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Perruchon C, Vasileiadis S, Papadopoulou ES, Karpouzas DG. Genome-Based Metabolic Reconstruction Unravels the Key Role of B12 in Methionine Auxotrophy of an Ortho-Phenylphenol-Degrading Sphingomonas haloaromaticamans. Front Microbiol 2020; 10:3009. [PMID: 31998277 PMCID: PMC6970198 DOI: 10.3389/fmicb.2019.03009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022] Open
Abstract
Auxotrophy to amino acids and vitamins is a common feature in the bacterial world shaping microbial communities through cross-feeding relations. The amino acid auxotrophy of pollutant-degrading bacteria could hamper their bioremediation potential, however, the underlying mechanisms of auxotrophy remain unexplored. We employed genome sequence-based metabolic reconstruction to identify potential mechanisms driving the amino acid auxotrophy of a Sphingomonas haloaromaticamans strain degrading the fungicide ortho-phenylphenol (OPP) and provided further verification for the identified mechanisms via in vitro bacterial assays. The analysis identified potential gaps in the biosynthesis of isoleucine, phenylalanine and tyrosine, while methionine biosynthesis was potentially effective, relying though in the presence of B12. Supplementation of the bacterium with the four amino acids in all possible combinations rescued its degrading capacity only with methionine. Genome sequence-based metabolic reconstruction and analysis suggested that the bacterium was incapable of de novo biosynthesis of B12 (missing genes for the construction of the corrin ring) but carried a complete salvage pathway for corrinoids uptake from the environment, transmembrane transportation and biosynthesis of B12. In line with this the bacterium maintained its degrading capacity and growth when supplied with environmentally relevant B12 concentrations (i.e., 0.1 ng ml–1). Using genome-based metabolic reconstruction and in vitro testing we unraveled the mechanism driving the auxotrophy of a pesticide-degrading S. haloaromaticamans. Further studies will investigate the corrinoids preferences of S. haloaromaticamans for optimum growth and OPP degradation.
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Affiliation(s)
- Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Yang Q, Yang Y, Tang Y, Wang X, Chen Y, Shen W, Zhan Y, Gao J, Wu B, He M, Chen S, Yang S. Development and characterization of acidic-pH-tolerant mutants of Zymomonas mobilis through adaptation and next-generation sequencing-based genome resequencing and RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:144. [PMID: 32817760 PMCID: PMC7427070 DOI: 10.1186/s13068-020-01781-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/04/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Acid pretreatment is a common strategy used to break down the hemicellulose component of the lignocellulosic biomass to release pentoses, and a subsequent enzymatic hydrolysis step is usually applied to release hexoses from the cellulose. The hydrolysate after pretreatment and enzymatic hydrolysis containing both hexoses and pentoses can then be used as substrates for biochemical production. However, the acid-pretreated liquor can also be directly used as the substrate for microbial fermentation, which has an acidic pH and contains inhibitory compounds generated during pretreatment. Although the natural ethanologenic bacterium Zymomonas mobilis can grow in a broad range of pH 3.5 ~ 7.5, cell growth and ethanol fermentation are still affected under acidic-pH conditions below pH 4.0. RESULTS In this study, adaptive laboratory evolution (ALE) strategy was applied to adapt Z. mobilis under acidic-pH conditions. Two mutant strains named 3.6M and 3.5M with enhanced acidic pH tolerance were selected and confirmed, of which 3.5M grew better than ZM4 but worse than 3.6M in acidic-pH conditions that is served as a reference strain between 3.6M and ZM4 to help unravel the acidic-pH tolerance mechanism. Mutant strains 3.5M and 3.6M exhibited 50 ~ 130% enhancement on growth rate, 4 ~ 9 h reduction on fermentation time to consume glucose, and 20 ~ 