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Journal articles on the topic 'CoA ligases'

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Published: 21 September 2024

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1

Villemur, Richard. "Coenzyme A ligases involved in anaerobic biodegradation of aromatic compounds." Canadian Journal of Microbiology 41, no. 10 (October 1, 1995): 855–61. http://dx.doi.org/10.1139/m95-118.

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Bacterial strains and consortia of bacteria have been isolated for their ability to degrade, under anaerobic conditions, homocyclic monoaromatic compounds, such as phenolic compounds, methylbenzenes, and aminobenzenes. As opposed to aerobic conditions where these compounds are degraded via dihydroxyl intermediates introduced by oxygenases, most of aromatic compounds under anaerobic conditions are metabolized via aromatic acid intermediates, such as nitrobenzoates, hydroxybenzoates, or phenylacetate. These aromatic acids are then transformed to benzoate before the reduction and the cleavage of the benzene ring to aliphatic acid products. One step of these catabolic pathways is the addition of a coenzyme A (CoA) residue to the carboxylic group of the aromatic acids by CoA ligases. This addition would facilitate the enzymatic transformation of the aromatic acids to benzoyl-CoA and the subsequent degradation steps of this latter molecule. Aromatic acid – CoA ligases have been characterized or detected from several bacterial strains that were grown under anaerobic conditions and from an anaerobic syntrophic consortium. They are also involved in the degradation of some aromatic compounds under aerobic conditions. They have molecular masses varying between 48 and 61 kDa, require ATP, Mg2+, and CoASH as cofactors, and have an optimum pH of 8.2–9.3. Amino acid sequence analyses of four aromatic acid–CoA ligases have revealed that they are related to an AMP-binding protein family. Aromatic acid – CoA ligases expressed in anaerobically grown bacterial cells are strictly regulated by the anaerobic conditions and the presence of aromatic acids.Key words: aromatic compounds, coenzyme A ligase, anaerobic microorganisms.

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2

Nolte, Johannes Christoph, Marc Schürmann, Catherine-Louise Schepers, Elvira Vogel, Jan Hendrik Wübbeler, and Alexander Steinbüchel. "Novel Characteristics of Succinate Coenzyme A (Succinate-CoA) Ligases: Conversion of Malate to Malyl-CoA and CoA-Thioester Formation of Succinate AnaloguesIn Vitro." Applied and Environmental Microbiology 80, no. 1 (October 18, 2013): 166–76. http://dx.doi.org/10.1128/aem.03075-13.

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ABSTRACTThree succinate coenzyme A (succinate-CoA) ligases (SucCD) fromEscherichia coli,Advenella mimigardefordensisDPN7T, andAlcanivorax borkumensisSK2 were characterized regarding their substrate specificity concerning succinate analogues. Previous studies had suggested that SucCD enzymes might be promiscuous toward succinate analogues, such as itaconate and 3-sulfinopropionate (3SP). The latter is an intermediate of the degradation pathway of 3,3′-dithiodipropionate (DTDP), a precursor for the biotechnical production of polythioesters (PTEs) in bacteria. ThesucCDgenes were expressed inE. coliBL21(DE3)/pLysS. The SucCD enzymes ofE. coliandA. mimigardefordensisDPN7Twere purified in the native state using stepwise purification protocols, while SucCD fromA. borkumensisSK2 was equipped with a C-terminal hexahistidine tag at the SucD subunit. Besides the preference for the physiological substrates succinate, itaconate, ATP, and CoA, high enzyme activity was additionally determined for both enantiomeric forms of malate, amounting to 10 to 21% of the activity with succinate.Kmvalues ranged from 2.5 to 3.6 mM forl-malate and from 3.6 to 4.2 mM ford-malate for the SucCD enzymes investigated in this study. Asl-malate-CoA ligase is present in the serine cycle for assimilation of C1compounds in methylotrophs, structural comparison of these two enzymes as members of the same subsubclass suggested a strong resemblance of SucCD tol-malate-CoA ligase and gave rise to the speculation that malate-CoA ligases and succinate-CoA ligases have the same evolutionary origin. Although enzyme activities were very low for the additional substrates investigated, liquid chromatography/electrospray ionization-mass spectrometry analyses proved the ability of SucCD enzymes to form CoA-thioesters of adipate, glutarate, and fumarate. Since all SucCD enzymes were able to activate 3SP to 3SP-CoA, we consequently demonstrated that the activation of 3SP is not a unique characteristic of the SucCD fromA. mimigardefordensisDPN7T. The essential role ofsucCDin the activation of 3SPin vivowas proved by genetic complementation.

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3

Lazo, O., M. Contreras, and I. Singh. "Topographical localization of peroxisomal acyl-CoA ligases: differential localization of palmitoyl-CoA and lignoceroyl-CoA ligases." Biochemistry 29, no. 16 (April 24, 1990): 3981–86. http://dx.doi.org/10.1021/bi00468a027.

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4

Singh, Inderjit, Oscar Lazo, and Miguel Contreras. "72 Topographical localization of Peroxisomal Acyl-CoA Ligases: Differential localization of Palmitoyl-CoA and Lignoceroyl-CoA Ligases." Pediatric Research 28, no. 3 (September 1990): 289. http://dx.doi.org/10.1203/00006450-199009000-00096.

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5

El-Said Mohamed, Magdy. "Biochemical and Molecular Characterization of Phenylacetate-Coenzyme A Ligase, an Enzyme Catalyzing the First Step in Aerobic Metabolism of Phenylacetic Acid inAzoarcus evansii." Journal of Bacteriology 182, no. 2 (January 15, 2000): 286–94. http://dx.doi.org/10.1128/jb.182.2.286-294.2000.

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ABSTRACT Phenylacetate-coenzyme A ligase (PA-CoA ligase; AMP forming, EC6.2.1.30 ), the enzyme catalyzing the first step in the aerobic degradation of phenylacetate (PA) in Azoarcus evansii, has been purified and characterized. The gene (paaK) coding for this enzyme was cloned and sequenced. The enzyme catalyzes the reaction of PA with CoA and MgATP to yield phenylacetyl-CoA (PACoA) plus AMP plus PPi. The enzyme was specifically induced after aerobic growth in a chemically defined medium containing PA or phenylalanine (Phe) as the sole carbon source. Growth with 4-hydroxyphenylacetate, benzoate, adipate, or acetate did not induce the synthesis of this enzyme. This enzymatic activity was detected very early in the exponential phase of growth, and a maximal specific activity of 76 nmol min−1mg of cell protein−1 was measured. After 117-fold purification to homogeneity, a specific activity of 48 μmol min−1 mg of protein−1 was achieved with a turnover number (catalytic constant) of 40 s−1. The protein is a monomer of 52 kDa and shows high specificity towards PA; other aromatic or aliphatic acids were not used as substrates. The apparent Km values for PA, ATP, and CoA were 14, 60, and 45 μM, respectively. The PA-CoA ligase has an optimum pH of 8 to 8.5 and a pI of 6.3. The enzyme is labile and requires the presence of glycerol for stabilization. The N-terminal amino acid sequence of the purified protein showed no homology with other reported PA-CoA ligases. The gene encoding this enzyme is 1,320 bp long and codes for a protein of 48.75 kDa (440 amino acids) which shows high similarity with other reported PA-CoA ligases. An amino acid consensus for an AMP binding motif (VX2SSGTTGXP) was identified. The biochemical and molecular characteristics of this enzyme are quite different from those of the isoenzyme catalyzing the same reaction under anaerobic conditions in the same bacterium.

