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Characterization of a Thiamin Diphosphatedependent

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Characterization of a Thiamin Diphosphatedependent Characterization of a thiamin diphosphate-dependent phenylpyruvate decarboxylase from Saccharomyces cerevisiae Malea M. Kneen1, Razvan Stan1, Alejandra Yep2, Ryan P. Tyler2, Choedchai Saehuan2,* and Michael J. McLeish1 1 Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, IN, USA 2 Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA Keywords The product of the ARO10 gene from Saccharomyces cerevisiae was ini- amino acid catabolism; Ehrlich pathway; tially identified as a thiamine diphosphate-dependent phenylpyruvate decar- homology model; mutagenesis; TPP boxylase with a broad substrate specificity. It was suggested that the enzyme could be responsible for the catabolism of aromatic and branched- Correspondence M. J. McLeish, Department of Chemistry chain amino acids, as well as methionine. In the present study, we report and Chemical Biology, Indiana University- the overexpression of the ARO10 gene product in Escherichia coli and the Purdue University Indianapolis, 402 North first detailed in vitro characterization of this enzyme. The enzyme is shown Blackford Street, Indianapolis, IN 46202, to be an efficient aromatic 2-keto acid decarboxylase, consistent with it USA playing a major in vivo role in phenylalanine, tryptophan and possibly also Fax: +1 317 274 4701 tyrosine catabolism. However, its substrate spectrum suggests that it is Tel: +1 317 274 6889 unlikely to play any significant role in the catabolism of the branched-chain E-mail: [email protected] amino acids or of methionine. A homology model was used to identify resi- *Present address dues likely to be involved in substrate specificity. Site-directed mutagenesis Department of Medical Technology, Faculty on those residues confirmed previous studies indicating that mutation of of Allied Health Sciences, Naresuan single residues is unlikely to produce the immediate conversion of an aro- University, Phitsanulok Thailand matic into an aliphatic 2-keto acid decarboxylase. In addition, the enzyme was compared with the phenylpyruvate decarboxylase from Azospiril- (Received 23 December 2010, revised 7 lum brasilense and the indolepyruvate decarboxylase from Enterobacter clo- March 2011, accepted 21 March 2011) acae. We show that the properties of the two phenylpyruvate doi:10.1111/j.1742-4658.2011.08103.x decarboxylases are similar in some respects yet quite different in others, and that the properties of both are distinct from those of the indolepyru- vate decarboxylase. Finally, we demonstrate that it is unlikely that replace- ment of a glutamic acid by leucine leads to discrimination between phenylpyruvate and indolepyruvate, although, in this case, it did lead to unexpected allosteric activation. Introduction The Ehrlich pathway, which permits the use of leucine, formation of the fusel alcohols and acids (Fig. 1) [1]. isoleucine, valine, methionine, tyrosine, tryptophan or Indeed, in Saccharomyces cerevisiae, the Ehrlich phenylalanine as a sole nitrogen source, leads to the pathway is the only route for phenylalanine and Abbreviations BFDC, benzoylformate decarboxylase; IPDC, indole-3-pyruvate decarboxylase; IPyA, indole-3-pyruvic acid; KdcA, keto acid decarboxylase; PDB, Protein Data Bank; PDC, pyruvate decarboxylase; PPA, phenylpyruvic acid; PPDC, phenylpyruvate decarboxylase; ThDP, thiamin diphosphate. 1842 FEBS Journal 278 (2011) 1842–1853 ª 2011 The Authors Journal compilation ª 2011 FEBS M. M. Kneen et al. Characterization of phenylpyruvate decarboxylase Fig. 1. The Ehrlich pathway: catabolism of amino acids to produce alcohols or carbox- ylic acids. tryptophan catabolism [2]. The amino acids are target genes [14]. Therefore, potentially, ARO10 and initially transaminated to 2-keto acids and, in the its associated genes may be responsible for the catabo- subsequent irreversible step, the 2-keto acids are de- lism of aromatic and branched-chain amino acids, as carboxylated by any of several thiamin diphosphate well as methionine. However, ScPPDC is essentially (ThDP)-dependent decarboxylases. Depending on the unable to utilize pyruvate [4]. redox state of the cell [3], the resulting aldehydes are As part of an ongoing project in our laboratory, we then converted by a suite of alcohol and aldehyde de- are interested in determining the rules that govern sub- hydrogenases to fusel alcohols or acids, respectively strate specificity in ThDP-dependent decarboxylases. [4]. The fusel products are finally excreted into the In the first instance, we focused on converting benzoyl- surrounding medium. In yeast-fermented foods and formate decarboxylase (BFDC) into a PDC, which beverages, these products are important contributors involved shifting the enzyme’s