Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering

Metabolic Engineering

Volumn 28, Issue , 2015, Pages 123-133

  Alonso Gutierrez, Jorge ^a,b   Kim, Eun Mi ^a,b   Batth, Tanveer S ^a,b   Cho, Nathan ^a,b,c   Hu, Qijun ^a,b,d   Chan, Leanne Jade G ^a,b   Petzold, Christopher J ^a,b   Hillson, Nathan J ^a,b   Adams, Paul D ^a,b,d   Keasling, Jay D ^a,b,d,e   Garcia Martin, Hector ^a,b   Lee, Taek Soon ^a,b  

^a JOINT BIOENERGY INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c Department of Civil and Environmental Engineering   (United States)

^d University of California at Berkeley   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Escherichia coli; Heterologous pathway; Metabolic engineering; Mevalonate pathway; Principal component analysis (PCA); Targeted proteomics

Indexed keywords

DATA HANDLING; ENZYMES; ESCHERICHIA COLI; GENE EXPRESSION; METABOLIC ENGINEERING; METABOLISM; MOLECULAR BIOLOGY; MOLECULES;

COMPUTATIONAL TOOLS; EXPRESSION LEVELS; HETEROLOGOUS PATHWAY; ISOPRENOIDS; MEVALONATE PATHWAY; PRODUCTION DATA; TARGET MOLECULE; TARGETED PROTEOMICS;

PRINCIPAL COMPONENT ANALYSIS;

ISOPRENOID; LIMONENE; MEVALONIC ACID; ESCHERICHIA COLI PROTEIN; TERPENE;

ARTICLE; ESCHERICHIA COLI; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; METABOLIC ENGINEERING; NONHUMAN; PRINCIPAL COMPONENT ANALYSIS; PRINCIPAL COMPONENT ANALYSIS OF PROTEOMICS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PROCEDURES;

ESCHERICHIA COLI;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; METABOLIC ENGINEERING; PROTEOMICS; TERPENES;

EID: 84921278263     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2014.11.011     Document Type: Article

References (49)

