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Song Z, He M, Zhao R, Qi L, Chen G, Yin WB, Li W. Molecular Evolution of Lysine Biosynthesis in Agaricomycetes. J Fungi (Basel) 2021; 8:jof8010037. [PMID: 35049977 PMCID: PMC8779187 DOI: 10.3390/jof8010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
As an indispensable essential amino acid in the human body, lysine is extremely rich in edible mushrooms. The α-aminoadipic acid (AAA) pathway is regarded as the biosynthetic pathway of lysine in higher fungal species in Agaricomycetes. However, there is no deep understanding about the molecular evolutionary relationship between lysine biosynthesis and species in Agaricomycetes. Herein, we analyzed the molecular evolution of lysine biosynthesis in Agaricomycetes. The phylogenetic relationships of 93 species in 34 families and nine orders in Agaricomycetes were constructed with six sequences of LSU, SSU, ITS (5.8 S), RPB1, RPB2, and EF1-α datasets, and then the phylogeny of enzymes involved in the AAA pathway were analyzed, especially homocitrate synthase (HCS), α-aminoadipate reductase (AAR), and saccharopine dehydrogenase (SDH). We found that the evolution of the AAA pathway of lysine biosynthesis is consistent with the evolution of species at the order level in Agaricomycetes. The conservation of primary, secondary, predicted tertiary structures, and substrate-binding sites of the enzymes of HCS, AAR, and SDH further exhibited the evolutionary conservation of lysine biosynthesis in Agaricomycetes. Our results provide a better understanding of the evolutionary conservation of the AAA pathway of lysine biosynthesis in Agaricomycetes.
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Affiliation(s)
- Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.S.); (M.H.); (R.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoqiang He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.S.); (M.H.); (R.Z.)
| | - Ruilin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.S.); (M.H.); (R.Z.)
| | - Landa Qi
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, China; (L.Q.); (G.C.)
| | - Guocan Chen
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, China; (L.Q.); (G.C.)
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.S.); (M.H.); (R.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.-B.Y.); (W.L.); Tel.: +86-10-6480-6170 (W.-B.Y.)
| | - Wei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.S.); (M.H.); (R.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.-B.Y.); (W.L.); Tel.: +86-10-6480-6170 (W.-B.Y.)
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Vowinckel J, Hartl J, Marx H, Kerick M, Runggatscher K, Keller MA, Mülleder M, Day J, Weber M, Rinnerthaler M, Yu JSL, Aulakh SK, Lehmann A, Mattanovich D, Timmermann B, Zhang N, Dunn CD, MacRae JI, Breitenbach M, Ralser M. The metabolic growth limitations of petite cells lacking the mitochondrial genome. Nat Metab 2021; 3:1521-1535. [PMID: 34799698 PMCID: PMC7612105 DOI: 10.1038/s42255-021-00477-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022]
Abstract
Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.
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Affiliation(s)
- Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Biognosys AG, Schlieren, Switzerland
| | - Johannes Hartl
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Hans Marx
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Martin Kerick
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Parasitology and Biomedicine 'López-Neyra' (IPBLN, CSIC), Granada, Spain
| | - Kathrin Runggatscher
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Manuela Weber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Andrea Lehmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Nianshu Zhang
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Turkey
| | - James I MacRae
- Metabolomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany.
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
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3
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Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily. Commun Biol 2021; 4:687. [PMID: 34099860 PMCID: PMC8184944 DOI: 10.1038/s42003-021-02147-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis. Seiya Watanabe et al. report the crystal structures of two distinct members of the Aconitase X subfamily, which contain [Fe-S] clusters different from other aconitases. This study provides insight into the molecular evolution of the aconitase superfamily.
