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Biotechnological potential of the ethylmalonyl-CoA pathway

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Abstract

The ethylmalonyl-CoA pathway is central to the carbon metabolism of many α-proteobacteria, like Rhodobacter sphaeroides and Methylobacterium extorquens as well as actinomycetes, like Streptomyces spp. Its function is to convert acetyl-CoA, a central carbon intermediate, to other precursor metabolites for cell carbon biosynthesis. In contrast to the glyoxylate cycle—another widely distributed acetyl-CoA assimilation strategy—the ethylmalonyl-CoA pathway contains many unique CoA-ester intermediates, such as (2R)- and (2S)-ethylmalonyl-CoA, (2S)-methylsuccinyl-CoA, mesaconyl-(C1)-CoA, and (2R, 3S)-methylmalyl-CoA. With this come novel catalysts that interconvert these compounds. Among these unique enzymes is a novel carboxylase that reductively carboxylates crotonyl-CoA, crotonyl-CoA carboxylase/reductase, and (3S)-malyl-CoA thioesterase. The latter represents the first example of a non-Claisen condensation enzyme of the malate synthase superfamily and defines a new class of thioesterases apart from the hotdog-fold and α/β-fold thioesterases. The biotechnological implications of the ethylmalonyl-CoA pathway are tremendous as one looks to tap into the potential of using these new intermediates and catalysts to produce value-added products.

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References

  • Alber BE, Spanheimer R, Ebenau-Jehle C, Fuchs G (2006) Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides. Mol Microbiol 61:297–309

    Article  CAS  Google Scholar 

  • Anthony C (1982) The biochemistry of methylotrophs. Academic, London

    Google Scholar 

  • Arai H, Roh JH, Kaplan S (2008) Transriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1. J Bacteriol 190:286–299

    Article  CAS  Google Scholar 

  • Barnes EM, Wakil SJ (1968) Studies of the mechanism of fatty acid synthesis. XIX. Preparation and general properties of palmityl thioesterase. J Biol Chem 243:2955–2962

    CAS  Google Scholar 

  • Bauer CE, Bird TH (1996) Regulatory circuits controlling photosynthesis gene expression. Cell 85:5–8

    Article  CAS  Google Scholar 

  • Benning MM, Wesenberg G, Liu R, Taylor KL, Dunaway-Mariano D, Holden HM (1998) The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. strain CBS-3. J Biol Chem 273:33572–33579

    Article  CAS  Google Scholar 

  • Berthold CL, Toyota CG, Richards NGJ, Lindqvist Y (2008) Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase. J Biol Chem 283:6519–6529

    Article  CAS  Google Scholar 

  • Buckel W, Dorn U, Semmler R (1981) Glutaconate CoA-transferase from Acidaminococcus fermentas. Eur J Biochem 118:315–321

    Article  CAS  Google Scholar 

  • Buckel W, Kratky C, Golding BT (2006) Stabilization of methylene radicals by cobalamin in coenzyme B12 dependent mutases. Chem Eur J 12:352–362

    Article  Google Scholar 

  • Cao J, Hang X, Zhao H, Gong W, Dunaway-Mariano D (2009) The mechanism of human hotdog-fold thioesterase 2 (hTHEM2) substarte recognition and catalysis illuminated by a structure and function based analysis. Biochemistry 48:1293–1304

    Article  CAS  Google Scholar 

  • Chan YA, Podevels AM, Kevany BM, Thomas MG (2009) Biosynthesis of polyketide synthase extender units. Nat Prod Rep 26:10–114

    Article  Google Scholar 

  • Chisterodova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499

    Article  Google Scholar 

  • Chistoserdova L, Lidstrom ME (1996) Molecular characterization of a chromosomal region involved in the oxidation of acetyl-CoA to glyoxylate in the isocitrate-lyase-negative methylotroph Methylobacterium extorquens AM1. Microbiology 142:1459–1468

    Article  Google Scholar 

  • Chistoserdova L, Chen S-W, Lapidus A, Lidstrom ME (2003) Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol 185:2980–2987

    Article  CAS  Google Scholar 

  • Cho H, Cronan JE (1993) Escherichia coli thioesterase I, molecular cloning and sequencing of the structural gene and identification as a periplasmic enzyme. J Biol Chem 268:9238–9245

    CAS  Google Scholar 

  • Choudhary M, Zabhua X, Fu YX, Kaplan S (2007) Genome analyses of three strains of Rhodobacter sphaeroides: evidence of rapid evolution of chromosome II. J Bacteriol 189:1914–1921

