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Fulton RL, Downs DM. Modulators of a robust and efficient metabolism: Perspective and insights from the Rid superfamily of proteins. Adv Microb Physiol 2023; 83:117-179. [PMID: 37507158 PMCID: PMC10642521 DOI: 10.1016/bs.ampbs.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Metabolism is an integrated network of biochemical pathways that assemble to generate the robust, responsive physiologies of microorganisms. Despite decades of fundamental studies on metabolic processes and pathways, our understanding of the nuance and complexity of metabolism remains incomplete. The ability to predict and model metabolic network structure, and its influence on cellular fitness, is complicated by the persistence of genes of unknown function, even in the best-studied model organisms. This review describes the definition and continuing study of the Rid superfamily of proteins. These studies are presented with a perspective that illustrates how metabolic complexity can complicate the assignment of function to uncharacterized genes. The Rid superfamily of proteins has been divided into eight subfamilies, including the well-studied RidA subfamily. Aside from the RidA proteins, which are present in all domains of life and prevent metabolic stress, most members of the Rid superfamily have no demonstrated physiological role. Recent progress on functional assignment supports the hypothesis that, overall, proteins in the Rid superfamily modulate metabolic processes to ensure optimal organismal fitness.
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Affiliation(s)
- Ronnie L Fulton
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, United States.
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2
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Ahn-Horst TA, Mille LS, Sun G, Morrison JH, Covert MW. An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control. NPJ Syst Biol Appl 2022; 8:30. [PMID: 35986058 PMCID: PMC9391491 DOI: 10.1038/s41540-022-00242-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Growth and environmental responses are essential for living organisms to survive and adapt to constantly changing environments. In order to simulate new conditions and capture dynamic responses to environmental shifts in a developing whole-cell model of E. coli, we incorporated additional regulation, including dynamics of the global regulator guanosine tetraphosphate (ppGpp), along with dynamics of amino acid biosynthesis and translation. With the model, we show that under perturbed ppGpp conditions, small molecule feedback inhibition pathways, in addition to regulation of expression, play a role in ppGpp regulation of growth. We also found that simulations with dysregulated amino acid synthesis pathways provide average amino acid concentration predictions that are comparable to experimental results but on the single-cell level, concentrations unexpectedly show regular fluctuations. Additionally, during both an upshift and downshift in nutrient availability, the simulated cell responds similarly with a transient increase in the mRNA:rRNA ratio. This additional simulation functionality should support a variety of new applications and expansions of the E. coli Whole-Cell Modeling Project.
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Affiliation(s)
- Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jerry H Morrison
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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Putative Horizontally Acquired Genes, Highly Transcribed during Yersinia pestis Flea Infection, Are Induced by Hyperosmotic Stress and Function in Aromatic Amino Acid Metabolism. J Bacteriol 2020; 202:JB.00733-19. [PMID: 32205462 PMCID: PMC7221256 DOI: 10.1128/jb.00733-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Distinct gene repertoires are expressed during Y. pestis infection of its flea and mammalian hosts. The functions of many of these genes remain predicted or unknown, necessitating their characterization, as this may provide a better understanding of Y. pestis specialized biological adaptations to the discrete environments of its two hosts. This study provides functional context to adjacently clustered horizontally acquired genes predominantly expressed in the flea host by deciphering their fundamental processes with regard to (i) transcriptional organization, (ii) transcription activation signals, and (iii) biochemical function. Our data support a role for these genes in osmoadaptation and aromatic amino acid metabolism, highlighting these as preferential processes by which Y. pestis gene expression is modulated during flea infection. While alternating between insects and mammals during its life cycle, Yersinia pestis, the flea-transmitted bacterium that causes plague, regulates its gene expression appropriately to adapt to these two physiologically disparate host environments. In fleas competent to transmit Y. pestis, low-GC-content genes y3555, y3551, and y3550 are highly transcribed, suggesting that these genes have a highly prioritized role in flea infection. Here, we demonstrate that y3555, y3551, and y3550 are transcribed as part of a single polycistronic mRNA comprising the y3555, y3554, y3553, y355x, y3551, and y3550 genes. Additionally, y355x-y3551-y3550 compose another operon, while y3550 can be also transcribed as a monocistronic mRNA. The expression of these genes is induced by hyperosmotic