In Vitro Reconstitution of Metabolic Pathways: Insights into Nature’s Chemical Logic

Abstract

In vitro analysis of metabolic pathways is becoming a powerful method for gaining a deeper understanding of nature’s core biochemical transformations. Through the astounding advances in biotechnology, the purification of the enzymatic components of a given metabolic pathway is becoming a tractable problem; such in vitro studies permit scientists to capture the fine details of the mechanisms, kinetics, and identities of organic products of enzymatic reactions. In this review, we describe eleven metabolic pathways that have been the subject of recently reported in vitro reconstitution studies. In addition, we have selected and analyzed a subset of four case studies within these eleven examples that exemplify the remarkable organic chemistry that occurs within biological systems. These examples serves as tangible reminders that nature’s biochemical routes obey the fundamental principles of organic chemistry, as their chemical mechanisms are reminiscent of those occurring in conventional synthetic organic routes. The illustrations of biosynthetic chemistry presented in this review might inspire the development of biomimetic chemistries involving abiotic chemical techniques.

1 Introduction

2 Bacterial Metabolites

2.1 Fatty Acids

2.2 Farnesene

2.3 O-Polysaccharides

3 Plant Metabolites

3.1 Dhurrin

3.2 Camalexin

4 Polyketides and Nonribosomal Peptides

4.1 Aromatic Polyketides

4.1.1 Actinorhodin-Derived Polyketides

4.1.2 Enterocin

4.2 Fungal Polyketides

4.2.1 Norsolorinic Acid

4.2.2 Dihydromonacolin L

4.3 Assembly Line Polyketides and Nonribosomal Peptides

4.3.1 6-Deoxyerythronolide B

4.3.2 Asperlicin

5 Discussion of Chemical Insights

5.1 Allylic Carbocation Chemistry Drives Farnesene Synthesis

5.2 Multifunctional Oxidation Chemistry of Cytochrome P450 Enzymes

5.3 A Remarkable Favorskiiase Enzyme Within Enterocin Biosynthesis

5.4 Diels–Alder Chemistry Appears in Biology

6 Concluding Remarks

Key words

biosynthesis - bioorganic chemistry - biomimetic synthesis - enzymes - antibiotics - medicinal chemistry - natural products