63% improvement on ethanol productivity than wild-type ZM4 at pH 3.8. Next-generation sequencing (NGS)-based whole-genome resequencing (WGR) and RNA-Seq technologies were applied to unravel the acidic-pH tolerance mechanism of mutant strains. WGR result indicated that compared to wild-type ZM4, 3.5M and 3.6M have seven and five single nucleotide polymorphisms (SNPs), respectively, among which four are shared in common. Additionally, RNA-Seq result showed that the upregulation of genes involved in glycolysis and the downregulation of flagellar and mobility related genes would help generate and redistribute cellular energy to resist acidic pH while keeping normal biological processes in Z. mobilis. Moreover, genes involved in RND efflux pump, ATP-binding cassette (ABC) transporter, proton consumption, and alkaline metabolite production were significantly upregulated in mutants under the acidic-pH condition compared with ZM4, which could help maintain the pH homeostasis in mutant strains for acidic-pH resistance. Furthermore, our results demonstrated that in mutant 3.6M, genes encoding F1F0 ATPase to pump excess protons out of cells were upregulated under pH 3.8 compared to pH 6.2. This difference might help mutant 3.6M manage acidic conditions better than ZM4 and 3.5M. A few gene targets were then selected for genetics study to explore their role in acidic pH tolerance, and our results demonstrated that the expression of two operons in the shuttle plasmids, ZMO0956-ZMO0958 encoding cytochrome bc1 complex and ZMO1428-ZMO1432 encoding RND efflux pump, could help Z. mobilis tolerate acidic-pH conditions. CONCLUSION An acidic-pH-tolerant mutant 3.6M obtained through this study can be used for commercial bioethanol production under acidic fermentation conditions. In addition, the molecular mechanism of acidic pH tolerance of Z. mobilis was further proposed, which can facilitate future research on rational design of synthetic microorganisms with enhanced tolerance against acidic-pH conditions. Moreover, the strategy developed in this study combining approaches of ALE, genome resequencing, RNA-Seq, and classical genetics study for mutant evolution and characterization can be applied in other industrial microorganisms.
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Affiliation(s)
- Qing Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Ying Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Xia Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Wei Shen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Junjie Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu, 610041 China
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu, 610041 China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
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Identification and Partial Characterization of an L-Tyrosine Aminotransferase (TAT) from Arabidopsis thaliana. Biochem Res Int 2010; 2010:549572. [PMID: 21188077 PMCID: PMC3005984 DOI: 10.1155/2010/549572] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/17/2010] [Indexed: 11/17/2022] Open
Abstract
The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes. Twenty six of these enzymes are classified as characterized meaning that the reaction(s) that the enzyme catalyzes are documented using experimental means. The remaining 18 enzymes are uncharacterized and are therefore deemed putative. Our laboratory is interested in elucidating the function(s) of the remaining putative aminotransferase enzymes. To this end, we have identified and partially characterized an aminotransferase (TAT) enzyme from Arabidopsis annotated by the locus tag At5g36160. The full-length cDNA was cloned and the purified recombinant enzyme was characterized using in vitro and in vivo experiments. In vitro analysis showed that the enzyme is capable of interconverting L-Tyrosine and 4-hydroxyphenylpyruvate, and L-Phenylalanine and phenylpyruvate. In vivo analysis by functional complementation showed that the gene was able to complement an E. coli with a background of aminotransferase mutations that confers auxotrophy for L-Tyrosine and L-Phenylalanine.