salinity stress, which serves as an explicit environmental stimulus that initiates transcriptional activity from the predicted y3550 promoter. Y3555 has homology to pyridoxal 5′-phosphate (PLP)-dependent aromatic aminotransferases, while Y3550 and Y3551 are homologous to the Rid protein superfamily (YjgF/YER057c/UK114) members that forestall damage caused by reactive intermediates formed during PLP-dependent enzymatic activity. We demonstrate that y3551 specifically encodes an archetypal RidA protein with 2-aminoacrylate deaminase activity but Y3550 lacks Rid deaminase function. Heterologous expression of y3555 generates a critical aspartate requirement in a Salmonella entericaaspC mutant, while its in vitro expression, and specifically its heterologous coexpression with y3550, enhances the growth rate of an Escherichia coli ΔaspC ΔtyrB mutant in a defined minimal amino acid-supplemented medium. Our data suggest that the y3555, y3551, and y3550 genes operate cooperatively to optimize aromatic amino acid metabolism and are induced under conditions of hyperosmotic salinity stress. IMPORTANCE Distinct gene repertoires are expressed during Y. pestis infection of its flea and mammalian hosts. The functions of many of these genes remain predicted or unknown, necessitating their characterization, as this may provide a better understanding of Y. pestis specialized biological adaptations to the discrete environments of its two hosts. This study provides functional context to adjacently clustered horizontally acquired genes predominantly expressed in the flea host by deciphering their fundamental processes with regard to (i) transcriptional organization, (ii) transcription activation signals, and (iii) biochemical function. Our data support a role for these genes in osmoadaptation and aromatic amino acid metabolism, highlighting these as preferential processes by which Y. pestis gene expression is modulated during flea infection.
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Xiong T, Jiang J, Bai Y, Fan TP, Zhao Y, Zheng X, Cai Y. Redox self-sufficient biocatalyst system for conversion of 3,4-Dihydroxyphenyl-L-alanine into (R)- or (S)-3,4-Dihydroxyphenyllactic acid. J Ind Microbiol Biotechnol 2019; 46:1081-1090. [PMID: 31201648 DOI: 10.1007/s10295-019-02200-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/29/2019] [Indexed: 01/06/2023]
Abstract
We developed an efficient multi-enzyme cascade reaction to produce (R)- or (S)-3,4-Dihydroxyphenyllactic acid [(R)- or (S)-Danshensu, (R)- or (S)-DSS] from 3,4-Dihydroxyphenyl-L-alanine (L-DOPA) in Escherichia coli by introducing tyrosine aminotransferase (tyrB), glutamate dehydrogenase (cdgdh) and D-aromatic lactate dehydrogenase (csldhD) or L-aromatic lactate dehydrogenase (tcldhL). First, the genes in the pathway were overexpressed and fine-tuned for (R)- or (S)-DSS production. The resulting strain, E. coli TGL 2.1 and E. coli TGL 2.2, which overexpressed tyrB with the stronger T7 promoter and cdgdh, csldhD or tcldhL with the weaker Trc promoter, E. coli TGL 2.1 yielded 57% increase in (R)-DSS production: 59.8 ± 2.9 mM. Meanwhile, E. coli TGL 2.2 yielded 54% increase in (S)-DSS production: 52.2 ± 2.4 mM. The optimal concentration of L-glutamate was found to be 20 mM for production of (R)- or (S)-DSS. Finally, L-DOPA were transformed into (R)- or (S)-DSS with an excellent enantiopure form (enantiomeric excess > 99.99%) and productivity of 6.61 mM/h and 4.48 mM/h, respectively.
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Affiliation(s)
- Tianzhen Xiong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jing Jiang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1T, UK
| | - Ye Zhao
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Feng LY, Xu JZ, Zhang WG. Improved l-Leucine Production in Corynebacterium glutamicum by Optimizing the Aminotransferases. Molecules 2018; 23:molecules23092102. [PMID: 30134636 PMCID: PMC6225143 DOI: 10.3390/molecules23092102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022] Open
Abstract
The production of branched-chain amino acids (BCAAs) is still challenging, therefore we rationally engineered Corynebacterium glutamicum FA-1 to increase the l-leucine production by optimizing the aminotransferases. Based on this, we investigated the effects of the native aminotransferases, i.e., branched-chain amino acid aminotransferase (BCAT; encoded by ilvE) and aspartate aminotransferase (AspB; encoded by aspB) on l-leucine production in C. glutamicum. The strain FA-1△ilvE still exhibited significant growth without leucine addition, while FA-1△ilvE△aspB couldn't, which indicated that AspB also contributes to L-leucine synthesis in vivo and the yield of leucine reached 20.81 ± 0.02 g/L. It is the first time that AspB has been characterized for l-leucine synthesis activity. Subsequently, the aromatic aminotransferase TyrB and the putative aspartate aminotransferases, the aspC, yhdR, ywfG gene products, were cloned, expressed and characterized for leucine synthesis activity in FA-1△ilvE△aspB. Only TyrB was able to synthesize l-leucine and the l-leucine production was 18.55 ± 0.42 g/L. The two putative branched-chain aminotransferase genes, ybgE and CaIlvE, were also cloned and expressed. Both genes products function efficiently in BCAAs biosynthesis. This is the first report of a rational modification of aminotransferase activity that improves the l-leucine production through optimizing the aminotransferases.