• References

• 1 Barnett J, Lichtenthaler F. Yeast 2001; 18: 363
• 2 Barnett JA. Yeast 2003; 20: 509
• 3 Berg JM, Tymoczko JL, Stryer L. Biochemistry . W. H. Freeman; New York: 2012. 7th ed
• 4 Raetz CR. H, Reynolds CM, Trent MS, Bishop RE. Annu. Rev. Biochem. 2007; 76: 295
• 5 Rock CO, Jackowski S. Biochem. Biophys. Res. Commun. 2002; 292: 1155
• 6 Cronan JE, Thomas J. Meth. Enzymol. 2009; 459: 395
• 7 Pfeifer BA, Khosla C. Microbiol. Mol. Biol. Rev. 2001; 65: 106
• 8 Yu X, Liu T, Zhu F, Khosla C. Proc. Natl. Acad. Sci. U. S. A. 2011; 108: 18643
• 9 Xiao X, Yu X, Khosla C. Biochemistry 2013; 52: 8304
• 10 Kuo J, Khosla C. Metab. Eng. 2014; 22: 53
• 11 Liu R, Zhu F, Lu L, Fu A, Lu J, Deng Z, Liu T. Metab. Eng. 2014; 22: 10
• 12 Voet D, Voet JG. Biochemistry . Wiley; Hoboken: 2004. 3rd ed. 942
• 13 Kirby J, Keasling JD. Annu. Rev. Plant Biol. 2009; 60: 335
• 14 Cane DE, Ikeda H. Acc. Chem. Res. 2012; 45: 463
• 15 Citron CA, Gleitzmann J, Laurenzano G, Pukall R, Dickschat JS. ChemBioChem 2012; 13: 202
• 16 Ajikumar P, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G. Mol. Pharmaceutics 2008; 5: 167
• 17 Zhu F, Zhong X, Hu M, Lu L, Deng Z, Liu T. Biotechnol. Bioeng. 2014; 111: 1396
• 18 Goldstein J, Brown M. Nature 1990; 343: 425
• 19 Raetz CR. H, Whitfield C. Annu. Rev. Biochem. 2002; 71: 635
• 20 Whitfield C, Larue K. Nat. Struct. Mol. Biol. 2008; 15: 121
• 21a Woodward R, Yi W, Li L, Zhao G, Eguchi H, Sridhar PR, Guo H, Song JK, Motari E, Cai L, Kelleher P, Liu X, Han W, Zhang W, Ding Y, Li M, Wang PG. Nat. Chem. Biol. 2010; 6: 418
• 21b Han W, Wu B, Li L, Zhao G, Woodward R, Pettit N, Cai L, Thon V, Wang PG. J. Biol. Chem. 2012; 287: 5357
• 22 Yi W, Shao J, Zhu L, Li M, Singh M, Lu Y, Lin S, Li H, Ryu K, Shen J, Guo H, Yao Q, Bush CA, Wang PG. J. Am. Chem. Soc. 2005; 127: 2040
• 23 Wink M. Annu. Plant Rev. 2010; 40: 1
• 24 Hartmann T. Phytochemistry 2007; 68: 2831
• 25 Salim AA, Chin Y, Kinghorn AD In Bioactive Molecules and Medicinal Plants . Ramawat KG, Mérillon J.-M. Springer; Berlin: 2008. Chap. 1 1
• 26 Vetter J. Toxicon 2000; 38: 11
• 27 Kahn RA, Bak S, Svendsen I, Halkier BA, Møller BL. Plant Physiol. 1997; 115: 1661
• 28 Møller B, Conn E. J. Biol. Chem. 1980; 255: 3049
• 29 Facchini P. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2001; 52: 29
• 30 Ahuja I, Kissen R, Bones AM. Trends Plant Sci. 2012; 17: 73
• 31 Møldrup ME, Geu-Flores F, Halkier BA. Plant Cell 2013; 25: 360
• 32 Klein AP, Anarat-Cappillino G, Sattely ES. Angew. Chem. Int. Ed. 2013; 52: 13625
• 33 Walsh CT. Antibiotics: Actions, Origins, Resistance . ASM Press; Washington: 2003
• 34 Carreras C, Pieper R, Khosla C. Top. Curr. Chem. 1997; 188: 85
• 35 Staunton J, Weissman KJ. Nat. Prod. Rep. 2001; 18: 380
• 36 Hopwood DA. Chem. Rev. 1997; 97: 2465
• 37 Fischbach MA, Walsh CT. Chem. Rev. 2006; 106: 3468
• 38 Walsh CT. Science 2004; 303: 1805
• 39 Walsh CT, O’Brien RV, Khosla C. Angew. Chem. Int. Ed. 2013; 52: 7098
• 40 Katz L, Donadio S. Annu. Rev. Microbiol. 1993; 47: 875
• 41 Hopwood D, Sherman D. Annu. Rev. Genet. 1990; 24: 37
• 42 McDaniel R, Ebert-Khosla S, Hopwood DA, Khosla C. Science 1993; 262: 1546
• 43 Shen B, Hutchinson CR. Science 1993; 262: 1535
• 44 Das A, Khosla C. Acc. Chem. Res. 2009; 42: 631
• 45 Fu H, Ebert-Khosla S, Hopwood DA, Khosla C. J. Am. Chem. Soc. 1994; 116: 4166