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Yoshida A, Tomita T, Atomi H, Kuzuyama T, Nishiyama M. Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. J Biol Chem 2016; 291:21630-21643. [PMID: 27566549 DOI: 10.1074/jbc.m116.743021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 08/24/2016] [Indexed: 11/06/2022] Open
Abstract
We recently discovered a biosynthetic system using a novel amino group carrier protein called LysW for lysine biosynthesis via α-aminoadipate (AAA), and revealed that this system is also utilized in the biosynthesis of arginine by Sulfolobus In the present study, we focused on the biosynthesis of lysine and ornithine in the hyperthermophilic archaeon Thermococcus kodakarensis, and showed that their biosynthesis is accomplished by a single set of metabolic enzymes. We also determined the crystal structure of the LysX family protein from T. kodakarensis, which catalyzes the conjugation of LysW with either AAA or glutamate, in a complex with LysW-γ-AAA. This crystal structure is the first example to show how LysX recognizes AAA as a substrate and provides a structural basis for the bifunctionality of the LysX family protein from T. kodakarensis Based on comparisons with other LysX family proteins, we propose a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities.
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Affiliation(s)
- Ayako Yoshida
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Takeo Tomita
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Haruyuki Atomi
- the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, and.,the Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076 Japan
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Makoto Nishiyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657,
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5
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Fazius F, Shelest E, Gebhardt P, Brock M. The fungal α-aminoadipate pathway for lysine biosynthesis requires two enzymes of the aconitase family for the isomerization of homocitrate to homoisocitrate. Mol Microbiol 2012; 86:1508-30. [PMID: 23106124 PMCID: PMC3556520 DOI: 10.1111/mmi.12076] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 11/30/2022]
Abstract
Fungi produce α-aminoadipate, a precursor for penicillin and lysine via the α-aminoadipate pathway. Despite the biotechnological importance of this pathway, the essential isomerization of homocitrate via homoaconitate to homoisocitrate has hardly been studied. Therefore, we analysed the role of homoaconitases and aconitases in this isomerization. Although we confirmed an essential contribution of homoaconitases from Saccharomyces cerevisiae and Aspergillus fumigatus, these enzymes only catalysed the interconversion between homoaconitate and homoisocitrate. In contrast, aconitases from fungi and the thermophilic bacterium Thermus thermophilus converted homocitrate to homoaconitate. Additionally, a single aconitase appears essential for energy metabolism, glutamate and lysine biosynthesis in respirating filamentous fungi, but not in the fermenting yeast S. cerevisiae that possesses two contributing aconitases. While yeast Aco1p is essential for the citric acid cycle and, thus, for glutamate synthesis, Aco2p specifically and exclusively contributes to lysine biosynthesis. In contrast, Aco2p homologues present in filamentous fungi were transcribed, but enzymatically inactive, revealed no altered phenotype when deleted and did not complement yeast aconitase mutants. From these results we conclude that the essential requirement of filamentous fungi for respiration versus the preference of yeasts for fermentation may have directed the evolution of aconitases contributing to energy metabolism and lysine biosynthesis.
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Affiliation(s)
- Felicitas Fazius
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Beutenbergstr. 11a, 07745 Jena, Germany
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Dairi T, Kuzuyama T, Nishiyama M, Fujii I. Convergent strategies in biosynthesis. Nat Prod Rep 2011; 28:1054-86. [PMID: 21547300 DOI: 10.1039/c0np00047g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review article focuses on how nature sometimes solves the same problem in the biosynthesis of small molecules but using very different approaches. Four examples, involving isopentenyl diphosphate, menaquinone, lysine, and aromatic polyketides, are highlighted that represent different strategies in convergent metabolism.
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Affiliation(s)
- Tohru Dairi
- Faculty of Engineering and Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
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7
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Abstract
Insect endosymbiont genomes reflect massive gene loss. Two Blattabacterium genomes display colinearity and similar gene contents, despite high orthologous gene divergence, reflecting over 140 million years of independent evolution in separate cockroach lineages. We speculate that distant homologs may replace the functions of some eliminated genes through broadened substrate specificity.
