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Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:4458-76. [PMID: 25911487 DOI: 10.1128/aem.00405-15] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/20/2015] [Indexed: 11/20/2022] Open
Abstract
Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit(-1) in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases.
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Cui JD, Qiu JQ, Fan XW, Jia SR, Tan ZL. Biotechnological production and applications of microbial phenylalanine ammonia lyase: a recent review. Crit Rev Biotechnol 2013; 34:258-68. [PMID: 23688066 DOI: 10.3109/07388551.2013.791660] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Phenylalanine ammonia lyase (PAL) catalyzes the nonoxidative deamination of l-phenylalanine to form trans-cinnamic acid and a free ammonium ion. It plays a major role in the catabolism of l-phenylalanine. The presence of PAL has been reported in diverse plants, some fungi, Streptomyces and few Cyanobacteria. In the past two decades, PAL has gained considerable significance in several clinical, industrial and biotechnological applications. Since its discovery, much knowledge has been gathered with reference to the enzyme's importance in phenyl propanoid pathway of plants. In contrast, there is little knowledge about microbial PAL. Furthermore, the commercial source of the enzyme has been mainly obtained from the fungi. This study focuses on the recent advances on the physiological role of microbial PAL and the improvements of PAL biotechnological production both from our laboratory and many others as well as the latest advances on the new applications of microbial PAL.
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Affiliation(s)
- Jian Dong Cui
- Research Center for Fermentation Engineering of Hebei, College of Bioscience and Bioengineering, Hebei University of Science and Technology , Shijiazhang , P R China
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Abstract
Phenylalanine ammonia lyase (PAL; E.C.4.3.1.5), which catalyses the biotransformation of l-phenylalanine to trans-cinnamic acid and ammonia, was first described in 1961 by Koukol and Conn. Since its discovery, much knowledge has been gathered with reference to the enzyme’s catabolic role in microorganisms and its importance in the phenyl propanoid pathway of plants. The 3-dimensional structure of the enzyme has been characterized using X-ray crystallography. This has led to a greater understanding of the mechanism of PAL-catalyzed reactions, including the discovery of a recently described cofactor, 3,5-dihydro-5-methyldiene-4H-imidazol-4-one. In the past 3 decades, PAL has gained considerable significance in several clinical, industrial, and biotechnological applications. The reversal of the normal physiological reaction can be effectively employed in the production of optically pure l-phenylalanine, which is a precursor of the noncalorific sweetener aspartame (l-phenylalanyl-l-aspartyl methyl ester). The enzyme’s natural ability to break down l-phenylalanine makes PAL a reliable treatment for the genetic condition phenylketonuria. In this mini-review, we discuss prominent details relating to the physiological role of PAL, the mechanism of catalysis, methods of determination and purification, enzyme kinetics, and enzyme activity in nonaqueous media. Two topics of current study on PAL, molecular biology and crystal structure, are also discussed.
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Affiliation(s)
- M Jason MacDonald
- Department of Chemistry, Cape Breton University, 1250 Grand Lake Road, Sydney, NS B1P 6L2, Canada
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Hwang EI, Kaneko M, Ohnishi Y, Horinouchi S. Production of plant-specific flavanones by Escherichia coli containing an artificial gene cluster. Appl Environ Microbiol 2003; 69:2699-706. [PMID: 12732539 PMCID: PMC154558 DOI: 10.1128/aem.69.5.2699-2706.2003] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In plants, chalcones are precursors for a large number of flavonoid-derived plant natural products and are converted to flavanones by chalcone isomerase or nonenzymatically. Chalcones are synthesized from tyrosine and phenylalanine via the phenylpropanoid pathway involving phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate:coenzyme A ligase (4CL), and chalcone synthase (CHS). For the purpose of production of flavanones in Escherichia coli, three sets of an artificial gene cluster which contained three genes of heterologous origins--PAL from the yeast Rhodotorula rubra, 4CL from the actinomycete Streptomyces coelicolor A3(2), and CHS from the licorice plant Glycyrrhiza echinata--were constructed. The constructions of the three sets were done as follows: (i) PAL, 4CL, and CHS were placed in that order under the control of the T7 promoter (P(T7)) and the ribosome-binding sequence (RBS) in the pET vector, where the initiation codons of 4CL and CHS were overlapped with the termination codons of the preceding genes; (ii) the three genes were transcribed by a single P(T7) in front of PAL, and each of the three contained the RBS at appropriate positions; and (iii) all three genes contained both P(T7) and the RBS. These pathways bypassed C4H, a cytochrome P-450 hydroxylase, because the bacterial 4CL enzyme ligated coenzyme A to both cinnamic acid and 4-coumaric acid. E. coli cells containing the gene clusters produced two flavanones, pinocembrin from phenylalanine and naringenin from tyrosine, in addition to their precursors, cinnamic acid and 4-coumaric acid. Of the three sets, the third gene cluster conferred on the host the highest ability to produce the flavanones. This is a new metabolic engineering technique for the production in bacteria of a variety of compounds of plant and animal origin.
