Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids

PeerJ

Volumn 2015, Issue 6, 2015, Pages

  Ford, Tyler J ^a   Way, Jeffrey C ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

CoA synthetase; Fatty acid metabolism; Fatty acids; Protein engineering

Indexed keywords

LONG CHAIN FATTY ACID;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SPECIFICITY; ESCHERICHIA COLI; FATTY ACID METABOLISM; FLUORESCENCE ACTIVATED CELL SORTING; GENE MUTATION; NONHUMAN; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; WESTERN BLOTTING;

EID: 84944734306     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.1040     Document Type: Article

References (45)

1. Akhtar MK, Dandapani H, Thiel K, Jones PR. 2015. Microbial Production of 1-octanol: a naturally excreted biofuel with diesel-like properties. Metabolic Engineering Communications 2:1-5 DOI 10.1016/j.meteno.2014.11.001.
2. Arnold K, Bordoli L, Kopp J, Schwede T. 2006. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195-201 DOI 10.1093/bioinformatics/bti770.
3. Benkert P, Biasini M, Schwede T. 2011. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27:343-350 DOI 10.1093/bioinformatics/btq662.
4. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. 2014. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research 42:W252-W258 DOI 10.1093/nar/gku340.
5. Black PN, DiRusso CC, Metzger AK, Heimert TL. 1992. Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. The Journal of Biological Chemistry 267:25513-25520.
6. Black PN, DiRusso CC, Sherin D, MacColl R, Knudsen J, Weimar JD. 2000. Affinity labeling fatty acyl-CoA synthetase with 9-p-azidophenoxy nonanoic acid and the identification of the fatty acid-binding site. The Journal of Biological Chemistry 275:38547-38553 DOI 10.1074/jbc. M006413200.
7. Black PN, Zhang Q, Weimar JD, DiRusso CC. 1997. Mutational analysis of a fatty acyl-coenzyme A synthetase signature motif identifies seven amino acid residues that modulate fatty acid substrate specificity. The Journal of Biological Chemistry 272:4896-4903 DOI 10.1074/jbc.272.8.4896.
8. Campbell JW, Morgan-Kiss RM, Cronan JE. 2003. A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic beta-oxidation pathway. Molecular Microbiology 47:793-805 DOI 10.1046/j.1365-2958.2003.03341.x.
9. Choi YJ, Lee SY. 2013. Microbial production of short-chain alkanes. Nature 502:571-574 DOI 10.1038/nature12536.
10. Chung CT, Niemela SL, Miller RH. 1989. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proceedings of the National Academy of Sciences of the United States of America 86:2172-2175 DOI 10.1073/pnas.86.7.2172.
11. Conti E, Franks NP, Brick P. 1996. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 4:287-298 DOI 10.1016/S0969-2126(96)00033-0.
12. Conti E, Stachelhaus T, Marahiel MA, Brick P. 1997. Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. The EMBO Journal 16:4174-4183 DOI 10.1093/emboj/16.14.4174.
13. Dehesh K, Edwards P, Hayes T, Cranmer AM, Fillatti J. 1996. Two novel thioesterases are key determinants of the bimodal distribution of acyl chain length of Cuphea palustris seed oil. Plant Physiology 110:203-210 DOI 10.1104/pp.110.1.203.
14. Dellomonaco C, Clomburg JM, Miller EN, Gonzalez R. 2011. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 476:355-359 DOI 10.1038/nature10333.
15. Doan TT, Carlsson AS, Hamberg M, Bulow L, Stymne S, Olsson P. 2009. Functional expression of five Arabidopsis fatty acyl-CoA reductase genes in Escherichia coli. Journal of Plant Physiology 166:787-796 DOI 10.1016/j.jplph.2008.10.003.
16. Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723 DOI 10.1002/elps.1150181505.
17. Gulick AM. 2009. Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase. ACS Chemical Biology 4:811-827 DOI 10.1021/cb900156h.
18. Gulick AM, Starai VJ, Horswill AR, Homick KM, Escalante-Semerena JC. 2003. The 1.75 A crystal structure of acetyl-CoA synthetase bound to adenosine-5'-propylphosphate and coenzyme A. Biochemistry 42:2866-2873 DOI 10.1021/bi0271603.
19. Handke P, Lynch SA, Gill RT. 2011. Application and engineering of fatty acid biosynthesis in Escherichia coli for advanced fuels and chemicals. Metabolic Engineering 13:28-37 DOI 10.1016/j.ymben.2010.10.007.
20. Hisanaga Y, Ago H, Nakagawa N, Hamada K, Ida K, Yamamoto M, Hori T, Arii Y, Sugahara M, Kuramitsu S, Yokoyama S, Miyano M. 2004. Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. The Journal of Biological Chemistry 279:31717-31726 DOI 10.1074/jbc. M400100200.