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Affiliation(s)
- Li-Yan Feng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A 2015; 112:929-34. [PMID: 25564669 DOI: 10.1073/pnas.1414218112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enzyme promiscuity toward substrates has been discussed in evolutionary terms as providing the flexibility to adapt to novel environments. In the present work, we describe an approach toward exploring such enzyme promiscuity in the space of a metabolic network. This approach leverages genome-scale models, which have been widely used for predicting growth phenotypes in various environments or following a genetic perturbation; however, these predictions occasionally fail. Failed predictions of gene essentiality offer an opportunity for targeting biological discovery, suggesting the presence of unknown underground pathways stemming from enzymatic cross-reactivity. We demonstrate a workflow that couples constraint-based modeling and bioinformatic tools with KO strain analysis and adaptive laboratory evolution for the purpose of predicting promiscuity at the genome scale. Three cases of genes that are incorrectly predicted as essential in Escherichia coli--aspC, argD, and gltA--are examined, and isozyme functions are uncovered for each to a different extent. Seven isozyme functions based on genetic and transcriptional evidence are suggested between the genes aspC and tyrB, argD and astC, gabT and puuE, and gltA and prpC. This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations.
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Saika A, Watanabe Y, Sudesh K, Tsuge T. Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxy-4-methylvalerate) by recombinant Escherichia coli expressing leucine metabolism-related enzymes derived from Clostridium difficile. J Biosci Bioeng 2014; 117:670-5. [DOI: 10.1016/j.jbiosc.2013.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/01/2022]
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Farrugia DN, Elbourne LDH, Hassan KA, Eijkelkamp BA, Tetu SG, Brown MH, Shah BS, Peleg AY, Mabbutt BC, Paulsen IT. The complete genome and phenome of a community-acquired Acinetobacter baumannii. PLoS One 2013; 8:e58628. [PMID: 23527001 PMCID: PMC3602452 DOI: 10.1371/journal.pone.0058628] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/05/2013] [Indexed: 01/19/2023] Open
Abstract
Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable of resistance to multiple antimicrobials. Community-acquired A. baumannii in contrast, comprise a minor proportion of all A. baumannii infections and are highly susceptible to antimicrobial treatment. However, these infections also present acute clinical manifestations associated with high reported rates of mortality. We report the complete 3.70 Mbp genome of A. baumannii D1279779, previously isolated from the bacteraemic infection of an Indigenous Australian; this strain represents the first community-acquired A. baumannii to be sequenced. Comparative analysis of currently published A. baumannii genomes identified twenty-four accessory gene clusters present in D1279779. These accessory elements were predicted to encode a range of functions including polysaccharide biosynthesis, type I DNA restriction-modification, and the metabolism of novel carbonaceous and nitrogenous compounds. Conversely, twenty genomic regions present in previously sequenced A. baumannii strains were absent in D1279779, including gene clusters involved in the catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii antibiotic resistance island, known to bestow resistance to multiple antimicrobials in nosocomial strains. Phenomic analysis utilising the Biolog Phenotype Microarray system indicated that A. baumannii D1279779 can utilise a broader range of carbon and nitrogen sources than international clone I and clone II nosocomial isolates. However, D1279779 was more sensitive to antimicrobial compounds, particularly beta-lactams, tetracyclines and sulphonamides. The combined genomic and phenomic analyses have provided insight into the features distinguishing A. baumannii isolated from community-acquired and nosocomial infections.