    Article  CAS  Google Scholar 

  • de Koning GJM, Kellerhals M, van Meurs C, Witholt B (1997) A process for the recovery of poly(hydroxyalkanoates) from Pseudomnas. Part 2: process, development and economic evaluation. Bioprocess Eng 17:15–21

    Article  Google Scholar 

  • Eraso JM, Kaplan S (1994) prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacetr sphaeroides. J Bacteriol 176:32–43

    CAS  Google Scholar 

  • Erb TJ (2009) The ethylmalonyl-CoA pathway: a novel acetyl-CoA assimilation strategy. Doctoral thesis, Albert-Ludwigs-Universität Freiburg

  • Erb TJ, Berg IA, Brecht V, Müller M, Fuchs G, Alber BE (2007) Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. Proc Natl Acad Sci USA 104:10631–10636

    Article  CAS  Google Scholar 

  • Erb TJ, Rétey J, Fuchs G, Alber BE (2008) Ethylmalonyl-CoA mutase from Rhodobacter sphaeroides defines a new subclass of coenzyme B12-dependent acyl-CoA mutases. J Biol Chem 283:32283–32293

    Article  CAS  Google Scholar 

  • Erb TJ, Brecht V, Fuchs G, Müller M, Alber BE (2009a) Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase. Proc Natl Acad Sci USA 106:8871–8876

    Article  CAS  Google Scholar 

  • Erb TJ, Fuchs G, Alber BE (2009b) (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Mol Microbiol 73:992–1008

    Article  CAS  Google Scholar 

  • Erb TJ, Frerichs-Revermann L, Fuchs G, Alber BE (2010) The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J Bacteriol 192:1249–1258

    Article  CAS  Google Scholar 

  • Eustáquio AS, McGlinchey RP, Liu Y, Hazzard C, Beer LL, Florova G, Alhamadsheh MM, Lechner A, Kale AJ, Kobayashi Y, Reynolds KA, Moore BS (2009) Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-l-methionine. Proc Natl Acad Sci USA 106:12295–12300

    Article  Google Scholar 

  • Fleck CB, Brock M (2008) Characterization of an acyl-CoA:carboxylate CoA-transferase from Aspergillus nidulans involved in propionyl-CoA detoxification. Mol Microbiol 68:642–656

    Article  CAS  Google Scholar 

  • Fuchs G (1999) Biosynthesis of building blocks, chapter 7. In: Lengeler JW, Drews G, Schlegel HG (eds) Biology of the prokaryotes. Thieme, Stuttgart, pp 114–116

    Google Scholar 

  • Gibson JL, Tabita FR (1993) Nucleotide sequence and functional analysis of CbbR, a positive regulator of the Calvin cycle operons of Rhodobacter sphaeroides. J Bacteriol 175:5778–5784

    CAS  Google Scholar 

  • Goulding CW, Bowers PM, Segelke B, Lekin T, Kim C-Y, Terwilliger TC, Eisenberg D (2007) The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function. J Mol Biol 365:275–283

    Article  CAS  Google Scholar 

  • Gu L, Wang B, Kulkarni A, Geders TW, Gri RV, Gerwick L, Håkansson K, Wipf P, Smith JL, Gerwick WH, Sherman DH (2009) Metamorphic enzyme assembly in polyketide diversification. Nature 459:731–735

    Article  CAS  Google Scholar 

  • Heider J (2001) A new family of CoA-transferases. FEBS Lett 509:345–349

    Article  CAS  Google Scholar 

  • Howard BR, Endrizzi JA, Remington SJ (2000) Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 Å resolution: mechanistic implications. Biochemistry 39:3156–3168

    Article  CAS  Google Scholar 

  • Ind AC, Porter SL, Brown MT, Byles ED, de Beyer JA, Godfrey SA, Armitage JP (2009) Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Appl Environ Microbiol 75:6613–6615

    Article  CAS  Google Scholar 

  • Joshi HM, Tabita FR (1996) A global two component signal transduction system that integrates the control of photosynthesis, carbon dioxide assimilation, and nitrogen fixation. Proc Natl Acad Sci USA 93:14515–14520

    Article  CAS  Google Scholar 

  • Kapritchkoff FM, Viotti AP, Alli RCP, Zuccolo M, Pradella JGC, Maiorano AE, Miranda EA, Bonomi A (2006) Enzymatic recovery and purification of ployhydroxybutyrate produced by Ralstonia eutropha. J Biotechnol 122:453–462