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6

Lamas-Maceiras, Mónica, Inmaculada Vaca, Esther Rodríguez, Javier Casqueiro, and Juan F. Martín. "Amplification and disruption of the phenylacetyl-CoA ligase gene of Penicillium chrysogenum encoding an aryl-capping enzyme that supplies phenylacetic acid to the isopenicillin N-acyltransferase." Biochemical Journal 395, no. 1 (March 15, 2006): 147–55. http://dx.doi.org/10.1042/bj20051599.

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A gene, phl, encoding a phenylacetyl-CoA ligase was cloned from a phage library of Penicillium chrysogenum AS-P-78. The presence of five introns in the phl gene was confirmed by reverse transcriptase-PCR. The phl gene encoded an aryl-CoA ligase closely related to Arabidopsis thaliana 4-coumaroyl-CoA ligase. The Phl protein contained most of the amino acids defining the aryl-CoA (4-coumaroyl-CoA) ligase substrate-specificity code and differed from acetyl-CoA ligase and other acyl-CoA ligases. The phl gene was not linked to the penicillin gene cluster. Amplification of phl in an autonomous replicating plasmid led to an 8-fold increase in phenylacetyl-CoA ligase activity and a 35% increase in penicillin production. Transformants containing the amplified phl gene were resistant to high concentrations of phenylacetic acid (more than 2.5 g/l). Disruption of the phl gene resulted in a 40% decrease in penicillin production and a similar reduction of phenylacetyl-CoA ligase activity. The disrupted mutants were highly susceptible to phenylacetic acid. Complementation of the disrupted mutants with the phl gene restored normal levels of penicillin production and resistance to phenylacetic acid. The phenylacetyl-CoA ligase encoded by the phl gene is therefore involved in penicillin production, although a second aryl-CoA ligase appears to contribute partially to phenylacetic acid activation. The Phl protein lacks a peptide-carrier-protein domain and behaves as an aryl-capping enzyme that activates phenylacetic acid and transfers it to the isopenicillin N acyltransferase. The Phl protein contains the peroxisome-targeting sequence that is also present in the isopenicillin N acyltransferase. The peroxisomal co-localization of these two proteins indicates that the last two enzymes of the penicillin pathway form a peroxisomal functional complex.

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7

Chen, Janice S., Brendan Colón, Brendon Dusel, Marika Ziesack, Jeffrey C. Way, and Joseph P. Torella. "Production of fatty acids inRalstonia eutrophaH16 by engineeringβ-oxidation and carbon storage." PeerJ 3 (December 7, 2015): e1468. http://dx.doi.org/10.7717/peerj.1468.

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Ralstonia eutrophaH16 is a facultatively autotrophic hydrogen-oxidizing bacterium capable of producing polyhydroxybutyrate (PHB)-based bioplastics. As PHB’s physical properties may be improved by incorporation of medium-chain-length fatty acids (MCFAs), and MCFAs are valuable on their own as fuel and chemical intermediates, we engineeredR. eutrophafor MCFA production. Expression ofUcFatB2, a medium-chain-length-specific acyl-ACP thioesterase, resulted in production of 14 mg/L laurate in wild-typeR. eutropha. Total fatty acid production (22 mg/L) could be increased up to 2.5-fold by knocking out PHB synthesis, a major sink for acetyl-CoA, or by knocking out the acyl-CoA ligasefadD3, an entry point for fatty acids intoβ-oxidation. As ΔfadD3mutants still consumed laurate, and because theR. eutrophagenome is predicted to encode over 50 acyl-CoA ligases, we employed RNA-Seq to identify acyl-CoA ligases upregulated during growth on laurate. Knockouts of the three most highly upregulated acyl-CoA ligases increased fatty acid yield significantly, with one strain (ΔA2794) producing up to 62 mg/L free fatty acid. This study demonstrates that homologousβ-oxidation systems can be rationally engineered to enhance fatty acid production, a strategy that may be employed to increase yield for a range of fuels, chemicals, and PHB derivatives inR. eutropha.

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8

Knights, K., and C. Drogemuller. "Xenobiotic-CoA Ligases: Kinetic and Molecular Characterization." Current Drug Metabolism 1, no. 1 (July 1, 2000): 49–66. http://dx.doi.org/10.2174/1389200003339261.

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9

Barragán, María J. López, Manuel Carmona, María T. Zamarro, Bärbel Thiele, Matthias Boll, Georg Fuchs, José L. García, and Eduardo Díaz. "The bzd Gene Cluster, Coding for Anaerobic Benzoate Catabolism, in Azoarcus sp. Strain CIB." Journal of Bacteriology 186, no. 17 (September 1, 2004): 5762–74. http://dx.doi.org/10.1128/jb.186.17.5762-5774.2004.

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ABSTRACT We report here that the bzd genes for anaerobic benzoate degradation in Azoarcus sp. strain CIB are organized as two transcriptional units, i.e., a benzoate-inducible catabolic operon, bzdNOPQMSTUVWXYZA, and a gene, bzdR, encoding a putative transcriptional regulator. The last gene of the catabolic operon, bzdA, has been expressed in Escherichia coli and encodes the benzoate-coenzyme A (CoA) ligase that catalyzes the first step in the benzoate degradation pathway. The BzdA enzyme is able to activate a wider range of aromatic compounds than that reported for other previously characterized benzoate-CoA ligases. The reduction of benzoyl-CoA to a nonaromatic cyclic intermediate is carried out by a benzoyl-CoA reductase (bzdNOPQ gene products) detected in Azoarcus sp. strain CIB extracts. The bzdW, bzdX, and bzdY gene products show significant similarity to the hydratase, dehydrogenase, and ring-cleavage hydrolase that act sequentially on the product of the benzoyl-CoA reductase in the benzoate catabolic pathway of Thauera aromatica. Benzoate-CoA ligase assays and transcriptional analyses based on lacZ-reporter fusions revealed that benzoate degradation in Azoarcus sp. strain CIB is subject to carbon catabolite repression by some organic acids, indicating the existence of a physiological control that connects the expression of the bzd genes to the metabolic status of the cell.