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Affiliation(s)
- Daniel N. Farrugia
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Liam D. H. Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Bart A. Eijkelkamp
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Melissa H. Brown
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Bhumika S. Shah
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Anton Y. Peleg
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Bridget C. Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- * E-mail:
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9
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Maloney GS, Kochevenko A, Tieman DM, Tohge T, Krieger U, Zamir D, Taylor MG, Fernie AR, Klee HJ. Characterization of the branched-chain amino acid aminotransferase enzyme family in tomato. PLANT PHYSIOLOGY 2010; 153:925-36. [PMID: 20435740 PMCID: PMC2899903 DOI: 10.1104/pp.110.154922] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 04/30/2010] [Indexed: 05/18/2023]
Abstract
Branched-chain amino acids (BCAAs) are synthesized in plants from branched-chain keto acids, but their metabolism is not completely understood. The interface of BCAA metabolism lies with branched-chain aminotransferases (BCAT) that catalyze both the last anabolic step and the first catabolic step. In this study, six BCAT genes from the cultivated tomato (Solanum lycopersicum) were identified and characterized. SlBCAT1, -2, -3, and -4 are expressed in multiple plant tissues, while SlBCAT5 and -6 were undetectable. SlBCAT1 and -2 are located in the mitochondria, SlBCAT3 and -4 are located in chloroplasts, while SlBCAT5 and -6 are located in the cytosol and vacuole, respectively. SlBCAT1, -2, -3, and -4 were able to restore growth of Escherichia coli BCAA auxotrophic cells, but SlBCAT1 and -2 were less effective than SlBCAT3 and -4 in growth restoration. All enzymes were active in the forward (BCAA synthesis) and reverse (branched-chain keto acid synthesis) reactions. SlBCAT3 and -4 exhibited a preference for the forward reaction, while SlBCAT1 and -2 were more active in the reverse reaction. While overexpression of SlBCAT1 or -3 in tomato fruit did not significantly alter amino acid levels, an expression quantitative trait locus on chromosome 3, associated with substantially higher expression of Solanum pennellii BCAT4, did significantly increase BCAA levels. Conversely, antisense-mediated reduction of SlBCAT1 resulted in higher levels of BCAAs. Together, these results support a model in which the mitochondrial SlBCAT1 and -2 function in BCAA catabolism while the chloroplastic SlBCAT3 and -4 function in BCAA synthesis.
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MESH Headings
- Amino Acids, Branched-Chain/biosynthesis
- Amino Acids, Branched-Chain/chemistry
- Biosynthetic Pathways
- Chromatography, High Pressure Liquid
- Cloning, Molecular
- DNA, Complementary/genetics
- Escherichia coli/growth & development
- Gene Expression Profiling
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genetic Complementation Test
- Inbreeding
- Kinetics
- Solanum lycopersicum/enzymology
- Solanum lycopersicum/genetics
- Multigene Family
- Organ Specificity/genetics
- Physical Chromosome Mapping
- Plants, Genetically Modified
- Protein Transport
- Quantitative Trait Loci/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reproducibility of Results
- Sequence Homology, Amino Acid
- Subcellular Fractions/enzymology
- Transaminases/genetics
- Transaminases/metabolism
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Marienhagen J, Kennerknecht N, Sahm H, Eggeling L. Functional analysis of all aminotransferase proteins inferred from the genome sequence of Corynebacterium glutamicum. J Bacteriol 2005; 187:7639-46. [PMID: 16267288 PMCID: PMC1280304 DOI: 10.1128/jb.187.22.7639-7646.2005] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty putative aminotransferase (AT) proteins of Corynebacterium glutamicum, or rather pyridoxal-5'-phosphate (PLP)-dependent enzymes, were isolated and assayed among others with L-glutamate, L-aspartate, and L-alanine as amino donors and a number of 2-oxo-acids as amino acceptors. One outstanding AT identified is AlaT, which has a broad amino donor specificity utilizing (in the order of preference) L-glutamate > 2-aminobutyrate > L-aspartate with pyruvate as acceptor. Another AT is AvtA, which utilizes L-alanine to aminate 2-oxo-isovalerate, the L-valine precursor, and 2-oxo-butyrate. A second AT active with the L-valine precursor and that of the other two branched-chain amino acids, too, is IlvE, and both enzyme activities overlap partially in vivo, as demonstrated by the analysis of deletion mutants. Also identified was AroT, the aromatic AT, and this and IlvE were shown to have comparable activities with phenylpyruvate, thus demonstrating the relevance of both ATs for L-phenylalanine synthesis. We also assessed the activity of two PLP-containing cysteine desulfurases, supplying a persulfide intermediate. One of them is SufS, which assists in the sulfur transfer pathway for the Fe-S cluster assembly. Together with the identification of further ATs and the additional analysis of deletion mutants, this results in an overview of the ATs within an organism that may not have been achieved thus far.