    Article  CAS  Google Scholar 

  • Kim BS, Cropp TA, Beck BJ, Sherman DH, Reynolds KA (2002) Biochemical evidence for an editing role of thioesterase II in the biosynthesis of the polyketide pikromycin. J Biol Chem 277:48028–48034

    Article  CAS  Google Scholar 

  • Koglin A, Löhr F, Bernhard F, Rogov VV, Frueh DP, Strieter ER, Mofid MR, Güntert P, Wagnaer G, Walsh CT, Marahiel MA, Dötsch V (2008) Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature 454:907–911

    Article  CAS  Google Scholar 

  • Kornberg HL, Krebs HA (1957) Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature 179:988–991

    Article  CAS  Google Scholar 

  • Kornberg HL, Phizackerley PJR, Sadler JR (1958) Synthesis of cell constituents from acetate by Escherichia coli. Biochem J 72:32P–33P

    Google Scholar 

  • Korotkova N, Lidstrom ME (2001) Connection between ploy-β-hydroxybutyrate biosynthesis and growth on C1 and C2 compounds in the methylotroph Methylobacterium extorquens AM1. J Bacteriol 183:1038–1046

    Article  CAS  Google Scholar 

  • Korotkova N, Lidstrom ME (2004) MeaB is a component of the methylmalonyl-CoA mutase complex required for protection of the enzyme from inactivation. J Biol Chem 279:13652–13658

    Article  CAS  Google Scholar 

  • Korotkova N, Chistoserdova L, Kuska V, Lidstrom ME (2002) Glyoxylate regeneration pathway in the methylotroph Methylobacterium extorquens AM1. J Bacteriol 184:1750–1758

    Article  CAS  Google Scholar 

  • Korotkova N, Lidstrom ME, Chistoserdova L (2005) Identification of genes involved in the glyoxylate regeneration cycle in Methylobacterium extorquens AM1, including two genes, meaC and meaD. J Bacteriol 187:1523–1526

    Article  CAS  Google Scholar 

  • Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM, Peterson KM (1995) Four derivatives of the braod-host range cloning vector pBBR1MCS carrying different antibiotic-resistance cassettes. Gene 166:175–176

    Article  CAS  Google Scholar 

  • Large PJ, Peel D, Quayle JR (1961) Microbial growth on C1 compounds. Biochem J 81:470–480

    CAS  Google Scholar 

  • Larsen RA, Wilson MM, Guss AM, Metcalf WW (2002) Genetic analysis of pigmant biosynthesis in Xanthobacter autrophicus Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria. Arch Microbiol 178:193–201

    Article  CAS  Google Scholar 

  • Li J, Derewenda U, Dauetr Z, Smith S, Derewenda ZS (2000) Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme. Nat Struct Biol 7:555–559

    Article  CAS  Google Scholar 

  • Lim S-K, Kim SJ, Cha SH, Oh Y-K, Rhee H-J, Kim M-S, Lee JK (2009) Complete genome sequence of Rhodobacter sphaeroides KD131. J Bacteriol 191:1118–1119

    Article  CAS  Google Scholar 

  • Lin CY, Smith S (1978) Properties of the thioesterase component obtained by limited trypsinization of the fatty acid synthetase multienzyme complex. J Biol Chem 253:1954–1962

    CAS  Google Scholar 

  • Liu Y, Hazzard C, Eustáquio AS, Reynolds KA, Moore BS (2009) Biosynthesis of salinosporamides from α, β-unsaturated fatty acids: implications for extending polyketide synthase diversity. J Am Chem Soc 131:10376–10377

    Article  CAS  Google Scholar 

  • Lo YC, Lin SC, Shaw JF, Liaw YC (2003) Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network. J Mol Biol 330:539–551

    Article  CAS  Google Scholar 

  • Marx A, Poetter M, Buchholz S, May A, Siegert H, Alber B, Fuchs G, Eggerling L (2007) Microbiological production of 3-hydroxybutyric acid. WO/2007/141208

  • Meister M, Saum S, Alber BE, Fuchs G (2005) L-Malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. J Bacteriol 187:1415–1425

    Article  CAS  Google Scholar 

  • Neidhardt FC, Ingraham JL, Schaechter M (1990) In: Physiology of the bacterial cell. Chapter 5: biosynthesis and fueling. Sinauer, Sunderland, pp 133–172

