Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

Nature Communications

Volumn 6, Issue , 2015, Pages

  Mak, Wai Shun ^a   Tran, Stephen ^b   Marcheschi, Ryan ^c   Bertolani, Steve ^a   Thompson, James ^d   Baker, David ^d   Liao, James C ^b,c   Siegel, Justin B ^a,e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of California   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DERIVATIVE; ENZYME; SUGAR; OXOACID;

ALCOHOL; BIOENGINEERING; BIOINFORMATICS; CATALYSIS; DATABASE; EFFICIENCY MEASUREMENT; ENZYME ACTIVITY; GENOMICS; MOLECULAR ANALYSIS; SUGAR;

ALCOHOL PRODUCTION; ARTICLE; BIOINFORMATICS; BIOSYNTHESIS; CATALYTIC EFFICIENCY; SEQUENCE DATABASE; BIOLOGY; CHEMICAL STRUCTURE; ESCHERICHIA COLI; GENETICS; GENOMICS; METABOLISM;

ALCOHOLS; BIOSYNTHETIC PATHWAYS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENOMICS; KETO ACIDS; MODELS, MOLECULAR;

EID: 84948178435     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms10005     Document Type: Article

References (34)

1. USA White House. National Bioeconomy Blueprint (The White House, 2012).
2. USDA, US. Bio-Based Products: Market Potential And Projections Through 2025 (US Department of Agriculture, 2008).
3. Zhang, K., Sawaya, M. R., Eisenberg, D. S. & Liao, J. C. Expanding metabolism for biosynthesis of non-natural alcohols. Proc. Natl Acad. Sci. USA 105, 20653-20658 (2008).
4. Marcheschi, R. J. et al. A synthetic recursive " + 1" pathway for carbon chain elongation. ACS Chem. Biol. 7, 689-697 (2012).
5. Erickson, B. & Winters, P. Perspective on opportunities in industrial biotechnology in renewable chemicals. Biotechnol. J. 7, 176-185 (2012).
6. Plaza, M. et al. Biochemical and molecular characterization of α-ketoisovalerate decarboxylase, an enzyme involved in the formation of aldehydes from amino acids by Lactococcus lactis. FEMS Microbiol. Lett. 238, 367-374 (2004).
7. Felnagle, E. A. et al. Engineering synthetic recursive pathways to generate non-natural small molecules. Nat. Chem. Biol. 8, 518-526 (2012).
8. Bayer, T. S. et al. Synthesis of methyl halides from biomass using engineered microbes. J. Am. Chem. Soc. 131, 6508-6515 (2009).
9. Heins, Richard A. et al. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem. Biol. 9, 2082-2091 (2014).
10. The National Academies. Industrialization of Biology: A Roadmap to Accelerate Advanced Manufacturing of Chemicals (The National Academis Press, 2015).
11. Richter, F. et al. De novo enzyme design using Rosetta3. PLoS ONE 6, e19230 (2011).
12. Finn, Robert D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230 (2013).
13. Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29-W37 (2011).
14. Song, Yifan et al. High-resolution comparative modeling with RosettaCM. Structure 21, 1735-1742 (2013).
15. Huang, Y. et al. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26, 680-682 (2010).
16. Zhang, Y. & Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33, 2302-2309 (2005).
17. Berthold, C. L. et al. Structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis provides insights into the structural basis for the chemoselective and enantioselective carboligation reaction. Acta Crystallogr. D 63, 1217-1224 (2007).
18. Bruning, M. et al. Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediatez . Biochemistry 48, 3258-3268 (2009).
19. Shen, C. R. & Liao, J. C. Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the ketoacid pathways. Metab. Eng. 10, 312-320 (2008).
20. Kell, D. B. et al. Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends Biotechnol. 33, 237-246 (2015).
21. Foo, J. L. et al. Improving microbial biogasoline production in Escherichia coli using tolerance engineering. mBio 5, e01932-14 (2014).
22. Brennan, T. C. R. et al. Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae. Biotechnol. Bioeng. 109, 2513-2522 (2012).
23. Schnoes, A. M. et al. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol. 5, e1000605 (2009).
24. Parekh, S. Strain improvement. Desk Encyclopedia of Microbiology (Academic Press, 2010).
25. Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649 (2012).
26. Shao, Y. et al. Advances in methods and algorithms in a modern quantum chemistry program package. Phys. Chem. Chem. Phys. 8, 3172-3191 (2006).
27. Oechem, T. K. version 1.7. 7 (OpenEye Scientific Software Inc, 2012).
28. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
29. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128 (2007).
30. Letunic, I. & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011).
31. Gibson, G. D. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
32. Datsenko, A. K. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640-6645 (2000).
33. Gasteiger, E. et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31, 3784-3788 (2003).
34. The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.