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10

Philpott, Helena K., Pamela J. Thomas, David Tew, Doug E. Fuerst, and Sarah L. Lovelock. "A versatile biosynthetic approach to amide bond formation." Green Chemistry 20, no. 15 (2018): 3426–31. http://dx.doi.org/10.1039/c8gc01697f.

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Combining N-acyltransferases and CoA ligases with desired substrate profiles allows the construction of non-natural biosynthetic pathways for the synthesis of structurally diverse secondary and tertiary amides in high yields.

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11

Sunstrum, Frederick G., Hannah L. Liu, Sharon Jancsik, Lufiani L. Madilao, Joerg Bohlmann, and Sandra Irmisch. "4-Coumaroyl-CoA ligases in the biosynthesis of the anti-diabetic metabolite montbretin A." PLOS ONE 16, no. 10 (October 7, 2021): e0257478. http://dx.doi.org/10.1371/journal.pone.0257478.

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Background Montbretins are rare specialized metabolites found in montbretia (Crocosmia x crocosmiiflora) corms. Montbretin A (MbA) is of particular interest as a novel therapeutic for type-2 diabetes and obesity. There is no scalable production system for this complex acylated flavonol glycoside. MbA biosynthesis has been reconstructed in Nicotiana benthamiana using montbretia genes for the assembly of MbA from its various different building blocks. However, in addition to smaller amounts of MbA, the therapeutically inactive montbretin B (MbB) was the major product of this metabolic engineering effort. MbA and MbB differ in a single hydroxyl group of their acyl side chains, which are derived from caffeoyl-CoA and coumaroyl-CoA, respectively. Biosynthesis of both MbA and MbB also require coumaroyl-CoA for the formation of the myricetin core. Caffeoyl-CoA and coumaroyl-CoA are formed in the central phenylpropanoid pathway by acyl activating enzymes (AAEs) known as 4-coumaroyl-CoA ligases (4CLs). Here we investigated a small family of montbretia AAEs and 4CLs, and their possible contribution to montbretin biosynthesis. Results Transcriptome analysis for gene expression patterns related to montbretin biosynthesis identified eight different montbretia AAEs belonging to four different clades. Enzyme characterization identified 4CL activity for two clade IV members, Cc4CL1 and Cc4CL2, converting different hydroxycinnamic acids into the corresponding CoA thioesters. Both enzymes preferred coumaric acid over caffeic acid as a substrate in vitro. While expression of montbretia AAEs did not enhance MbA biosynthesis in N. benthamiana, we demonstrated that both Cc4CLs can be used to activate coumaric and caffeic acid towards flavanone biosynthesis in yeast (Saccharomyces cerevisiae). Conclusions Montbretia expresses two functional 4CLs, but neither of them is specific for the formation of caffeoyl-CoA. Based on differential expression analysis and phylogeny Cc4CL1 is most likely involved in MbA biosynthesis, while Cc4CL2 may contribute to lignin biosynthesis. Both Cc4CLs can be used for flavanone production to support metabolic engineering of MbA in yeast.

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12

Arora, Pooja, Archana Vats, Priti Saxena, Debasisa Mohanty, and Rajesh S. Gokhale. "Promiscuous Fatty Acyl CoA Ligases Produce Acyl-CoA and Acyl-SNAC Precursors for Polyketide Biosynthesis." Journal of the American Chemical Society 127, no. 26 (July 2005): 9388–89. http://dx.doi.org/10.1021/ja052991s.

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13

Klempien, Antje, Yasuhisa Kaminaga, Anthony Qualley, Dinesh A. Nagegowda, Joshua R. Widhalm, Irina Orlova, Ajit Kumar Shasany, et al. "Contribution of CoA Ligases to Benzenoid Biosynthesis in Petunia Flowers." Plant Cell 24, no. 5 (May 2012): 2015–30. http://dx.doi.org/10.1105/tpc.112.097519.

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14

Singh, Inderjit, Alok Bhushan, Nand Kishore Relan, and Takashi Hashimoto. "Acyl-CoA ligases from rat brain microsomes: An immunochemical study." Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism 963, no. 3 (December 1988): 509–14. http://dx.doi.org/10.1016/0005-2760(88)90319-0.

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15

Coleman, James P., L. Lynn Hudson, Susan L. McKnight, John M. Farrow, M. Worth Calfee, Claire A. Lindsey, and Everett C. Pesci. "Pseudomonas aeruginosa PqsA Is an Anthranilate-Coenzyme A Ligase." Journal of Bacteriology 190, no. 4 (December 14, 2007): 1247–55. http://dx.doi.org/10.1128/jb.01140-07.

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ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen which relies on several intercellular signaling systems for optimum population density-dependent regulation of virulence genes. The Pseudomonas quinolone signal (PQS) is a 3-hydroxy-4-quinolone with a 2-alkyl substitution which is synthesized by the condensation of anthranilic acid with a 3-keto-fatty acid. The pqsABCDE operon has been identified as being necessary for PQS production, and the pqsA gene encodes a predicted protein with homology to acyl coenzyme A (acyl-CoA) ligases. In order to elucidate the first step of the 4-quinolone synthesis pathway in P. aeruginosa, we have characterized the function of the pqsA gene product. Extracts prepared from Escherichia coli expressing PqsA were shown to catalyze the formation of anthraniloyl-CoA from anthranilate, ATP, and CoA. The PqsA protein was purified as a recombinant His-tagged polypeptide, and this protein was shown to have anthranilate-CoA ligase activity. The enzyme was active on a variety of aromatic substrates, including benzoate and chloro and fluoro derivatives of anthranilate. Inhibition of PQS formation in vivo was observed for the chloro- and fluoroanthranilate derivatives, as well as for several analogs which were not PqsA enzymatic substrates. These results indicate that the PqsA protein is responsible for priming anthranilate for entry into the PQS biosynthetic pathway and that this enzyme may serve as a useful in vitro indicator for potential agents to disrupt quinolone signaling in P. aeruginosa.

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16

Knights, Kathleen M., and Benjamin J. Roberts. "Xenobiotic acyl-CoA formation: evidence of kinetically distinct hepatic microsomal long-chain fatty acid and nafenopin-CoA ligases." Chemico-Biological Interactions 90, no. 3 (March 1994): 215–23. http://dx.doi.org/10.1016/0009-2797(94)90011-6.

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17

Luís, Paula B. M., Jos Ruiter, Lodewijk IJlst, Isabel Tavares de Almeida, Marinus Duran, Ronald J. A. Wanders, and Margarida F. B. Silva. "Valproyl-CoA inhibits the activity of ATP- and GTP-dependent succinate:CoA ligases." Journal of Inherited Metabolic Disease 37, no. 3 (October 24, 2013): 353–57. http://dx.doi.org/10.1007/s10545-013-9657-4.