1. Abdi H., Williams L.J. Principal Component Analysis 2010, 2:433-459. (Wiley Interdisciplinary Reviews: Computational Statistics). 10.1002/wics.101.
2. Ajikumar P.K., Xiao W.-H., Tyo K.E.J., Wang Y., Simeon F., Leonard E., Mucha O., Phon T.H., Pfeifer B., Stephanopoulos G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 2010, 330:70-74. 10.1126/science.1191652.
3. Alonso-Gutierrez J., Chan R., Batth T.S., Adams P.D., Keasling J.D., Petzold C.J., Lee T.S. Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Metab. Eng. 2013, 19:33-41. 10.1016/j.ymben.2013.05.004.
4. Alter O., Brown P.O., Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA 2000, 97:10101-10106.
5. Anderson J.C., Dueber J.E., Leguia M., Wu G.C., Goler J.A., Arkin A.P., Keasling J.D. BglBricks: a flexible standard for biological part assembly. J. Biol. Eng. 2010, 4:1. 10.1186/1754-1611-4-1.
6. Anthony J.R., Anthony L.C., Nowroozi F., Kwon G., Newman J.D., Keasling J.D. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab. Eng. 2009, 11:13-19.
7. Atsumi S., Hanai T., Liao J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86. (86-U13.). 10.1038/Nature06450.
8. Batth T.S., Singh P., Ramakrishnan V.R., Sousa M.M.L., Chan L.J.G., Tran H.M., Luning E.G., Pan E.H.Y., Vuu K.M., Keasling J.D., Adams P.D., Petzold C.J. A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins. Metab. Eng. 2014, 26:48-56. 10.1016/j.ymben.2015.08.004.
9. Bokinsky G., Peralta-Yahya P.P., George A., Holmes B.M., Steen E.J., Dietrich J., Lee T.S., Tullman-Ercek D., Voigt C.A., Simmons B.A., Keasling J.D. Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc. Natl. Acad. Sci. USA 2011, 108:19949-19954.
10. Burke C., Croteau R. Geranyl diphosphate synthase from Abies grandis: cDNA isolation, functional expression, and characterization. Arch. Biochem. Biophys. 2002, 405:130-136.
11. Cangelosi R., Goriely A. Component retention in principal component analysis with application to cDNA microarray data. Biol. Direct 2007, 2:2. 10.1186/1745-6150-2-2.
12. Casadaban M.J., Cohen S.N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J. Mol. Biol. 1980, 138:179-207.
13. Crescenzi M., Giuliani A. The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data. FEBS Lett. 2001, 507:114-118.
14. Dahl R.H., Zhang F., Alonso-Gutierrez J., Baidoo E., Batth T.S., Redding-Johanson A.M., Petzold C.J., Mukhopadhyay A., Lee T.S., Adams P.D., Keasling J.D. Engineering dynamic pathway regulation using stress-response promoters. Nat. Biotechnol. 2013, 1-10. 10.1038/nbt.2689.
15. Dellomonaco C., Clomburg J.M., Miller E.N., Gonzalez R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 2011, 476:355-359. 10.1038/nature10333.
16. Di Ventura B., Lemerle C., Michalodimitrakis K., Serrano L. From in vivo to in silico biology and back. Nature 2006, 443:527-533. 10.1038/nature05127.
17. Dueber J.E., Wu G.C., Malmirchegini G.R., Moon T.S., Petzold C.J., Ullal A.V., Prather K.L.J., Keasling J.D. Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 2009, 27:753-759. 10.1038/nbt.1557.
18. Francis D.M., Page R. Strategies to optimize protein expression in E. coli. Current Protocols in Protein Science 2010, (Chapter 5, Unit 5.24.1-29). 10.1002/0471140864.ps0524s61.
19. Goh E.B., Baidoo E.E.K., Keasling J.D., Beller H.R. Engineering of bacterial methyl ketone synthesis for biofuels. Appl. Environ. Microbiol. 2012, 78:70-80.
20. Ham T.S., Dmytriv Z., Plahar H., Chen J., Hillson N.J., Keasling J.D. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 2012, 40:e141. 10.1093/nar/gks531.
21. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 1983, 166:557-580.
22. Holter N.S., Mitra M., Maritan A., Cieplak M., Banavar J.R., Fedoroff N.V. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl. Acad. Sci. USA 2000, 97:8409-8414. 10.1073/pnas.150242097.
23. Holtz W.J., Keasling J.D. Engineering static and dynamic control of synthetic pathways. Cell 2010, 140:19-23. 10.1016/j.cell.2009.12.029.
24. Hyatt D.C., Youn B., Zhao Y., Santhamma B., Coates R.M., Croteau R.B., Kang C. Structure of limonene synthase, a simple model for terpenoid cyclase catalysis. Proc. Natl. Acad. Sci. USA 2007, 104:5360-5365. 10.1073/pnas.0700915104.
25. Juminaga D., Baidoo E.E.K., Redding-Johanson A.M., Batth T.S., Burd H., Mukhopadhyay A., Petzold C.J., Keasling J.D. Modular engineering of L-tyrosine production in Escherichia coli. Appl. Environ. Microbiol. 2012, 78:89-98.