  • Peyraud R, Kiefer P, Christen P, Massou S, Portais JC, Vorholt JA (2009) Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics. Proc Nat Acad Sci USA 106:4846–4851

    Article  CAS  Google Scholar 

  • Pickart CM, Jencks WP (1979) Formation of stable anhydrides from CoA transferase and hydroxamic acids. J Biol Chem 254:9120–9129

    CAS  Google Scholar 

  • Quandt J, Hynes MF (1993) Versatile suicide vectors which allow direct selection for gene replacement in Gram-negative bacteria. Gene 127:15–21

    Article  CAS  Google Scholar 

  • Rétey J (1990) Enzymatic reaction selectively by negative catalysis or how do enzymes deal with highly reactive intermediates. Angew Chem Int Ed 29:355–361

    Article  Google Scholar 

  • Roh JH, Smith WE, Kaplan S (2004) Effects of oxygen and light intensity on transcriptome expression in Rhodobacter sphaeroides 2.4.1. Redox active gene epression profile. J Biol Chem 279:9146–9155

    Article  CAS  Google Scholar 

  • Rohwerder T, Müller RH (2010) Biosynthesis of 2-hydroxyisobutyric acid (2-HIBA) from renewable carbon. Microb Cell Fact 25:13

    Article  Google Scholar 

  • Schäfer A, Tauch A, Jager W, Kalinowski J, Thierbach G, Puhler A (1994) Small mobilizable multipurpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145:69–73

    Article  Google Scholar 

  • Schrader J, Schilling M, Holtmann D, Sell D, Filho MV, Marx A, Vorholt JA (2008) Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol 27:107–115

    Article  Google Scholar 

  • Schwarzer D, Mootz HD, Linne U, Marahiel MA (2002) Regeneration of misprimed nonribosomal peptide synthases by type II thioesterases. Proc Natl Acad Sci USA 99:14083–14088

    Article  CAS  Google Scholar 

  • Sganga MW, Bauer CE (1992) Regulatory factors controlling photosynthetic reaction center and light-harvesting gene expression in Rhodobacter capsulatus. Cell 68:945–954

    Article  CAS  Google Scholar 

  • Smith LM, Meijer WG, Dijkuizen L, Goodwin PM (1996) A protein having similarity with methylmalonyl-CoA mutase is required for the assimilation of methanol and ethanol by Methylobacterium extorquens AM1. Microbiology 142:675–684

    Article  CAS  Google Scholar 

  • Thoden JB, Holden HM, Zhuang Z, Dunaway-Mariano D (2002) X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase. J Biol Chem 277:27468–27476

    Article  CAS  Google Scholar 

  • Thoden JB, Zhuang Z, Dunaway-Mariano D, Holden HM (2003) The structure of 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU. J Biol Chem 278:43709–43716

    Article  CAS  Google Scholar 

  • Vlasie MD, Banerjee R (2004) When a spectator turns killer: suicidal electron transfer from cobalamin in methylmalonyl-CoA mutase. Biochemistry 43:8410–8417

    Article  CAS  Google Scholar 

  • Wang XD, Falcone L, Tabita FR (1993) Reductive pentose phosphate-independent CO2 fixation in Rhodobacter sphaeroides and evidence that ribulose bisphosphate carboxylase/oxygenase activity serves to maintain the redox balance of the cell. J Bacteriol 175:3372–3379

    CAS  Google Scholar 

  • Zarzycki J, Schlichting A, Strychalsky N, Müller M, Alber BE, Fuchs G (2008) Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J Bacteriol 190:1366–1374

    Article  CAS  Google Scholar 

  • Zhuang Z, Gartemann K-H, Eichnelaub R, Dunaway-Mariano (2003) Characterization of the 4-hydroxybenzoyl-coenzyme A tioesterase from Arthrobacter sp. strain SU. Appl Environ Microbiol 69:2707–2711

    Article  Google Scholar 

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Acknowledgments

This research has been supported by the Deutsche Forschungsgemeinschaft (AL677/1-1) and by Evonik-Degussa GmbH in the past and is currently generously funded by the National Science Foundation (MCB0842892). I would like to thank Chuck Daniels for very helpful comments on the manuscript.

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  1. The Department of Microbiology, Ohio State University, 484 West 12th Ave, Room 417, Columbus, OH, USA

    Birgit E. Alber

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Alber, B.E. Biotechnological potential of the ethylmalonyl-CoA pathway. Appl Microbiol Biotechnol 89, 17–25 (2011). https://doi.org/10.1007/s00253-010-2873-z

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