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18

Peters, Franziska, Michael Rother, and Matthias Boll. "Selenocysteine-Containing Proteins in Anaerobic Benzoate Metabolism of Desulfococcus multivorans." Journal of Bacteriology 186, no. 7 (April 1, 2004): 2156–63. http://dx.doi.org/10.1128/jb.186.7.2156-2163.2004.

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ABSTRACT The sulfate-reducing bacterium Desulfococcus multivorans uses various aromatic compounds as sources of cell carbon and energy. In this work, we studied the initial steps in the aromatic metabolism of this strictly anaerobic model organism. An ATP-dependent benzoate coenzyme A (CoA) ligase (AMP plus PPi forming) composed of a single 59-kDa subunit was purified from extracts of cells grown on benzoate. Specific activity was highest with benzoate and some benzoate derivatives, whereas aliphatic carboxylic acids were virtually unconverted. The N-terminal amino acid sequence showed high similarities with benzoate CoA ligases from Thauera aromatica and Azoarcus evansii. When cultivated on benzoate, cells strictly required selenium and molybdenum, whereas growth on nonaromatic compounds, such as cyclohexanecarboxylate or lactate, did not depend on the presence of the two trace elements. The growth rate on benzoate was half maximal with 1 nM selenite present in the growth medium. In molybdenum- and/or selenium-depleted cultures, growth on benzoate could be induced by addition of the missing trace elements. In extracts of cells grown on benzoate in the presence of [75Se]selenite, three radioactively labeled proteins with molecular masses of ∼100, 30, and 27 kDa were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The 100- and 30-kDa selenoproteins were 5- to 10-fold induced in cells grown on benzoate compared to cells grown on lactate. These results suggest that the dearomatization process in D. multivorans is not catalyzed by the ATP-dependent Fe-S enzyme benzoyl-CoA reductase as in facultative anaerobes but rather involves unknown molybdenum- and selenocysteine-containing proteins.

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19

Berger, Martine, Nelson L. Brock, Heiko Liesegang, Marco Dogs, Ines Preuth, Meinhard Simon, Jeroen S. Dickschat, and Thorsten Brinkhoff. "Genetic Analysis of the Upper Phenylacetate Catabolic Pathway in the Production of Tropodithietic Acid by Phaeobacter gallaeciensis." Applied and Environmental Microbiology 78, no. 10 (March 9, 2012): 3539–51. http://dx.doi.org/10.1128/aem.07657-11.

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ABSTRACTProduction of the antibiotic tropodithietic acid (TDA) depends on the central phenylacetate catabolic pathway, specifically on the oxygenase PaaABCDE, which catalyzes epoxidation of phenylacetyl-coenzyme A (CoA). Our study was focused on genes of the upper part of this pathway leading to phenylacetyl-CoA as precursor for TDA.Phaeobacter gallaeciensisDSM 17395 encodes two genes with homology to phenylacetyl-CoA ligases (paaK1andpaaK2), which were shown to be essential for phenylacetate catabolism but not for TDA biosynthesis and phenylalanine degradation. Thus, inP. gallaeciensisanother enzyme must produce phenylacetyl-CoA from phenylalanine. Using random transposon insertion mutagenesis of apaaK1-paaK2double mutant we identified a gene (ior1) with similarity toiorAandiorBin archaea, encoding an indolepyruvate:ferredoxin oxidoreductase (IOR). Theior1mutant was unable to grow on phenylalanine, and production of TDA was significantly reduced compared to the wild-type level (60%). Nuclear magnetic resonance (NMR) spectroscopic investigations using13C-labeled phenylalanine isotopomers demonstrated that phenylalanine is transformed into phenylacetyl-CoA by Ior1. Using quantitative real-time PCR, we could show that expression ofior1depends on the adjacent regulator IorR. Growth on phenylalanine promotes production of TDA, induces expression ofior1(27-fold) andpaaK1(61-fold), and regulates the production of TDA. Phylogenetic analysis showed that the aerobic type of IOR as found in many roseobacters is common within a number of different phylogenetic groups of aerobic bacteria such asBurkholderia,Cupriavidis, andRhizobia, where it may also contribute to the degradation of phenylalanine.

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Lavhale, Santosh G., Rakesh S. Joshi, Yashwant Kumar, and Ashok P. Giri. "Functional insights into two Ocimum kilimandscharicum 4-coumarate-CoA ligases involved in phenylpropanoid biosynthesis." International Journal of Biological Macromolecules 181 (June 2021): 202–10. http://dx.doi.org/10.1016/j.ijbiomac.2021.03.129.

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21

Knights, Kathleen. "Long-Chain-Fatty-Acid CoA Ligases: The Key to Fatty Acid Activation, Formation of Xenobiotic Acyl-CoA Thioesters and Lipophilic Xenobiotic Conjugates." Current Medicinal Chemistry-Immunology, Endocrine & Metabolic Agents 3, no. 3 (September 1, 2003): 235–44. http://dx.doi.org/10.2174/1568013033483384.

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22

Go, Maybelle Kho, Jeng Yeong Chow, Vivian Wing Ngar Cheung, Yan Ping Lim, and Wen Shan Yew. "Establishing a Toolkit for Precursor-Directed Polyketide Biosynthesis: Exploring Substrate Promiscuities of Acid-CoA Ligases." Biochemistry 51, no. 22 (May 22, 2012): 4568–79. http://dx.doi.org/10.1021/bi300425j.

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23

Lazo, O., M. Contreras, Y. Yoshida, AK Singh, W. Stanley, M. Weise, and I. Singh. "Cellular oxidation of lignoceric acid is regulated by the subcellular localization of lignoceroyl-CoA ligases." Journal of Lipid Research 31, no. 4 (April 1990): 583–95. http://dx.doi.org/10.1016/s0022-2275(20)42826-3.

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24

Vessey, Donald A., Jie Hu, and Michael Kelley. "Interaction of salicylate and ibuprofen with the carboxylic acid: CoA ligases from bovine liver mitochondria." Journal of Biochemical Toxicology 11, no. 2 (1996): 73–78. http://dx.doi.org/10.1002/(sici)1522-7146(1996)11:2<73::aid-jbt4>3.0.co;2-r.

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25

Babbitt, Patricia C., George L. Kenyon, Brian M. Martin, Hugues Charest, Michel Slyvestre, Jeffrey D. Scholten, Kai Hsuan Chang, Po Huang Liang, and Debra Dunaway-Mariano. "Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases." Biochemistry 31, no. 24 (June 1992): 5594–604. http://dx.doi.org/10.1021/bi00139a024.