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Affiliation(s)
- Jan Marienhagen
- Institute of Biotechnology, Research Centre Juelich, Germany
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11
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Fernandez FJ, Vega MC, Lehmann F, Sandmeier E, Gehring H, Christen P, Wilmanns M. Structural studies of the catalytic reaction pathway of a hyperthermophilic histidinol-phosphate aminotransferase. J Biol Chem 2004; 279:21478-88. [PMID: 15007066 DOI: 10.1074/jbc.m400291200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In histidine biosynthesis, histidinol-phosphate aminotransferase catalyzes the transfer of the amino group from glutamate to imidazole acetol-phosphate producing 2-oxoglutarate and histidinol phosphate. In some organisms such as the hyperthermophile Thermotoga maritima, specific tyrosine and aromatic amino acid transaminases have not been identified to date, suggesting an additional role for histidinol-phosphate aminotransferase in other transamination reactions generating aromatic amino acids. To gain insight into the specific function of this transaminase, we have determined its crystal structure in the absence of any ligand except phosphate, in the presence of covalently bound pyridoxal 5'-phosphate, of the coenzyme histidinol phosphate adduct, and of pyridoxamine 5'-phosphate. The enzyme accepts histidinol phosphate, tyrosine, tryptophan, and phenylalanine, but not histidine, as substrates. The structures provide a model of how these different substrates could be accommodated by histidinol-phosphate aminotransferase. Some of the structural features of the enzyme are more preserved between the T. maritima enzyme and a related threonine-phosphate decarboxylase from S. typhimurium than with histidinol-phosphate aminotransferases from different organisms.
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Affiliation(s)
- Francisco J Fernandez
- EMBL c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Building 25A, D-22603 Hamburg, Germany
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12
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Schmitz G, Downs DM. Reduced transaminase B (IlvE) activity caused by the lack of yjgF is dependent on the status of threonine deaminase (IlvA) in Salmonella enterica serovar Typhimurium. J Bacteriol 2004; 186:803-10. [PMID: 14729707 PMCID: PMC321505 DOI: 10.1128/jb.186.3.803-810.2004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The YjgF/YER057c/UK114 family is a highly conserved class of proteins that is represented in the three domains of life. Thus far, a biochemical function demonstrated for these proteins in vivo or in vitro has yet to be defined. In several organisms, strains lacking a YjgF homolog have a defect in branched-chain amino acid biosynthesis. This study probes the connection between yjgF and isoleucine biosynthesis in Salmonella enterica. In strains lacking yjgF the specific activity of transaminase B, catalyzing the last step in the synthesis of isoleucine, was reduced. In the absence of yjgF, transaminase B activity could be restored by inhibiting threonine deaminase, the first enzymatic step in isoleucine biosynthesis. Strains lacking yjgF showed an increased sensitivity to sulfometruron methyl, a potent inhibitor of acetolactate synthase. Based on work described here and structural reports in the literature, we suggest a working model in which YjgF has a role in protecting the cell from toxic effects of imbalanced ketoacid pools.
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Affiliation(s)
- George Schmitz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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GAO SONG, STEELE JAMESL. PURIFICATION AND CHARACTERIZATION OF OLIGOMERIC SPECIES OF AN AROMATIC AMINO ACID AMINOTRANSFERASE FROM LACTOCOCCUS LACTIS SUBSP. LACTIS S3. J Food Biochem 1998. [DOI: 10.1111/j.1745-4514.1998.tb00239.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Beschle HG, Süssmuth R, Lingens F. Conversion of chloramphenicol degradation products by tyrosine aminotransferase from Flavobacteria. HOPPE-SEYLER'S ZEITSCHRIFT FUR PHYSIOLOGISCHE CHEMIE 1982; 363:439-44. [PMID: 6122637 DOI: 10.1515/bchm2.1982.363.1.439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The tyrosine aminotransferase of Flavobacterium strain CB 60, strain CB 6 and F. devorans r - a partially purified enzyme was used - is able to deaminate oxidatively p-aminophenylalanine and the intermediate products of chloramphenicol degradation p-nitrophenylserine and p-aminophenylserine. The aminotransferases of the strains CB 6 and CB 60 also convert p-aminophenylserinol. p-Nitrophenylserinol only reacts with the enzyme from strain CB 6. Determination of substrate specificity from strain CB 6 shows that an alcoholic group in C3 position (ring proximal) and to a lower degree an alcoholic group in C1 position (ring distal) decrease the turnover rate. Based on its broad substrate specificity the tyrosine aminotransferase has the ability not only to metabolize physiological compounds but also degradation products of chloramphenicol.