26. Keasling J.D. Manufacturing molecules through metabolic engineering. Science 2010, 330:1355-1358. 10.1126/science.1193990.
27. Lee J.W., Na D., Park J.M., Lee J., Choi S., Lee S.Y. Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol. 2012, 8:536-546. 10.1038/nchembio.970.
28. Lee T.S., Krupa R.A., Zhang F., Hajimorad M., Holtz W.J., Prasad N., Lee S.K., Keasling J.D. BglBrick vectors and datasheets: a synthetic biology platform for gene expression. J. Biol. Eng. 2011, 5:12. 10.1186/1754-1611-5-12.
29. MacLean B., Tomazela D.M., Shulman N., Chambers M., Finney G.L., Frewen B., Kern R. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26:966-968.
30. Maier T., Güell M., Serrano L. Correlation of mRNA and protein in complex biological samples. FEBS Lett. 2009, 583:3966-3973. 10.1016/j.febslet.2009.10.036.
31. Martin V.J.J., Pitera D.J., Withers S.T., Newman J.D., Keasling J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 21:796-802. 10.1038/Nbt833.
32. Misra J., Schmitt W., Hwang D., Hsiao L.-L., Gullans S., Stephanopoulos G., Stephanopoulos G. Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res. 2002, 12:1112-1120. 10.1101/gr.225302.
33. Moon T.S., Dueber J.E., Shiue E., Prather K.L.J. Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab. Eng. 2010, 12:298-305. 10.1016/j.ymben.2010.01.003.
34. Mutalik V.K., Guimaraes J.C., Cambray G., Lam C., Christoffersen M.J., Mai Q.-A., Tran A.B., Paull M., Keasling J.D., Arkin A.P., Endy D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 2013, 10:354-360. 10.1038/nmeth.2404.
35. Özaydin B., Burd H., Lee T.S., Keasling J.D. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab. Eng. 2013, 15:174-183. 10.1016/j.ymben.2012.07.010.
36. Pearson K. On lines and planes of closest fit to systems of points in space. Philos. Mag. 1901, 2:559-572.
37. Peralta-Yahya P.P., Ouellet M., Chan R., Mukhopadhyay A., Keasling J.D., Lee T.S. Identification and microbial production of a terpene-based advanced biofuel. Nat. Commun. 2011, 2:483. 10.1038/ncomms1494.
38. Peralta-Yahya P.P., Zhang F., del Cardayre S.B., Keasling J.D. Microbial engineering for the production of advanced biofuels. Nature 2012, 488:320-328. 10.1038/nature11478.
39. Pitera D.J., Paddon C.J., Newman J.D., Keasling J.D. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng. 2007, 9:193-207. 10.1016/J.Ymben.2006.11.002.
40. Redding-Johanson A.M., Batth T.S., Chan R., Krupa R., Szmidt H.L., Adams P.D., Keasling J.D., Lee T.S., Mukhopadhyay A., Petzold C.J. Targeted proteomics for metabolic pathway optimization: application to terpene production. Metab. Eng. 2011, 13:194-203.
41. Rossell S., Solem C., Jensen P.R., Heijnen J.J. Towards a quantitative prediction of the fluxome from the proteome. Metab. Eng. 2011, 13:253-262. 10.1016/j.ymben.2011.01.010.
42. Silva J.C., Gorenstein M.V., Li G.-Z., Vissers J.P.C., Geromanos S.J. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5:144-156. 10.1074/mcp.M500230-MCP200.
43. Stephanopoulos G. Synthetic biology and metabolic engineering. ACS Synth. Biol. 2012, 1:514-525. 10.1021/sb300094q.
44. Tsuruta H., Paddon C.J., Eng D., Lenihan J.R., Horning T., Anthony L.C., Regentin R., Keasling J.D., Renninger N.S., Newman J.D. High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One 2009, 4:e4489. 10.1371/journal.pone.0004489.
45. Wall M.E., Rechtsteiner A., Rocha L.M. Chapter 5 singular value decomposition and principal component analysis. A Practical Approach to Microarray Data Analysis 2003, 91-109. Kluwer, Norwell, MA. D.P. Berrar, W. Dubitzky, M. Granzow (Eds.).
46. Woolston B.M., Edgar S., Stephanopoulos G. Metabolic engineering: past and future. Annu. Rev. Chem. Biomol. Eng. 2013, 4:259-288. 10.1146/annurev-chembioeng-061312-103312.
47. Xu P., Gu Q., Wang W., Wong L., Bower A.G.W., Collins C.H., Koffas M.a G. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat. Commun. 2013, 4:1409. 10.1038/ncomms2425.
48. Yadav V.G., De Mey M., Lim C.G., Ajikumar K., Stephanopoulos G. The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab. Eng. 2013, 14:233-241. 10.1016/j.ymben.2012.02.001.
49. Zhang F., Carothers J.M., Keasling J.D. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 2012, 30:1-7. 10.1038/nbt.2149.