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Braun SD, Hofmann J, Wensing A, Ullrich MS, Weingart H, Völksch B, Spiteller D. Identification of the biosynthetic gene cluster for 3-methylarginine, a toxin produced by Pseudomonas syringae pv. syringae 22d/93. Appl Environ Microbiol 2010; 76:2500-8. [PMID: 20190091 PMCID: PMC2849186 DOI: 10.1128/aem.00666-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Accepted: 02/16/2010] [Indexed: 11/20/2022] Open
Abstract
The epiphyte Pseudomonas syringae pv. syringae 22d/93 (Pss22d) produces the rare amino acid 3-methylarginine (MeArg), which is highly active against the closely related soybean pathogen Pseudomonas syringae pv. glycinea. Since these pathogens compete for the same habitat, Pss22d is a promising candidate for biocontrol of P. syringae pv. glycinea. The MeArg biosynthesis gene cluster codes for the S-adenosylmethionine (SAM)-dependent methyltransferase MrsA, the putative aminotransferase MrsB, and the amino acid exporter MrsC. Transfer of the whole gene cluster into Escherichia coli resulted in heterologous production of MeArg. The methyltransferase MrsA was overexpressed in E. coli as a His-tagged protein and functionally characterized (K(m), 7 mM; k(cat), 85 min(-1)). The highly selective methyltransferase MrsA transfers the methyl group from SAM into 5-guanidino-2-oxo-pentanoic acid to yield 5-guanidino-3-methyl-2-oxo-pentanoic acid, which then only needs to be transaminated to result in the antibiotic MeArg.
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Affiliation(s)
- S. D. Braun
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - J. Hofmann
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - A. Wensing
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - M. S. Ullrich
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - H. Weingart
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - B. Völksch
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - D. Spiteller
- Institute of Microbiology, Microbial Phytopathology, University of Jena, Neugasse 25, 07743 Jena, Germany, Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany, Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Strasse 8, 07745 Jena, Germany
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Recombinant expression of twelve evolutionarily diverse subfamily Ialpha aminotransferases. Protein Expr Purif 2007; 57:34-44. [PMID: 17964807 DOI: 10.1016/j.pep.2007.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 09/02/2007] [Accepted: 09/03/2007] [Indexed: 11/24/2022]
Abstract
Aminotransferases are essential enzymes involved in the central metabolism of all organisms. The Ialpha subfamily of aspartate and tyrosine aminotransferases (AATases and TATases) is the best-characterized grouping, but only eight enzymes from this subfamily, representing relatively little sequence diversity, have been experimentally characterized for substrate specificity (i.e., AATase vs. TATase). Genome annotation, based on this limited dataset, provides tentative assignments for all sequenced members of this subfamily. This procedure is, however, subject to error, particularly when the experimental basis set is limited. To address this problem we cloned twelve additional subfamily Ialpha enzymes from an evolutionarily divergent set of organisms. Nine were purified to homogeneity after heterologous expression in Escherichia coli in native, intein-tagged or His(6)-tagged forms. The two Saccharomyces cerevisiae isoforms were recombinantly produced in yeast. The effects of the C-terminal tags on expression, purification and enzyme activity are discussed.
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Fani R, Brilli M, Liò P. Inference from proteobacterial operons shows piecewise organization: a reply to Price et al. J Mol Evol 2006; 63:577-80. [PMID: 16955235 DOI: 10.1007/s00239-006-0074-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 03/29/2006] [Indexed: 10/24/2022]
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Sivaraman J, Li Y, Larocque R, Schrag JD, Cygler M, Matte A. Crystal structure of histidinol phosphate aminotransferase (HisC) from Escherichia coli, and its covalent complex with pyridoxal-5'-phosphate and l-histidinol phosphate. J Mol Biol 2001; 311:761-76. [PMID: 11518529 DOI: 10.1006/jmbi.2001.4882] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The biosynthesis of histidine is a central metabolic process in organisms ranging from bacteria to yeast and plants. The seventh step in the synthesis of histidine within eubacteria is carried out by a pyridoxal-5'-phosphate (PLP)-dependent l-histidinol phosphate aminotransferase (HisC, EC 2.6.1.9). Here, we report the crystal structure of l-histidinol phosphate aminotransferase from Escherichia coli, as a complex with pyridoxamine-5'-phosphate (PMP) at 1.5 A resolution, as the internal aldimine with PLP, and in a covalent, tetrahedral complex consisting of PLP and l-histidinol phosphate attached to Lys214, both at 2.2 A resolution. This covalent complex resembles, in structural terms, the gem-diamine intermediate that is formed transiently during conversion of the internal to external