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8
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Teves F, Lamas-Maceiras M, García-Estrada C, Casqueiro J, Naranjo L, Ullán RV, Scervino JM, Wu X, Velasco-Conde T, Martín JF. Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress. MICROBIOLOGY-SGM 2009; 155:3881-3892. [PMID: 19696106 DOI: 10.1099/mic.0.031005-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The lysine biosynthetic pathway has to supply large amounts of alpha-aminoadipic acid for penicillin biosynthesis in Penicillium chrysogenum. In this study, we have characterized the P. chrysogenum L2 mutant, a lysine auxotroph that shows highly increased expression of several lysine biosynthesis genes (lys1, lys2, lys3, lys7). The L2 mutant was found to be deficient in homoaconitase activity since it was complemented by the Aspergillus nidulans lysF gene. We have cloned a gene (named lys3) that complements the L2 mutation by transformation with a P. chrysogenum genomic library, constructed in an autonomous replicating plasmid. The lys3-encoded protein showed high identity to homoaconitases. In addition, we cloned the mutant lys3 allele from the L2 strain that showed a G(1534) to A(1534) point mutation resulting in a Gly(495) to Asp(495) substitution. This mutation is located in a highly conserved region adjacent to two of the three cysteine residues that act as ligands to bind the iron-sulfur cluster required for homoaconitase activity. The L2 mutant accumulates homocitrate. Deletion of the lys1 gene (homocitrate synthase) in the L2 strain prevented homocitrate accumulation and reverted expression levels of the four lysine biosynthesis genes tested to those of the parental prototrophic strain. Homocitrate accumulation seems to act as a sensor of lysine-pathway distress, triggering overexpression of four of the lysine biosynthesis genes.
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Affiliation(s)
- Franco Teves
- Área de Microbiología, Departamento de Biología Molecular, Facultad de CC. Biológicas y Ambientales, Universidad de León, Campus de Vegazana s/n, 24071 Leon, Spain
| | - Mónica Lamas-Maceiras
- Área de Microbiología, Departamento de Biología Molecular, Facultad de CC. Biológicas y Ambientales, Universidad de León, Campus de Vegazana s/n, 24071 Leon, Spain
| | - Carlos García-Estrada
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain
| | - Javier Casqueiro
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain.,Área de Microbiología, Departamento de Biología Molecular, Facultad de CC. Biológicas y Ambientales, Universidad de León, Campus de Vegazana s/n, 24071 Leon, Spain
| | - Leopoldo Naranjo
- Área de Microbiología, Departamento de Biología Molecular, Facultad de CC. Biológicas y Ambientales, Universidad de León, Campus de Vegazana s/n, 24071 Leon, Spain
| | - Ricardo V Ullán
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain
| | - José-Martín Scervino
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain
| | - Xiaobin Wu
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain
| | - Tania Velasco-Conde
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain
| | - Juan F Martín
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 León, Spain.,Área de Microbiología, Departamento de Biología Molecular, Facultad de CC. Biológicas y Ambientales, Universidad de León, Campus de Vegazana s/n, 24071 Leon, Spain
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9
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Tomita T, Miyagawa T, Miyazaki T, Fushinobu S, Kuzuyama T, Nishiyama M. Mechanism for multiple-substrates recognition of α-aminoadipate aminotransferase fromThermus thermophilus. Proteins 2009; 75:348-59. [DOI: 10.1002/prot.22245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Hernández-Montes G, Díaz-Mejía JJ, Pérez-Rueda E, Segovia L. The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. Genome Biol 2008; 9:R95. [PMID: 18541022 PMCID: PMC2481427 DOI: 10.1186/gb-2008-9-6-r95] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 05/06/2008] [Accepted: 06/09/2008] [Indexed: 12/13/2022] Open
Abstract
A core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids is predicted using comparative genomics. Background Twenty amino acids comprise the universal building blocks of proteins. However, their biosynthetic routes do not appear to be universal from an Escherichia coli-centric perspective. Nevertheless, it is necessary to understand their origin and evolution in a global context, that is, to include more 'model' species and alternative routes in order to do so. We use a comparative genomics approach to assess the origins and evolution of alternative amino acid biosynthetic network branches. Results By tracking the taxonomic distribution of amino acid biosynthetic enzymes, we predicted a core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids, suggesting that this core occurred in ancient cells, before the separation of the three cellular domains of life. Additionally, we detail the distribution of two types of alternative branches to this core: analogs, enzymes that catalyze the same reaction (using the same metabolites) and belong to different superfamilies; and 'alternologs', herein defined as branches that, proceeding via different metabolites, converge to the same end product. We suggest that the origin of alternative branches is closely related to different environmental metabolite sources and life-styles among species. Conclusion The multi-organismal seed strategy employed in this work improves the precision of dating and determining evolutionary relationships among amino acid biosynthetic branches. This strategy could be extended to diverse metabolic routes and even other biological processes. Additionally, we introduce the concept of 'alternolog', which not only plays an important role in the relationships between structure and function in biological networks, but also, as shown here, has strong implications for their evolution, almost equal to paralogy and analogy.
