-threonine production. Biosci. Biotechnol. Biochem. 65:1149-1154.
21. Ohnishi, J., et al. 2002. A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant. Appl. Microbiol. Biotechnol. 58:217-223.
22. Omori, K., Y. Imai, S. I. Suzuki, and S. Komatsubara. 1993. Nucleotide sequence of the Serratia marcescens threonine operon and analysis of the threonine operon mutations which alter feedback inhibition of both aspartokinase I and homoserine dehydrogenase I. J. Bacteriol. 175:785-794.
23. Sano, K., and I. Shiio. 1970. Microbial production of L-lysine III. Production by mutants resistant to S-(2-aminoethyl)-L-cysteine. J. Gen. Appl. Microbiol. 16:373-391.
24. Sindelar, G., and V. F. Wendisch. 2007. Improving lysine production by Corynebacterium glutamicum through DNA microarray-based identification of novel target genes. Appl. Microbiol. Biotechnol. 74:677-689.
25. Smock, R. G., and L. M. Gierasch. 2009. Sending signals dynamically. Science 324:198-203.
26. Stephanopoulos, G. 1999. Metabolic fluxes and metabolic engineering. Metab. Eng. 1:1-11.
27. Suel, G. M., S. W. Lockless, M. A. Wall, and R. Ranganathan. 2003. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10:59-69.
28. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
29. Tsai, C. J., A. Sol, and R. Nussinov. 2009. Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol. Biosyst. 5:207-216.
30. 2-type aspartate kinase from Corynebacterium glutamicum. J. Mol. Biol. 368: 521-536.
31. 2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum. J. Biol. Chem. 285:27477-27486.