aldimine.HisC is a dimeric enzyme with a mass of approximately 80 kDa. Like most PLP-dependent enzymes, each HisC monomer consists of two domains, a larger PLP-binding domain having an alpha/beta/alpha topology, and a smaller domain. An N-terminal arm contributes to the dimerization of the two monomers. The PLP-binding domain of HisC shows weak sequence similarity, but significant structural similarity with the PLP-binding domains of a number of PLP-dependent enzymes. Residues that interact with the PLP cofactor, including Tyr55, Asn157, Asp184, Tyr187, Ser213, Lys214 and Arg222, are conserved in the family of aspartate, tyrosine and histidinol phosphate aminotransferases. The imidazole ring of l-histidinol phosphate is bound, in part, through a hydrogen bond with Tyr110, a residue that is substituted by Phe in the broad substrate specific HisC enzymes from Zymomonas mobilis and Bacillus subtilis. Comparison of the structures of the HisC internal aldimine, the PMP complex and the HisC l-histidinol phosphate complex reveal minimal changes in protein or ligand structure. Proton transfer, required for conversion of the gem-diamine to the external aldimine, does not appear to be limited by the distance between substrate and lysine amino groups. We propose that the tetrahedral complex has resulted from non-productive binding of l-histidinol phosphate soaked into the HisC crystals, resulting in its inability to be converted to the external aldimine at the HisC active site.
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Affiliation(s)
- J Sivaraman
- Biotechnology Research Institute, 6100 Royalmount Ave., Montreal, H4P 2R2 and, Canada
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Calhoun DH, Bonner CA, Gu W, Xie G, Jensen RA. The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa. Genome Biol 2001; 2:RESEARCH0030. [PMID: 11532214 PMCID: PMC55327 DOI: 10.1186/gb-2001-2-8-research0030] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Revised: 05/21/2001] [Accepted: 06/13/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chorismate mutases of the AroQ homology class are widespread in the Bacteria and the Archaea. Many of these exist as domains that are fused with other aromatic-pathway catalytic domains. Among the monofunctional AroQ proteins, that from Erwinia herbicola was previously shown to have a cleavable signal peptide and located in the periplasmic compartment. Whether or not this might be unique to E. herbicola was unknown. RESULTS The gene coding for the AroQ protein was cloned from Salmonella typhimurium, and the AroQ protein purified from both S. typhimurium and Pseudomonas aeruginosa was shown to have a periplasmic location. The periplasmic chorismate mutases (denoted *AroQ) are shown to be a distinct subclass of AroQ, being about twice the size of cytoplasmic AroQ proteins. The increased size is due to a carboxy-terminal extension of unknown function. In addition, a so-far novel aromatic aminotransferase was shown to be present in the periplasm of P. aeruginosa. CONCLUSIONS Our analysis has detected a number of additional *aroQ genes. The joint presence of *AroQ, cyclohexadienyl dehydratase and aromatic aminotransferase in the periplasmic compartment of P. aeruginosa comprises a complete chorismate-to-phenylalanine pathway and accounts for the "hidden overflow pathway" to phenylalanine described previously.
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Affiliation(s)
- David H Calhoun
- Department of Chemistry, City College of New York, New York, NY 10031, USA
| | - Carol A Bonner
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
| | - Wei Gu
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
| | - Gary Xie
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Roy A Jensen
- Department of Chemistry, City College of New York, New York, NY 10031, USA
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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Gu W, Song J, Bonner CA, Xie G, Jensen RA. PhhC is an essential aminotransferase for aromatic amino acid catabolism in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 11):3127-3134. [PMID: 9846749 DOI: 10.1099/00221287-144-11-3127] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The phhC gene of Pseudomonas aeruginosa encodes a protein which is a member of the Family I aminotransferases. At high expression levels in the heterologous Escherichia coli system, PhhC can compensate for the absence of AspC (which functions in L-aspartate biosynthesis) and TyrB (which functions in aromatic biosynthesis). In the native organism, PhhC is essential for catabolism of either L-tyrosine or L-phenylalanine, as demonstrated by gene inactivation. This catabolic function of PhhC is consistent with its inclusion as the distal gene in the inducible phenylalanine hydroxylase operon. The presence of PhhC for catabolism of aromatic amino acids is required in spite of an existing multiplicity of other P. aeruginosa aminotransferases having a similar pattern of broad substrate specificity in vitro. This implies a spatial orientation of PhhC that effectively specializes it for aromatic amino acid catabolism.