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Affiliation(s)
- Georgina Hernández-Montes
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av, Universidad, Col, Chamilpa, Cuernavaca, Morelos, México
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11
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Fondi M, Brilli M, Emiliani G, Paffetti D, Fani R. The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. BMC Evol Biol 2007; 7 Suppl 2:S3. [PMID: 17767731 PMCID: PMC1963480 DOI: 10.1186/1471-2148-7-s2-s3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution. RESULTS The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted. CONCLUSION The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall.
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Affiliation(s)
- Marco Fondi
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, Via Romana 17\19, Firenze, Italia
| | - Matteo Brilli
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, Via Romana 17\19, Firenze, Italia
| | - Giovanni Emiliani
- Dipartimento di Scienze e Tecnologie Ambientali Forestali, Università di Firenze, Via S. Bonaventura 13, Firenze, Italia
| | - Donatella Paffetti
- Dipartimento di Scienze e Tecnologie Ambientali Forestali, Università di Firenze, Via S. Bonaventura 13, Firenze, Italia
| | - Renato Fani
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, Via Romana 17\19, Firenze, Italia
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12
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Alhapel A, Darley DJ, Wagener N, Eckel E, Elsner N, Pierik AJ. Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc Natl Acad Sci U S A 2006; 103:12341-6. [PMID: 16894175 PMCID: PMC1562527 DOI: 10.1073/pnas.0601635103] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The anaerobic soil bacterium Eubacterium barkeri catabolizes nicotinate to pyruvate and propionate via a unique fermentation. A full molecular characterization of nicotinate fermentation in this organism was accomplished by the following results: (i) A 23.2-kb DNA segment with a gene cluster encoding all nine enzymes was cloned and sequenced, (ii) two chiral intermediates were discovered, and (iii) three enzymes were found, completing the hitherto unknown part of the pathway. Nicotinate dehydrogenase, a (nonselenocysteine) selenium-containing four-subunit enzyme, is encoded by ndhF (FAD subunit), ndhS (2 x [2Fe-2S] subunit), and by the ndhL/ndhM genes. In contrast to all enzymes of the xanthine dehydrogenase family, the latter two encode a two-subunit molybdopterin protein. The 6-hydroxynicotinate reductase, catalyzing reduction of 6-hydroxynicotinate to 1,4,5,6-tetrahydro-6-oxonicotinate, was purified and shown to contain a covalently bound flavin cofactor, one [2Fe-2S](2+/1+) and two [4Fe-4S](2+/1+) clusters. Enamidase, a bifunctional Fe-Zn enzyme belonging to the amidohydrolase family, mediates hydrolysis of 1,4,5,6-tetrahydro-6-oxonicotinate to ammonia and (S)-2-formylglutarate. NADH-dependent reduction of the latter to (S)-2-(hydroxymethyl)glutarate is catalyzed by a member of the 3-hydroxyisobutyrate/phosphogluconate dehydrogenase family. A [4Fe-4S]-containing serine dehydratase-like enzyme is predicted to form 2-methyleneglutarate. After the action of the coenzyme B(12)-dependent 2-methyleneglutarate mutase and 3-methylitaconate isomerase, an aconitase and isocitrate lyase family pair of enzymes, (2R,3S)-dimethylmalate dehydratase and lyase, completes the pathway. Genes corresponding to the first three enzymes of the E. barkeri nicotinate catabolism were identified in nine Proteobacteria.