• 46 Carreras C, Khosla C. Biochemistry 1998; 37: 2084
• 47 Tang Y, Tsai S.-C, Khosla C. J. Am. Chem. Soc. 2003; 125: 12708
• 48 Zawada RJ. X, Khosla C. J. Biol. Chem. 1997; 272: 16184
• 49 Zawada RJ. X, Khosla C. Chem. Biol. 1999; 6: 607
• 50 Akey DL, Gehret JJ, Khare D, Smith JL. Nat. Prod. Rep. 2012; 29: 1038
• 51 Moore BS, Kalaitzis JA, Xiang L. Antonie Van Leeuwenhoek 2005; 87: 49
• 52 Watts KR, Tenney K, Crews P. Curr. Opin. Biotechnol. 2010; 21: 808
• 53 Cheng Q, Xiang L, Izumikawa M, Meluzzi D, Moore BS. Nat. Chem. Biol. 2007; 3: 557
• 54 Xiang L, Kalaitzis JA, Moore BS. Proc. Natl. Acad. Sci. U. S. A. 2004; 101: 15609
• 55 Akhrem AA, Ustynyuk TK, Titov YA. Russ. Chem. Rev. 1970; 39: 732
• 56 Teufel R, Miyanaga A, Michaudel Q, Stull F, Louie G, Noel JP, Baran PS, Palfey B, Moore BS. Nature 2013; 503: 552
• 57 Simpson TJ, Cox RJ In Wiley Encyclopedia of Chemical Biology . Begley TP. Wiley; Oxford: 2009. doi: 10.1002/9780470048672.wecb458
• 58 Crawford JM, Townsend CA. Nat. Rev. Microbiol. 2010; 8: 879
• 59 Crawford JM, Thomas PM, Scheerer JR, Vagstad AL, Kelleher NL, Townsend CA. Science 2008; 320: 243
• 60 Vagstad AL, Bumpus SB, Belecki K, Kelleher NL, Townsend CA. J. Am. Chem. Soc. 2012; 134: 6865
• 61 Ma SM, Li JW.-H, Choi JW, Zhou H, Lee KK. M, Moorthie VA, Xie X, Kealey JT, Da Silva NA, Vederas JC, Tang Y. Science 2009; 326: 589
• 62 Xu W, Chooi Y.-H, Choi JW, Li S, Vederas JC, Da Silva NA, Tang Y. Angew. Chem. Int. Ed. 2013; 52: 6472
• 63 Meehan MJ, Xie X, Zhao X, Xu W, Tang Y, Dorrestein PC. Biochemistry 2011; 50: 287
• 64 Khosla C, Tang Y, Chen AY, Schnarr NA, Cane DE. Annu. Rev. Biochem. 2007; 76: 195
• 65 Cortes J, Haydock S, Roberts G. Nature 1990; 348: 176
• 66 Donadio S, Staver M, McAlpine J. Science 1991; 252: 675
• 67 Gokhale RS, Tsuji SY, Cane DE, Khosla C. Science 1999; 284: 482
• 68 Broadhurst RW, Nietlispach D, Wheatcroft MP, Leadlay PF, Weissman KJ. Chem. Biol. 2003; 10: 723
• 69 Wong FT, Chen AY, Cane DE, Khosla C. Biochemistry 2010; 49: 95
• 70 Kapur S, Chen A, Cane D, Khosla C. Proc. Natl. Acad. Sci. U. S. A. 2010; 107: 22066
• 71 Kapur S, Lowry B, Yuzawa S, Kenthirapalan S, Chen AY, Cane DE, Khosla C. Proc. Natl. Acad. Sci. U. S. A. 2012; 109: 4110
• 72 Lowry B, Robbins T, Weng C.-H, O’Brien RV, Cane DE, Khosla C. J. Am. Chem. Soc. 2013; 135: 16809
• 73 Dunn BJ, Khosla C. J. R. Soc., Interface 2013; 10: 20130297 ; doi: 10.1098/rsif.2013.0297
• 74 Sattely ES, Fischbach MA, Walsh CT. Nat. Prod. Rep. 2008; 25: 757
• 75 Gao X, Jiang W, Jiménez-Osés G, Choi MS, Houk KN, Tang Y, Walsh CT. Chem. Biol. 2013; 20: 870
• 76 Naredla RR, Klumpp DA. Chem. Rev. 2013; 113: 6905
• 77 Faraldos JA, Gonzalez V, Li A, Yu F, Köksal M, Christianson DW, Alleman RA. J. Am. Chem. Soc. 2012; 134: 20844
• 78 Nicolaou KC, Kang Q, Wu TR, Lim CS, Chen DY.-K. J. Am. Chem. Soc. 2010; 132: 7540
• 79 Meunier B, de Visser SP, Shaik S. Chem. Rev. 2004; 104: 3947
• 80 Coon MJ. Annu. Rev. Pharmacol. Toxicol. 2005; 45: 1
• 81 Denisov IG, Makris TM, Sligar SG, Schlichting I. Chem. Rev. 2005; 105: 2253
• 82 Sibbesen O, Koch B, Halkier BA, Møller BL. J. Biol. Chem. 1995; 270: 3506
• 83 Nicolaou KC, Snyder SA, Montagnon T, Vassilikogiannakis G. Angew. Chem. Int. Ed. 2002; 41: 1668
• 84 Woodward RB, Katz T. Tetrahedron 1959; 5: 70
• 85 Stocking EM, Williams RM. Angew. Chem. Int. Ed. 2003; 42: 3078