Purification, characterization, DNA sequence and cloning of a pimeloyl-CoA synthetase from Pseudomonas mendocina 35

Binieda, Andrew; Fuhrmann, Martin; Lehner, Bruno; Rey-Berthod, Claudine; Frutiger-Hughes, Séverine; Hughes, Graham J.; Shaw, Nicholas M.

doi:10.1042/bj3400793

Cited by 16 publications

(10 citation statements)

References 14 publications

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“…strain HR167. In addition, the FerA amino acid sequence did show 31% identity with pimeloyl-CoA synthetase of Pseudomonas mendocina 35, which is involved in biotin synthesis (3).…”

Section: Resultsmentioning

confidence: 99%

Cloning and Characterization of the Ferulic Acid Catabolic Genes of Sphingomonas paucimobilis SYK-6

Masai

Harada

Peng

et al. 2002

Appl Environ Microbiol

103

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Sphingomonas paucimobilis SYK-6 degrades ferulic acid to vanillin, and it is further metabolized through the protocatechuate 4,5-cleavage pathway. We obtained a Tn5 mutant of SYK-6, FA2, which was able to grow on vanillic acid but not on ferulic acid. A cosmid which complemented the growth deficiency of FA2 on ferulic acid was isolated. . On the basis of the enzyme activity of E. coli carrying each of these genes, ferA and ferB were shown to encode a feruloyl-CoA synthetase and feruloyl-CoA hydratase/lyase, respectively. p-coumaric acid, caffeic acid, and sinapinic acid were converted to their corresponding benzaldehyde derivatives by the cell extract containing FerA and FerB, thereby indicating their broad substrate specificities. We found a ferB homolog, ferB2, upstream of a 5-carboxyvanillic acid decarboxylase gene (ligW) involved in the degradation of 5,5-dehydrodivanillic acid. The deduced amino acid sequence of ferB2 showed 49% identity with ferB, and its gene product showed feruloyl-CoA hydratase/lyase activity with a substrate specificity similar to that of FerB. Insertional inactivation of each fer gene in S. paucimobilis SYK-6 suggested that the ferA gene is essential and that ferB and ferB2 genes are involved in ferulic acid degradation.

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“…strain HR167. In addition, the FerA amino acid sequence did show 31% identity with pimeloyl-CoA synthetase of Pseudomonas mendocina 35, which is involved in biotin synthesis (3).…”

Section: Resultsmentioning

confidence: 99%

Cloning and Characterization of the Ferulic Acid Catabolic Genes of Sphingomonas paucimobilis SYK-6

Masai

Harada

Peng

et al. 2002

Appl Environ Microbiol

103

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“…BioW and BioC represent two major types of enzymes involved in the synthesis of pimeloylCoA, a biotin precursor. Moreover, another type of pimeloylCoA synthetase, namely, PauA, was found recently in Pseudomonas mendocina (Binieda et al 1999). In contrast to BioW, PauA belongs to the newly recognized superfamily of acylCoA synthetases (Sanchez et al 2000) and is involved in catabolism rather than biosynthesis.…”

Section: Discussionmentioning

confidence: 99%

Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea

Rodionov

Миронов²,

Gelfand³

2002

Genome Res.

182

230

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Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional BirA protein, which acts both as a biotin–protein ligase and as a transcriptional repressor of the biotin operon. Little is known about regulation of biotin biosynthesis in other bacteria. Using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the BirA regulon in most available bacterial genomes. Existence of an N-terminal DNA-binding domain in BirA strictly correlates with the presence of putative BirA-binding sites upstream of biotin operons. The predicted BirA-binding sites are well conserved among various eubacterial and archaeal genomes. The possible role of the hypothetical genes bioY and yhfS–yhfT, newly identified members of the BirA regulon, in the biotin metabolism is discussed. Based on analysis of co-occurrence of the biotin biosynthetic genes and bioY in complete genomes, we predict involvement of the transmembrane protein BioY in biotin transport. Various nonorthologous substitutes of the bioC-coupled gene bioH from E. coli, observed in several genomes, possibly represent the existence of different pathways for pimeloyl-CoA biosynthesis. Another interesting result of analysis of operon structures and BirA sites is that some biotin-dependent carboxylases from Rhodobacter capsulatus, actinomycetes, and archaea are possibly coregulated with BirA. BirA is the first example of a transcriptional regulator with a conserved binding signal in eubacteria and archaea

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“…Acyl-CoA ligases involved in the b-oxidation of fatty acids, including FadD from E. coli (Kameda & Nunn, 1981), have been described that are active with a broad range of fatty acids; however, these enzymes were not reported to have been tested for activity with dicarboxylic acids. Pimelyl-CoA is the first committed intermediate in the synthesis of the vitamin biotin, and several pimelate-CoA ligases have been purified and characterized in the course of efforts to develop a biotechnological process for the production of biotin (Binieda et al, 1999;Ploux et al, 1992). PimA shares approximately 30 % amino acid identity with these proteins, but the region of identity is mainly confined to the shared AMPbinding domain common to CoA ligases.…”

Section: Discussionmentioning

confidence: 99%

The pimFABCDE operon from Rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation

Harrison

Harwood

2005

Microbiology

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Bacteria in anoxic environments typically convert aromatic compounds derived from pollutants or green plants to benzoyl-CoA, and then to the C 7 dicarboxylic acid derivative 3-hydroxypimelyl-CoA. Inspection of the recently completed genome sequence of the purple nonsulfur phototroph Rhodopseudomonas palustris revealed one predicted cluster of genes for the b-oxidation of dicarboxylic acids. These genes, annotated as pimFABCDE, are predicted to encode acyl-CoA ligase, enoyl-CoA hydratase, acyl-CoA dehydrogenase and acyl-CoA transferase enzymes, which should allow the conversion of odd-chain dicarboxylic acids to glutaryl-CoA, and even-chain dicarboxylic acids to succinyl-CoA. A mutant strain that was deleted in the pim gene cluster grew at about half the rate of the wild-type parent when benzoate or pimelate was supplied as the sole carbon source. The mutant grew five times more slowly than the wild-type on the C 14 dicarboxylic acid tetradecanedioate. The mutant was unimpaired in growth on the C 8 -fatty acid caprylate. The acyl-CoA ligase predicted to be encoded by the pimA gene was purified, and found to be active with C 7-C 14 dicarboxylic and fatty acids. The expression of a pimA-lacZ chromosomal gene fusion increased twofold when cells were grown in the presence of straight-chain C 7-C 14 dicarboxylic and fatty acids. These results suggest that the b-oxidation enzymes encoded by the pim gene cluster are active with medium-chain-length dicarboxylic acids, including pimelate. However, the finding that the pim operon deletion mutant is still able to grow on dicarboxylic acids, albeit at a slower rate, indicates that R. palustris has additional genes that can also specify the degradation of these compounds.

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Purification, characterization, DNA sequence and cloning of a pimeloyl-CoA synthetase from Pseudomonas mendocina 35

Cited by 16 publications

References 14 publications

Cloning and Characterization of the Ferulic Acid Catabolic Genes of Sphingomonas paucimobilis SYK-6

Cloning and Characterization of the Ferulic Acid Catabolic Genes of Sphingomonas paucimobilis SYK-6

Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea

The pimFABCDE operon from Rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation

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