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26

Baran, Marzena, Kimberly D. Grimes, Paul A. Sibbald, Peng Fu, Helena I. M. Boshoff, Daniel J. Wilson, and Courtney C. Aldrich. "Development of small-molecule inhibitors of fatty acyl-AMP and fatty acyl-CoA ligases in Mycobacterium tuberculosis." European Journal of Medicinal Chemistry 201 (September 2020): 112408. http://dx.doi.org/10.1016/j.ejmech.2020.112408.

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27

Xu, Jaiwei, Haifang Zhao, and Tao Wang. "Suppression of retinal degeneration by two novel ERAD ubiquitin E3 ligases SORDD1/2 in Drosophila." PLOS Genetics 16, no. 11 (November 2, 2020): e1009172. http://dx.doi.org/10.1371/journal.pgen.1009172.

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Mutations in the gene rhodopsin are one of the major causes of autosomal dominant retinitis pigmentosa (adRP). Mutant forms of Rhodopsin frequently accumulate in the endoplasmic reticulum (ER), cause ER stress, and trigger photoreceptor cell degeneration. Here, we performed a genome-wide screen to identify suppressors of retinal degeneration in a Drosophila model of adRP, carrying a point mutation in the major rhodopsin, Rh1 (Rh1G69D). We identified two novel E3 ubiquitin ligases SORDD1 and SORDD2 that effectively suppressed Rh1G69D-induced photoreceptor dysfunction and retinal degeneration. SORDD1/2 promoted the ubiquitination and degradation of Rh1G69D through VCP (valosin containing protein) and independent of processes reliant on the HRD1 (HMG-CoA reductase degradation protein 1)/HRD3 complex. We further demonstrate that SORDD1/2 and HRD1 function in parallel and in a redundant fashion to maintain rhodopsin homeostasis and integrity of photoreceptor cells. These findings identify a new ER-associated protein degradation (ERAD) pathway and suggest that facilitating SORDD1/2 function may be a therapeutic strategy to treat adRP.

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28

McInerney, Michael J., Lars Rohlin, Housna Mouttaki, UnMi Kim, Rebecca S. Krupp, Luis Rios-Hernandez, Jessica Sieber, et al. "The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth." Proceedings of the National Academy of Sciences 104, no. 18 (April 18, 2007): 7600–7605. http://dx.doi.org/10.1073/pnas.0610456104.

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Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaerobic flow of carbon in the biosphere. The completed genome sequence of Syntrophus aciditrophicus SB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium, provides a glimpse of the composition and architecture of the electron transfer and energy-transducing systems needed to exist on marginal energy economies of a syntrophic lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature of syntrophic metabolism is the need for reverse electron transport; the presence of a unique Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish this task. Previously undescribed approaches to degrade fatty and aromatic acids, including multiple AMP-forming CoA ligases and acyl-CoA synthetases seem to be present as ways to form and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus, although nutritionally self-sufficient, seems to be a syntrophic specialist with limited fermentative and respiratory metabolism. Genomic analysis confirms the S. aciditrophicus metabolic and regulatory commitment to a nonconventional mode of life compared with our prevailing understanding of microbiology.

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Dong, Yanpeng, Huiqian Du, Chunxu Gao, Ting Ma, and Lu Feng. "Characterization of two long-chain fatty acid CoA ligases in the Gram-positive bacterium Geobacillus thermodenitrificans NG80-2." Microbiological Research 167, no. 10 (December 2012): 602–7. http://dx.doi.org/10.1016/j.micres.2012.05.001.

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Vessey, Donald A., Michael Kelley, Eva Lau, and Shirley Z. Zhang. "Monovalent cation effects on the activity of the xenobiotic/medium-chain fatty acid: CoA ligases are substrate specific." Journal of Biochemical and Molecular Toxicology 14, no. 3 (2000): 162–68. http://dx.doi.org/10.1002/(sici)1099-0461(2000)14:3<162::aid-jbt6>3.0.co;2-8.

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Krawiec, Brian J., Gerald J. Nystrom, Robert A. Frost, Leonard S. Jefferson, and Charles H. Lang. "AMP-activated protein kinase agonists increase mRNA content of the muscle-specific ubiquitin ligases MAFbx and MuRF1 in C2C12 cells." American Journal of Physiology-Endocrinology and Metabolism 292, no. 6 (June 2007): E1555—E1567. http://dx.doi.org/10.1152/ajpendo.00622.2006.

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The hypothesis of the present study was that exposure of differentiated muscle cells to agonists of the AMP-activated protein kinase (AMPK) would increase the mRNA content of the muscle-specific ubiquitin ligases muscle atrophy F-box (MAFbx) and muscle RING finger 1 (MuRF1). C2C12 cells were incubated with incremental doses of 5-aminoimidazol-4-carboximide ribonucleoside (AICAR) or metformin for 24 h. Both MAFbx and MuRF1 mRNA increased dose dependently in response to these AMPK activators. AICAR, metformin, and 2-deoxy-d-glucose produced time-dependent alterations in ubiquitin ligase expression, typified by a biphasic pattern of expression marked by an acute repression followed by a sustained induction. AMPK-activating treatments in conjunction with dexamethasone produced a pronounced synergistic effect on ligase mRNA expression at later time points. This cooperative response occurred in the absence of a dexamethasone-dependent increase in AMPK expression or activity, as determined by immunoblotting for phosphorylation and expression of AMPKα and its downstream target acetyl-CoA carboxylase (ACC). These responses elicited by AMPK activation singly or in combination with dexamethasone did not extend to the mRNA expression of the UBR box family E3s UBR1/E3αI and UBR2/E3αII. Treatment with the AMPK inhibitor compound C prevented increases in MAFbx and MuRF1 mRNA in response to serum deprivation, as well as AICAR and dexamethasone treatment individually or jointly. Stimulation of AMPK activity in vivo via AICAR injection increased both MAFbx and MuRF1 mRNA in murine skeletal muscle. These data suggest that activation of AMPK in skeletal muscle results in a specific upregulation of MAFbx and MuRF1, responses that are reminiscent of the proposed atrophic transcriptional program executed under various conditions of skeletal muscle wasting. Therefore, AMPK may be a critical component of the intercalated network of signaling pathways governing skeletal muscle atrophy, where its input acts to modify anti- and proatrophic signals to influence gene expression in reaction to catabolic perturbations.

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Vessey, Donald A., and Michael Kelley. "Characterization of the monovalent and divalent cation requirements for the xenobiotic carboxylic acid: CoA ligases of bovine liver mitochondria." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1382, no. 2 (February 1998): 243–48. http://dx.doi.org/10.1016/s0167-4838(97)00163-5.