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Affiliation(s)
- Eui Il Hwang
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masafumi Kaneko
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sueharu Horinouchi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding author. Mailing address: Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. Phone: 81 3 5841 5123. Fax: 81 3 5841 8021. E-mail:
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Langer B, Langer M, Rétey J. Methylidene-imidazolone (MIO) from histidine and phenylalanine ammonia-lyase. ADVANCES IN PROTEIN CHEMISTRY 2002; 58:175-214. [PMID: 11665488 DOI: 10.1016/s0065-3233(01)58005-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- B Langer
- Lehrstuhl Biochemie Im Institut für Organische Chemie, Universität Karlsruhe, Karlsruhe, Germany
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Nehls U, Ecke M, Hampp R. Sugar- and nitrogen-dependent regulation of an Amanita muscaria phenylalanine ammonium lyase gene. J Bacteriol 1999; 181:1931-3. [PMID: 10074091 PMCID: PMC93597 DOI: 10.1128/jb.181.6.1931-1933.1999] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/1998] [Accepted: 01/12/1999] [Indexed: 11/20/2022] Open
Abstract
The cDNA of a key enzyme of secondary metabolism, phenylalanine ammonium lyase, was identified for an ectomycorrhizal fungus by differential screening of a mycorrhizal library. The gene was highly expressed in hyphae grown at low external monosaccharide concentrations, but its expression was 30-fold reduced at elevated concentrations. Gene repression was regulated by hexokinase.
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Affiliation(s)
- U Nehls
- Universität Tübingen, Botanisches Institut, Physiologische Okologie der Pflanzen, 72076 Tübingen, Germany.
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Alonso J, Barredo JL, Díez B, Mellado E, Salto F, García JL, Cortés E. D-amino-acid oxidase gene from Rhodotorula gracilis (Rhodosporidium toruloides) ATCC 26217. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 4):1095-1101. [PMID: 9579082 DOI: 10.1099/00221287-144-4-1095] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete nucleotide sequence of the DAO1 gene encoding D-amino-acid oxidase (DAAO) in the yeast Rhodotorula gracilis (Rhodosporidium toruloides) ATCC 26217 has been determined. The primary structure of DAAO was deduced from the nucleotide sequence of a cDNA clone that covered the entire amino acid coding sequence. Comparison of cDNA and genomic sequences of DAO1 revealed the presence of five introns. Because this is the first gene of strain ATCC 26217 that has been cloned so far, the nucleotide sequences of these introns were compared to those from other fungi. Upstream of the structural gene there was a stretch of C + T-rich DNA similar to that found in the promoter region of a number of yeast genes. The cDNA gene, which encoded a protein of 368 amino acids (molecular mass 40 kDa), was overexpressed in Escherichia coli under the control of the strong lipoprotein promoter. Interestingly, a significant fraction (13-62%) of the total DAAO activity was recovered in its apoenzyme form, the percentage depending on the culture conditions. This fact allowed a rapid purification of the recombinant DAAO by affinity chromatography. The high level of expression achieved in E. coli and the possibility of modifying its catalytic properties by protein engineering provide a new model for the study of this enzyme.
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Affiliation(s)
- Jorge Alonso
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain
| | - José L Barredo
- Laboratorio de Ingeniería Genética, Antibióticos SA, León, Spain
| | - Bruno Díez
- Laboratorio de Ingeniería Genética, Antibióticos SA, León, Spain
| | | | - Francisco Salto
- Laboratorio de Ingeniería Genética, Antibióticos SA, León, Spain
| | - José L García
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain
| | - Estrella Cortés
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain
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Rétey J. Enzymatic catalysis by Friedel-Crafts-type reactions. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1996; 83:439-47. [PMID: 8947915 DOI: 10.1007/bf01144012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Although most enzymes work in aqueous medium, at their active sites they can adjust the polarity to meet the requirements of the reactions they catalyse. Thus, a Friedel-Crafts-type electrophilic substitution which is normally conducted in water-free media, can be used to activate the substrate for chemically difficult transformations. It is shown that histidine and phenylalanine ammonia lyases which contain the rare prosthetic group dehydroalanine, make use of a Friedel-Crafts-type reaction which was formerly thought to occur only in rather abiotic conditions. While histidine ammonia-lyase catalyses the first step of histidine degradation in most cells, phenylalanine ammonia-lyase is an important plant enzyme, producing cinnamic acid which is the precursor of lignins, coumarins and flavonoids responsible for the marvelous colours of many flowers.