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15
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Jensen RA, Calhoun DH. Intracellular roles of microbial aminotransferases: overlap enzymes across different biochemical pathways. Crit Rev Microbiol 1981; 8:229-66. [PMID: 7009061 DOI: 10.3109/10408418109085080] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
Species of coryneform bacteria (Corynebacterium glutamicum, Brevibacterium flavum, and B. ammoniagenes) are capable of transaminating all three of the aromatic pathway intermediates; prephenate, phenylpyruvate, and 4-hydroxy-phenylpyruvate. Two molecular species of aromatic aminotransferase (denoted aminotransferase I and aminotransferase II) were partially purified from C. glutamicum and B. flavum, whereas a single aromatic aminotransferase was isolated from B. ammoniagenes. In both C. glutamicum and B. flavum, aromatic aminotransferase I and aromatic aminotransferase II have molecular weights of about 155,000 and 260,000 respectively. The two aromatic aminotransferases from C. glutamicum and B. flavum, although exhibiting a similar spectrum of overlapping specificities, differ substantially in substrate preference. Pyridoxal-5'-phosphate is tightly associated with these aminotransferases, since little loss of activity was detected when partially purified enzyme preparations were assayed in the absence of exogenous pyridoxal-5'-phosphate. The aminotransferases are quite sensitive to inhibition by phenylhydrazine. This has practical application when assay of prephenate dehydratase is desired in the presence of aromatic aminotransferase activity since potentially trivial interference can be negated by selective phenylhydrazine inhibition of aromatic aminotransferase activity. At 0.1 mM concentrations of phenylhydrazine, 90% inhibitions of aminotransferase activities were achieved in partially purified preparations of B. flavum and C. glutamicum.
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Lee-Peng FC, Hermodson MA, Kohlhaw GB. Transaminase B from Escherichia coli: quaternary structure, amino-terminal sequence, substrate specificity, and absence of a separate valine-alpha-ketoglutarate activity. J Bacteriol 1979; 139:339-45. [PMID: 378964 PMCID: PMC216874 DOI: 10.1128/jb.139.2.339-345.1979] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transaminase B (branched-chain amino acid aminotransferase, EC 2.6.1.42), the ilvE gene product, was purified to apparent homogeneity from an Escherichia coli K-12 strain which carries the ilvE gene both on the host chromosome and on a plasmid. The oligomeric structure of the enzyme, as determined by analytical ultracentrifugation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was confirmed to be that of a hexamer with a molecular weight of about 182,000 and apparently identical subunits. Cross-linking with dimethylsuberimidate yielded trimers, dimers, and monomers, but essentially no species of higher molecular weight. These results are consistent with a double-trimer arrangement of the subunits in native enzyme. The amino-terminal sequence was found to be: Gly Thr Lys Lys Ala Asp Tyr Ile (Trp) Phe Asn Gly (Thr) (Met) Val. Purified transaminase B catalyzed transamination between alpha-ketoglutarate and l-isoleucine, l-leucine, l-valine, and, to a lesser extent, l-phenylalanine and l-tyrosine, the latter reacting very sluggishly. The enzyme was free of aspartate transaminase and of transaminase C. The apparent K(m) values for the branched-chain alpha-ketoacids were smaller than those for the corresponding amino acids. The lowest K(m) was recorded for dl-alpha-keto-beta-methyl-n-valerate, and the highest was recorded for l-valine. The ratio of the valine- and isoleucine-alpha-ketoglutarate activities did not change significantly during purification, and both activities were quantitatively removed from crude extract by antibody raised against purified transaminase B. These observations argue against the existence of a separate valine-alpha-ketoglutarate transaminase. Anti-E. coli transaminase B antibody cross-reacted with crude extract from Salmonella typhimurium, but not with extract obtained from Pseudomonas aeruginosa.
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