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Law, Adrienne, and Martin J. Boulanger. "Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis PathogenBurkholderia cenocepaciaJ2315." Journal of Biological Chemistry 286, no. 17 (March 8, 2011): 15577–85. http://dx.doi.org/10.1074/jbc.m111.219683.

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van der Sluis, Rencia. "Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B." Molecular Genetics and Genomics 293, no. 5 (June 14, 2018): 1279–92. http://dx.doi.org/10.1007/s00438-018-1460-3.

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35

Jo, Y., P. C. W. Lee, P. V. Sguigna, and R. A. DeBose-Boyd. "Sterol-induced degradation of HMG CoA reductase depends on interplay of two Insigs and two ubiquitin ligases, gp78 and Trc8." Proceedings of the National Academy of Sciences 108, no. 51 (December 5, 2011): 20503–8. http://dx.doi.org/10.1073/pnas.1112831108.

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Wilhovsky, Sharon, Richard Gardner, and Randolph Hampton. "HRDGene Dependence of Endoplasmic Reticulum-associated Degradation." Molecular Biology of the Cell 11, no. 5 (May 2000): 1697–708. http://dx.doi.org/10.1091/mbc.11.5.1697.

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Work from several laboratories has indicated that many different proteins are subject to endoplasmic reticulum (ER) degradation by a common ER-associated machinery. This machinery includes ER membrane proteins Hrd1p/Der3p and Hrd3p and the ER-associated ubiquitin-conjugating enzymes Ubc7p and Ubc6p. The wide variety of substrates for this degradation pathway has led to the reasonable hypothesis that the HRD (Hmg CoA reductase degradation) gene-encoded proteins are generally involved in ER protein degradation in eukaryotes. We have tested this model by directly comparing the HRD dependency of the ER-associated degradation for various ER membrane proteins. Our data indicated that the role of HRD genes in protein degradation, even in this highly defined subset of proteins, can vary from absolute dependence to complete independence. Thus, ER-associated degradation can occur by mechanisms that do not involve Hrd1p or Hrd3p, despite their apparently broad envelope of substrates. These data favor models in which the HRD gene-encoded proteins function as specificity factors, such as ubiquitin ligases, rather than as factors involved in common aspects of ER degradation.

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Gao, Shuai, Xin-Yan Liu, Rong Ni, Jie Fu, Hui Tan, Ai-Xia Cheng, and Hong-Xiang Lou. "Molecular cloning and functional analysis of 4-coumarate: CoA ligases from Marchantia paleacea and their roles in lignin and flavanone biosynthesis." PLOS ONE 19, no. 1 (January 8, 2024): e0296079. http://dx.doi.org/10.1371/journal.pone.0296079.

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Phenylpropanoids play important roles in plant physiology and the enzyme 4-coumarate: coenzyme A ligase (4CL) catalyzes the formation of thioesters. Despite extensive characterization in various plants, the functions of 4CLs in the liverwort Marchantia paleacea remain unknown. Here, four 4CLs from M. paleacea were isolated and functionally analyzed. Heterologous expression in Escherichia coli indicated the presence of different enzymatic activities in the four enzymes. Mp4CL1 and Mp4CL2 were able to convert caffeic, p-coumaric, cinnamic, ferulic, dihydro-p-coumaric, and 5-hydroxyferulic acids to their corresponding CoA esters, while Mp4CL3 and Mp4CL4 catalyzed none. Mp4CL1 transcription was induced when M. paleacea thalli were treated with methyl jasmonate (MeJA). The overexpression of Mp4CL1 increased the levels of lignin in transgenic Arabidopsis. In addition, we reconstructed the flavanone biosynthetic pathway in E. coli. The pathway comprised Mp4CL1, co-expressed with chalcone synthase (CHS) from different plant species, and the efficiency of biosynthesis was optimal when both the 4CL and CHS were obtained from the same species M. paleacea.

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Roberts, B. J., and K. M. Knights. "Differential induction of rat hepatic microsomal and peroxisomal long-chain and nafenopin-CoA ligases by clofibric acid and di-(2-ethylhexyl)phthalate." Xenobiotica 25, no. 5 (January 1995): 469–76. http://dx.doi.org/10.3109/00498259509061866.

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Jo, Youngah, Isamu Z. Hartman, and Russell A. DeBose-Boyd. "Ancient ubiquitous protein-1 mediates sterol-induced ubiquitination of 3-hydroxy-3-methylglutaryl CoA reductase in lipid droplet–associated endoplasmic reticulum membranes." Molecular Biology of the Cell 24, no. 3 (February 2013): 169–83. http://dx.doi.org/10.1091/mbc.e12-07-0564.

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Sterol-induced binding to Insigs in endoplasmic reticulum (ER) membranes triggers ubiquitination of the cholesterol biosynthetic enzyme 3-hydroxy-3-methylglutaryl CoA reductase. This ubiquitination, which is mediated by Insig-associated ubiquitin ligases gp78 and Trc8, is obligatory for extraction of reductase from lipid droplet–associated ER membranes into the cytosol for proteasome-mediated, ER-associated degradation (ERAD). In this study, we identify lipid droplet–associated, ancient, ubiquitous protein-1 (Aup1) as one of several proteins that copurify with gp78. RNA interference (RNAi) studies show that Aup1 recruits the ubiquitin-conjugating enzyme Ubc7 to lipid droplets and facilitates its binding to both gp78 and Trc8. The functional significance of these interactions is revealed by the observation that RNAi-mediated knockdown of Aup1 blunts sterol-accelerated ubiquitination of reductase, which appears to occur in lipid droplet–associated membranes and subsequent ERAD of the enzyme. In addition, Aup1 knockdown inhibits ERAD of Insig-1, another substrate for gp78, as well as that of membrane-bound precursor forms of sterol-regulatory, element-binding protein-1 and -2, transcription factors that modulate expression of genes encoding enzymes required for cholesterol synthesis. Considered together, these findings not only implicate a role for Aup1 in maintenance of intracellular cholesterol homeostasis, but they also highlight the close connections among ERAD, lipid droplets, and lipid droplet–associated proteins.

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Elsabrouty, Rania, Youngah Jo, Tammy T. Dinh, and Russell A. DeBose-Boyd. "Sterol-induced dislocation of 3-hydroxy-3-methylglutaryl coenzyme A reductase from membranes of permeabilized cells." Molecular Biology of the Cell 24, no. 21 (November 2013): 3300–3308. http://dx.doi.org/10.1091/mbc.e13-03-0157.