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Affiliation(s)
- J Rétey
- Institut für Organische Chemie, Universität Karlsruhe, Germany
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Appert C, Logemann E, Hahlbrock K, Schmid J, Amrhein N. Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 225:491-9. [PMID: 7925471 DOI: 10.1111/j.1432-1033.1994.00491.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Near-full-length cDNAs for the four phenylalanine ammonia-lyase (PAL) isoenzymes in parsley (Petroselium crispum Nym.) were cloned and the complete amino acid sequences deduced. Fusion proteins with glutathione S-transferase were expressed in Escherichia coli, purified and cleaved. All of the resulting phenylalanine ammonia-lyase proteins, as well as the fusion proteins, were catalytically active. The turnover number of one selected isoenzyme, PAL-1, was estimated to be around 22 s-1 for each active site. In contrast to a certain degree of differential expression in various parts of parsley plants, the four phenylalanine ammonia-lyase isoenzymes exhibited very similar apparent Km values for L-phenylalanine (15-24.5 microM) as well as identical temperature (58 degrees C) and pH (8.5) optima. All of them were competitively inhibited by (E)-cinnamate with similar efficiency (Ki values: 9.1-21.5 microM), lacked cooperative behaviour, and accepted L-tyrosine as a substrate with low affinity (Km values: 2.6-7.8 mM). These results suggest that the occurrence of multiple gene copies has a function other than encoding isoenzymes with different enzyme kinetic properties.
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Affiliation(s)
- C Appert
- Institut für Pflanzenwissenschaften, Eidgenössische Technische Hochschule Zürich, Switzerland
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Schuster B, Rétey J. Serine-202 is the putative precursor of the active site dehydroalanine of phenylalanine ammonia lyase. Site-directed mutagenesis studies on the enzyme from parsley (Petroselinum crispum L.). FEBS Lett 1994; 349:252-4. [PMID: 8050576 DOI: 10.1016/0014-5793(94)00681-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To investigate the possible role of serine as a precursor of dehydroalanine at the active site of phenylalanine ammonia lyase, two serines, conserved in all known PAL and histidase sequences, were changed to alanine by site-directed mutagenesis. The resulting mutant genes were subcloned into the expression vector pT7.7 and the gene products were assayed for PAL activity. Mutant PALMutS209A showed the same catalytic property as wild-type PAL, whereas mutant PALMutS202A was devoid of catalytic activity, indicating that serine-202 is the most likely precursor of the active site dehydroalanine.
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Affiliation(s)
- B Schuster
- Department of Biochemistry, University of Karlsruhe, Germany
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Rasmussen OF, Oerum H. Analysis of the gene for phenylalanine ammonia-lyase from Rhodosporidium toruloides. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1991; 1:207-11. [PMID: 1773059 DOI: 10.3109/10425179109020772] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have cloned and sequenced the pal gene encoding phenylalanine ammonia-lyase (PAL) from Rhodosporidium toruloides strain CBS14. Our data imply a different start codon and thus a different amino acid sequence for the N-terminus of PAL as compared to the previously published sequence for pal from R. toruloides strain IF00559. Primer extension analysis shows three transcription initiation sites with non-translated leaders of 24-35 nucleotides. Upstream of these initiation sites is a long stretch rich in pyrimidines. PAL from R. toruloides is 78% and 37% homologous to PAL from Rhodotorula rubra and Petroselinum crispum, respectively. Alignment of the PAL sequences is related to data of enzyme function.
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Taylor RG, Lambert MA, Sexsmith E, Sadler SJ, Ray PN, Mahuran DJ, McInnes RR. Cloning and expression of rat histidase. Homology to two bacterial histidases and four phenylalanine ammonia-lyases. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)44737-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Dixon RA, Harrison MJ. Activation, structure, and organization of genes involved in microbial defense in plants. ADVANCES IN GENETICS 1990; 28:165-234. [PMID: 2239449 DOI: 10.1016/s0065-2660(08)60527-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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