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Affiliation(s)
- Wei Gu
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 3261 1-0700, USA
| | - Jian Song
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 3261 1-0700, USA
| | - Carol A Bonner
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 3261 1-0700, USA
| | - Gang Xie
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 3261 1-0700, USA
| | - Roy A Jensen
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 3261 1-0700, USA
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Gu W, Williams DS, Aldrich HC, Xie G, Gabriel DW, Jensen RA. The aroQ and pheA domains of the bifunctional P-protein from Xanthomonas campestris in a context of genomic comparison. MICROBIAL & COMPARATIVE GENOMICS 1998; 2:141-58. [PMID: 9689222 DOI: 10.1089/omi.1.1997.2.141] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The gene (denoted aroQp.pheA) encoding the bifunctional P-protein (chorismate mutase-P/prephenate dehydratase) from Xanthomonas campestris was cloned. aroQp.pheA is essential for L-phenylalanine biosynthesis. DNA sequencing of the smallest subclone capable of functional complementation of an Escherichia coli phenylalanine auxotroph revealed a putative open reading frame (ORF) of 1200 bp that would encode a 43,438-Da protein. AroQp.PheA exhibited 51% amino acid identity with a Pseudomonas stutzeri homologoue and greater than 30% identities with AroQp.PheA proteins from Haemophilus influenzae, Neisseria gonorrhoeae, and a number of enteric bacteria. AroQp.PheA from X. campestris, when expressed in E. coli, possesses a 40-residue amino-terminal extension that is lysine-rich and that is absent in all of the AroQp.PheA homologues known at present. About 95% of AroQp.PheA was particulate and readily sedimented by low-speed centrifugation. Soluble preparations of cloned AroQp.PheA exhibited a native molecular mass of 81,000 Da, indicating that the active enzyme species is a homodimer. These preparations were unstable after purification of about 40-fold, even in the presence of glycerol, which was an effective protectant before fractionation. When AroQp.PheA was overproduced by a T7 translation vector, unusual inclusion bodies having a macromolecular structure consisting of protein fibrils were observed by electron microscopy. Insoluble protein collected at low-speed centrifugation possessed high catalytic activity. The single band obtained via SDS-PAGE was used to confirm the translational start via N-terminal amino acid sequencing. A perspective on the evolutionary relationships of monofunctional AroQ and PheA proteins and the AroQp.PheA family of proteins is presented. A serC gene located immediately upstream of X. campestris aroQp.pheA appears to reflect a conserved gene organization, and both may belong to a single transcriptional unit.
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Affiliation(s)
- W Gu
- Department of Microbiology and Cell Science, University of Florida, Gainesville, USA
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Jensen RA, Gu W. Evolutionary recruitment of biochemically specialized subdivisions of Family I within the protein superfamily of aminotransferases. J Bacteriol 1996; 178:2161-71. [PMID: 8636014 PMCID: PMC177921 DOI: 10.1128/jb.178.8.2161-2171.1996] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- R A Jensen
- Department of Microbiology and Cell Science, University of Florida, Gainesville 32611, USA
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12
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Alifano P, Fani R, Liò P, Lazcano A, Bazzicalupo M, Carlomagno MS, Bruni CB. Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Microbiol Rev 1996; 60:44-69. [PMID: 8852895 PMCID: PMC239417 DOI: 10.1128/mr.60.1.44-69.1996] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- P Alifano
- Dipartimento di Biologia e Patologia Cellulare e Molecolare L. Califano, Università degli Studi di Napoli Federico II, Italy
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