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The polytopic endoplasmic reticulum (ER)–localized enzyme 3-hydroxy-3-methylglutaryl CoA reductase catalyzes a rate-limiting step in the synthesis of cholesterol and nonsterol isoprenoids. Excess sterols cause the reductase to bind to ER membrane proteins called Insig-1 and Insig-2, which are carriers for the ubiquitin ligases gp78 and Trc8. The resulting gp78/Trc8-mediated ubiquitination of reductase marks it for recognition by VCP/p97, an ATPase that mediates subsequent dislocation of reductase from ER membranes into the cytosol for proteasomal degradation. Here we report that in vitro additions of the oxysterol 25-hydroxycholesterol (25-HC), exogenous cytosol, and ATP trigger dislocation of ubiquitinated and full-length forms of reductase from membranes of permeabilized cells. In addition, the sterol-regulated reaction requires the action of Insigs, is stimulated by reagents that replace 25-HC in accelerating reductase degradation in intact cells, and is augmented by the nonsterol isoprenoid geranylgeraniol. Finally, pharmacologic inhibition of deubiquitinating enzymes markedly enhances sterol-dependent ubiquitination of reductase in membranes of permeabilized cells, leading to enhanced dislocation of the enzyme. Considered together, these results establish permeabilized cells as a viable system in which to elucidate mechanisms for postubiquitination steps in sterol-accelerated degradation of reductase.

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Viviani, V. R., R. A. Prado, D. R. Neves, D. Kato, and J. A. Barbosa. "A Route from Darkness to Light: Emergence and Evolution of Luciferase Activity in AMP-CoA-Ligases Inferred from a Mealworm Luciferase-like Enzyme." Biochemistry 52, no. 23 (May 30, 2013): 3963–73. http://dx.doi.org/10.1021/bi400141u.

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Vessey, Donald A., Michael Kelley, and Robert S. Warren. "Characterization of the CoA ligases of human liver mitochondria catalyzing the activation of short- and medium-chain fatty acids and xenobiotic carboxylic acids." Biochimica et Biophysica Acta (BBA) - General Subjects 1428, no. 2-3 (August 1999): 455–62. http://dx.doi.org/10.1016/s0304-4165(99)00088-4.

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43

Bains, Jasleen, and Martin J. Boulanger. "Biochemical and Structural Characterization of the Paralogous Benzoate CoA Ligases from Burkholderia xenovorans LB400: Defining the Entry Point into the Novel Benzoate Oxidation (box) Pathway." Journal of Molecular Biology 373, no. 4 (November 2007): 965–77. http://dx.doi.org/10.1016/j.jmb.2007.08.008.

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44

Robinson, Serina L., Barbara R. Terlouw, Megan D. Smith, Sacha J. Pidot, Timothy P. Stinear, Marnix H. Medema, and Lawrence P. Wackett. "Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia." Journal of Biological Chemistry 295, no. 44 (August 21, 2020): 14826–39. http://dx.doi.org/10.1074/jbc.ra120.013528.

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Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.

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45

Erzurumlu, Yalcin, Deniz Catakli, and Hatice Kubra Dogan. "Circadian Oscillation Pattern of Endoplasmic Reticulum Quality Control (ERQC) Components in Human Embryonic Kidney HEK293 Cells." Journal of Circadian Rhythms 21 (April 3, 2023): 1. http://dx.doi.org/10.5334/jcr.219.

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The circadian clock regulates the “push-pull” of the molecular signaling mechanisms that arrange the rhythmic organization of the physiology to maintain cellular homeostasis. In mammals, molecular clock genes tightly arrange cellular rhythmicity. It has been shown that this circadian clock optimizes various biological processes, including the cell cycle and autophagy. Hence, we explored the dynamic crosstalks between the circadian rhythm and endoplasmic reticulum (ER)-quality control (ERQC) mechanisms. ER-associated degradation (ERAD) is one of the most important parts of the ERQC system and is an elaborate surveillance system that eliminates misfolded proteins. It regulates the steady-state levels of several physiologically crucial proteins, such as 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) and the metastasis suppressor KAI1/CD82. However, the circadian oscillation of ERQC members and their roles in cellular rhythmicity requires further investigation. In the present study, we provided a thorough investigation of the circadian rhythmicity of the fifteen crucial ERQC members, including gp78, Hrd1, p97/VCP, SVIP, Derlin1, Ufd1, Npl4, EDEM1, OS9, XTP3B, Sel1L, Ufd2, YOD1, VCIP135 and FAM8A1 in HEK293 cells. We found that mRNA and protein accumulation of the ubiquitin conjugation, binding and processing factors, retrotranslocation-dislocation, substrate recognition and targeting components of ERQC exhibit oscillation under the control of the circadian clock. Moreover, we found that Hrd1 and gp78 have a possible regulatory function on Bmal1 turnover. The findings of the current study indicated that the expression level of ERQC components is fine-tuned by the circadian clock and major ERAD E3 ligases, Hrd1 and gp78, may influence the regulation of circadian oscillation by modulation of Bmal1 stability.

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Du, Yuanxu, Shuo Gao, Hui Ma, Siqi Lu, Zhenhua Zhang, and Mengmeng Zhao. "Catalytic Behavior of Cobalt Complexes Bearing Pyridine–Oxime Ligands in Isoprene Polymerization." Polymers 15, no. 24 (December 10, 2023): 4660. http://dx.doi.org/10.3390/polym15244660.

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Several cobalt(II) complexes Co1–Co3 bearing pyridine–oxime ligands (L1 = pyridine-2-aldoxime for Co1; L2 = 6-methylpyridine-2-aldoxime for Co2; L3 = phenyl-2-pyridylketoxime for Co3) and picolinaldehyde O-methyl oxime (L4)-supported Co4 were synthesized and well characterized by FT-IR, mass spectrum and elemental analysis. The single-crystal X-ray diffraction of complex Co2 reveals that the cobalt center of CoCl2 is coordinated with two 6-methylpyridine-2-aldoxime ligands binding with Npyridine and Noxime atoms, which feature a distorted octahedral structure. These Co complexes Co1–Co4 displayed extremely high activity toward isoprene polymerization upon activation with small amount of AlClEt2 in toluene, giving polyisoprene with high activity up to 16.3 × 105 (mol of Co)−1(h)−1. And, the generated polyisoprene displayed high molecular weights and narrow molecular distribution with a cis-1,4-enriched selectivity. The type of cobalt complexes, cocatalyst and reaction temperature all have effects on the polymerization activity but not on the microstructure of polymer.

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47

Zhuang, Zhihao, Karl-Heinz Gartemann, Rudolf Eichenlaub, and Debra Dunaway-Mariano. "Characterization of the 4-Hydroxybenzoyl-Coenzyme A Thioesterase from Arthrobacter sp. Strain SU." Applied and Environmental Microbiology 69, no. 5 (May 2003): 2707–11. http://dx.doi.org/10.1128/aem.69.5.2707-2711.2003.