preference from binding to flavors, both desirable and undesirable [1]. Recently, a phenyl group to binding a methyl group [15,16]. interest in this pathway has extended to a potential Although the results obtained from those studies have role in the production of biofuels. Branched-chain been promising, with a 11 000-fold improvement in alcohols have significant advantages, such as higher pyruvate utilization by BFDC [16], the experimental energy density and lower hygroscopicity, over ethanol design has been complicated by differences in the posi- [5]. Consequently, there is considerable attention being tion of the catalytic residues in the two decarboxylases paid to those enzymes that are involved in the produc- [17]. ScPPDC is more similar to S. cerevisiae PDC1 tion of branched-chain 2-keto acids [5,6]. (32% identity, 45% similarity) than is BFDC (18% S. cerevisiae expresses several ThDP-dependent identity, 33% similarity), and it was considered that decarboxylases that permit the assimilation of the aro- ScPPDC may prove to be a more tractable subject for matic and branched-chain amino acids [7–9]. The three conversion to a PDC. ScPPDC may also be considered pyruvate decarboxylase (PDC) isoforms, PDC1 [10], an attractive target for manipulation of the production PDC5 [11] and PDC6 [12], are the best-studied of these of fusel alcohols for the food, cosmetics and biofuel enzymes. The presence of PDC-independent decarbox- industries [1], as well as being useful for stereospecific ylase activity in S. cerevisiae was suggested by the abil- carboligation reactions [18]. ity of PDC-deletion strains to metabolize both In the present study, we report the overexpression of branched-chain and aromatic amino acids [8]. This the ARO10 gene product in Escherichia coli and the ability was traced to the ARO10 gene, also known as first detailed in vitro characterization of this enzyme YDR380w, which was induced by tryptophan through (UniProt ID: Q06408). The initial steps towards under- the same mechanism as ARO9, the gene encoding aro- standing the factors influencing decarboxylation of matic aminotransferase II [13]. The latter enzyme cata- shorter chain-length substrates are also reported. lyzes the first step in aromatic amino acid catabolism Finally, we test the proposal [19] that a single residue and is induced by aromatic amino acids via the tran- may be used to differentiate between the phenylpyru- scription factor Aro80 [13]. Subsequently, ARO10 was vate decarboxylases and the indolepyruvate decarboxy- found to be inducible by growth on phenylalanine as a lases (IPDCs). sole nitrogen source, and it was shown that the ARO10 gene product, ScPPDC, was a phenylpyruvate Results and Discussion decarboxylase with a broad substrate specificity [4]. In addition to being upregulated by methionine and leu- The ARO10 gene product has been identified as a phe- cine [4], transcriptome analyses of S. cerevisiae cells nylpyruvate decarboxylase with a broad spectrum of grown on various nitrogen sources showed that isoleu- activity [3,4]. PPDCs have been reported in a range of cine and threonine also trigger transcription of Aro80 bacterial species, including Achromobacter eurydice FEBS Journal 278 (2011) 1842–1853 ª 2011 The Authors Journal compilation ª 2011 FEBS 1843 Characterization of phenylpyruvate decarboxylase M. M. Kneen et al. [20], Acinetobacter calcoaceticus [21], Pseudomonas put- from P. putida (57.4 kDa) when run on the same gel ida [22], Nocardia sp. 239 [23] and Thauera aromatica (Fig. 2). Reassuringly, ESI-MS analysis provided a [23,24], although none of these enzymes has been char- molecular mass of 72 122.2 kDa. This corresponded acterized in detail. PPDC activity has also been well with the calculated molecular mass of ScPPDC- observed in crude extracts of Aspergillus niger [25] and His lacking the two N-terminal residues, Met and Ala blast searches [26] indicate that PPDCs are likely to (72 113.6 kDa). The N-terminal sequence of ScPPDC- exist in other fungal species. Similar to the latter His was determined to be PVTIEKFV, corresponding enzymes, at approximately 72 kDa, the ScPPDC is to residues 3–10 of the expected ScPPDC sequence, predicted to be almost 20% larger than most ThDP- confirming that the N-terminal Met and Ala were dependent decarboxylases. Nonetheless, the signature indeed absent. Although cleavage of the terminal Met features of a ThDP-dependent enzyme are maintained. was not unexpected, the loss of the alanine residue was In the present study, the gene encoding ScPPDC initially surprising. However, the literature revealed was amplified from S. cerevisiae genomic DNA and several examples in which the presence of proline as visualized as an approximately 1.9 kb band on a 0.8% the antepenultimate residue led to the removal of both agarose gel. This corresponded
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