21. Hu Y, Gai Y, Yin L, Wang X, Feng C, Feng L, Li D, Jiang XN, Wang DC. 2010. Crystal structures of a Populus tomentosa 4-coumarate: CoA ligase shed light on its enzymatic mechanisms. The Plant Cell 22:3093-3104 DOI 10.1105/tpc.109.072652.
22. Iram SH, Cronan JE. 2006. The beta-oxidation systems of Escherichia coli and Salmonella enterica are not functionally equivalent. Journal of Bacteriology 188:599-608 DOI 10.1128/JB.188.2.599-608.2006.
23. Kameda K, Nunn WD. 1981. Purification and characterization of acyl coenzyme A synthetase from Escherichia coli. The Journal of Biological Chemistry 256:5702-5707.
24. Karchin R, Cline M, Karplus K. 2004. Evaluation of local structure alphabets based on residue burial. Proteins 55:508-518 DOI 10.1002/prot.20008.
25. Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. 2003. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins 51:504-514 DOI 10.1002/prot.10369.
26. Karplus K. 2009. SAM-T08, HMM-based protein structure prediction. Nucleic Acids Research 37:W492-W497 DOI 10.1093/nar/gkp403.
27. Karplus K, Hu B. 2001. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics 17:713-720 DOI 10.1093/bioinformatics/17.8.713.
28. Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. 2001. What is the value added by human intervention in protein structure prediction?. Proteins (Suppl 5):86-91 DOI 10.1002/prot.10021.
29. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. 2003. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 53(Suppl 6):491-496 DOI 10.1002/prot.10540.
30. Karplus K, Katzman S, Shackleford G, Koeva M, Draper J, Barnes B, Soriano M, Hughey R. 2005. SAM-T04: what is new in protein-structure prediction for CASP6. Proteins 61(Suppl 7):135-142 DOI 10.1002/prot.20730.
31. Knothe G. 2009. Improving biodiesel fuel properties by modifying fatty ester composition. Energy and Environmental Science 2:759-766 DOI 10.1039/b903941d.
32. Kochan G, Pilka ES, von Delft F, Oppermann U, Yue WW. 2009. Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A. Journal of Molecular Biology 388:997-1008 DOI 10.1016/j.jmb.2009.03.064.
33. Mangroo D, Gerber GE. 1993. Fatty acid uptake in Escherichia coli: regulation by recruitment of fatty acyl-CoA synthetase to the plasma membrane. Biochemistry and Cell Biology 71:51-56 DOI 10.1139/o93-008.
34. Morgan-Kiss RM, Cronan JE. 2004. The Escherichia coli fadK (ydiD) gene encodes an anerobically regulated short chain acyl-CoA synthetase. The Journal of Biological Chemistry 279:37324-37333 DOI 10.1074/jbc. M405233200.
35. Overath P, Pauli G, Schairer HU. 1969. Fatty acid degradation in Escherichia coli. An inducible acyl-CoA synthetase, the mapping of old-mutations, and the isolation of regulatory mutants. European Journal of Biochemistry/FEBS 7:559-574 DOI 10.1111/j.1432-1033.1969.tb19644.x.
36. Roy A, Kucukural A, Zhang Y. 2010. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols 5:725-738 DOI 10.1038/nprot.2010.5.
37. Salanitro JP, Wegener WS. 1971. Growth of Escherichia coli on short-chain fatty acids: growth characteristics of mutants. Journal of Bacteriology 108:885-892.
38. Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9:671-675 DOI 10.1038/nmeth.2089.
39. Shackelford G, Karplus K. 2007. Contact prediction using mutual information and neural nets. Proteins 69(Suppl 8):159-164 DOI 10.1002/prot.21791.
40. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, Del Cardayre SB, Keasling JD. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559-562 DOI 10.1038/nature08721.
41. Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. 2013. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proceedings of the National Academy of Sciences of the United States of America 110:11290-11295 DOI 10.1073/pnas.1307129110.
42. Voelker TA, Davies HM. 1994. Alteration of the specificity and regulation of fatty acid synthesis of Escherichia coli by expression of a plant medium-chain acyl-acyl carrier protein thioesterase. Journal of Bacteriology 176:7320-7327.
43. Yang JY, Yan RX, Roy A, Xu D, Poisson J, Zhang Y. 2015. The I-TASSER Suite: protein structure and function prediction. Nature Methods 12:7-8 DOI 10.1038/nmeth.3213.
44. Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40 DOI 10.1186/1471-2105-9-40.
45. Zhang F, Carothers JM, Keasling JD. 2012. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nature Biotechnology 30:354-359 DOI 10.1038/nbt.2149.