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ABSTRACT The Arthrobacter sp. strain SU 4-chlorobenzoate (4-CBA) dehalogenation pathway converts 4-CBA to 4-hydroxybenzoate (4-HBA). The pathway operon contains the genes fcbA, fcbB, and fcbC (A. Schmitz, K. H. Gartemann, J. Fiedler, E. Grund, and R. Eichenlaub, Appl. Environ. Microbiol. 58:4068-4071, 1992). Genes fcbA and fcbB encode 4-CBA-coenzyme A (CoA) ligase and 4-CBA-CoA dehalogenase, respectively, whereas the function of fcbC is not known. We subcloned fcbC and expressed it in Escherichia coli, and we purified and characterized the FcbC protein. A substrate activity screen identified benzoyl-CoA thioesters as the most active substrates. Catalysis of 4-HBA-CoA hydrolysis to 4-HBA and CoA occurred with a k cat of 6.7 s−1 and a Km of 1.2 μM. The k cat pH rate profile for 4-HBA-CoA hydrolysis indicated optimal activity over a pH range of 6 to 10. The amino acid sequence of the FcbC protein was compared to other sequences contained in the protein sequence data banks. A large number of sequence homologues of unknown function were identified. On the other hand, the 4-HBA-CoA thioesterases isolated from 4-CBA-degrading Pseudomonas strains did not share significant sequence identity with the FcbC protein, indicating early divergence of the thioesterase-encoding genes.

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48

Hawkins, Aaron B., Michael W. W. Adams, and Robert M. Kelly. "Conversion of 4-Hydroxybutyrate to Acetyl Coenzyme A and Its Anapleurosis in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Carbon Fixation Pathway." Applied and Environmental Microbiology 80, no. 8 (February 14, 2014): 2536–45. http://dx.doi.org/10.1128/aem.04146-13.

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ABSTRACTThe extremely thermoacidophilic archaeonMetallosphaera sedula(optimum growth temperature, 73°C, pH 2.0) grows chemolithoautotrophically on metal sulfides or molecular hydrogen by employing the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) carbon fixation cycle. This cycle adds two CO2molecules to acetyl coenzyme A (acetyl-CoA) to generate 4HB, which is then rearranged and cleaved to form two acetyl-CoA molecules. Previous metabolic flux analysis showed that two-thirds of central carbon precursor molecules are derived from succinyl-CoA, which is oxidized to malate and oxaloacetate. The remaining one-third is apparently derived from acetyl-CoA. As such, the steps beyond succinyl-CoA are essential for completing the carbon fixation cycle and for anapleurosis of acetyl-CoA. Here, the final four enzymes of the 3HP/4HB cycle, 4-hydroxybutyrate-CoA ligase (AMP forming) (Msed_0406), 4-hydroxybutyryl-CoA dehydratase (Msed_1321), crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase (Msed_0399), and acetoacetyl-CoA β-ketothiolase (Msed_0656), were produced recombinantly inEscherichia coli, combinedin vitro, and shown to convert 4HB to acetyl-CoA. Metabolic pathways connecting CO2fixation and central metabolism were examined using a gas-intensive bioreactor system in whichM. sedulawas grown under autotrophic (CO2-limited) and heterotrophic conditions. Transcriptomic analysis revealed the importance of the 3HP/4HB pathway in supplying acetyl-CoA to anabolic pathways generating intermediates inM. sedulametabolism. The results indicated that flux between the succinate and acetyl-CoA branches in the 3HP/4HB pathway is governed by 4-hydroxybutyrate-CoA ligase, possibly regulated posttranslationally by the protein acetyltransferase (Pat)/Sir2-dependent system. Taken together, this work confirms the final four steps of the 3HP/4HB pathway, thereby providing the framework for examining connections between CO2fixation and central metabolism inM. sedula.

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Wong, Gail A., James D. Bergstrom, and John Edmond. "Acetoacetyl-CoA ligase activity in the isolated rat hepatocyte: Effects of 25-hydroxycholesterol and high density lipoprotein." Bioscience Reports 7, no. 3 (March 1, 1987): 217–24. http://dx.doi.org/10.1007/bf01124792.

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The activity of acetoacetyl-CoA (AcAc-CoA) ligase (E.C.6.2.1.16) in hepatocytes from rats was shown to be the same as the activity in homogenates of their livers. In hepatocytes treated with 25-hydroxycholesterol, AcAc-CoA ligase, 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase and rates of sterol synthesis were substantially decreased. Hepatocytes treated with high density lipoprotein (HDL) exhibited a 2 to 4 fold induction of HMG-CoA reductase activity; however an accompanying increase in AcAc-CoA ligase activity and the rate of cholesterol synthesis was not observed. We conclude (a) that increases in the activity of HMG-CoA reductase when mediated by HDL in hepatocytes do not result in a corresponding change in the capacity for sterol synthesis and (b) that changes in the activity state of HMG-CoA reductase can be dissociated from that of AcAc-CoA ligase.

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Schühle, Karola, Johannes Gescher, Ulrich Feil, Michael Paul, Martina Jahn, Hermann Schägger, and Georg Fuchs. "Benzoate-Coenzyme A Ligase from Thauera aromatica: an Enzyme Acting in Anaerobic and Aerobic Pathways." Journal of Bacteriology 185, no. 16 (August 15, 2003): 4920–29. http://dx.doi.org/10.1128/jb.185.16.4920-4929.2003.

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ABSTRACT In the denitrifying member of the β-Proteobacteria Thauera aromatica, the anaerobic metabolism of aromatic acids such as benzoate or 2-aminobenzoate is initiated by the formation of the coenzyme A (CoA) thioester, benzoyl-CoA and 2-aminobenzoyl-CoA, respectively. Both aromatic substrates were transformed to the acyl-CoA intermediate by a single CoA ligase (AMP forming) that preferentially acted on benzoate. This benzoate-CoA ligase was purified and characterized as a 57-kDa monomeric protein. Based on V max/Km , the specificity constant for 2-aminobenzoate was 15 times lower than that for benzoate; this may be the reason for the slower growth on 2-aminobenzoate. The benzoate-CoA ligase gene was cloned and sequenced and was found not to be part of the gene cluster encoding the general benzoyl-CoA pathway of anaerobic aromatic metabolism. Rather, it was located in a cluster of genes coding for a novel aerobic benzoate oxidation pathway. In line with this finding, the same CoA ligase was induced during aerobic growth with benzoate. A deletion mutant not only was unable to grow anaerobically on benzoate or 2-aminobenzoate, but also aerobic growth on benzoate was affected. This suggests that benzoate induces a single benzoate-CoA ligase. The product of benzoate activation, benzoyl-CoA, then acts as inducer of separate anaerobic or aerobic pathways of benzoyl-CoA, depending on whether oxygen is lacking or present.

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