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Affiliation(s)
- Ashraf Alhapel
- Laboratorium für Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universität, D-35032 Marburg, Germany
| | - Daniel J. Darley
- Laboratorium für Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universität, D-35032 Marburg, Germany
| | - Nadine Wagener
- Laboratorium für Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universität, D-35032 Marburg, Germany
| | - Elke Eckel
- Laboratorium für Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universität, D-35032 Marburg, Germany
| | - Nora Elsner
- Laboratorium für Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universität, D-35032 Marburg, Germany
| | - Antonio J. Pierik
- Laboratorium für Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universität, D-35032 Marburg, Germany
- *To whom correspondence should be addressed. E-mail:
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13
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Jia Y, Tomita T, Yamauchi K, Nishiyama M, Palmer D. Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus. Biochem J 2006; 396:479-85. [PMID: 16524361 PMCID: PMC1482822 DOI: 10.1042/bj20051711] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
HACN (homoaconitase) is a member of a family of [4Fe-4S] cluster-dependent enzymes that catalyse hydration/dehydration reactions. The best characterized example of this family is the ubiquitous ACN (aconitase), which catalyses the dehydration of citrate to cis-aconitate, and the subsequent hydration of cis-aconitate to isocitrate. HACN is an enzyme from the alpha-aminoadipate pathway of lysine biosynthesis, and has been identified in higher fungi and several archaea and one thermophilic species of bacteria, Thermus thermophilus. HACN catalyses the hydration of cis-homoaconitate to (2R,3S)-homoisocitrate, but the HACN-catalysed dehydration of (R)-homocitrate to cis-homoaconitate has not been observed in vitro. We have synthesized the substrates and putative substrates for this enzyme, and in the present study report the first steady-state kinetic data for recombinant HACN from T. thermophilus using a (2R,3S)-homoisocitrate dehydrogenase-coupled assay. We have also examined the products of the reaction using HPLC. We do not observe HACN-catalysed 'homocitrate dehydratase' activity; however, we have observed that ACN can catalyse the dehydration of (R)-homocitrate to cis-homoaconitate, but HACN is required for subsequent conversion of cis-homoaconitate into homoisocitrate. This suggests that the in vivo process for conversion of homocitrate into homoisocitrate requires two enzymes, in simile with the propionate utilization pathway from Escherichia coli. Surprisingly, HACN does not show any activity when cis-aconitate is substituted for the substrate, even though other enzymes from the alpha-aminoadipate pathway can accept analogous tricarboxylic acid-cycle substrates. The enzyme shows no apparent feedback inhibition by L-lysine.
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Affiliation(s)
- Yunhua Jia
- *Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
| | - Takeo Tomita
- †Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuma Yamauchi
- †Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- †Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - David R. J. Palmer
- *Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
- To whom correspondence should be addressed (email )
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14
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Kwon ES, Jeong JH, Roe JH. Inactivation of homocitrate synthase causes lysine auxotrophy in copper/zinc-containing superoxide dismutase-deficient yeast Schizosaccharomyces pombe. J Biol Chem 2005; 281:1345-51. [PMID: 16299000 DOI: 10.1074/jbc.m506611200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe lacking copper/zinc-containing superoxide dismutase (CuZn-SOD) is auxotrophic for lysine and sulfurous amino acids under aerobic growth conditions. A multicopy suppressor gene (phx1+) that restored the growth of CuZn-SOD-deficient cells on minimal medium was isolated. It encodes a putative DNA-binding protein with a conserved homeobox domain. Overproduction of Phx1 increased the amount of several proteins, and one of those turned out to be a putative homocitrate synthase (HCS) encoded by the lys4+ gene in S. pombe as judged by mass spectrometric analysis. Consistent with this observation, overexpression of the lys4+ gene increased HCS enzyme activity and was sufficient to suppress the lysine requirement of the CuZn-SOD-deficient cells. Enzyme activity and Western blot analyses revealed that the activity and protein level of HCS were dramatically reduced upon depletion of CuZn-SOD. Treatment of exponentially growing S. pombe cells with paraquat, a superoxide generator, caused a decrease in the amount of Lys4 protein as expected. These results led us to conclude that HCS, the first enzyme in the alpha-aminoadipate-mediated pathway for lysine synthesis common in fungi and some bacteria, is a labile target of oxidative stress caused by CuZn-SOD depletion and that its synthesis is positively regulated by the putative transcriptional regulator Phx1.
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Affiliation(s)
- Eun-Soo Kwon
- Laboratory of Molecular Microbiology, School of Biological Sciences, Seoul National University, Korea
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15
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Guo S, Garrad RC, Bhattacharjee JK. Functional analysis through site-directed mutations and phylogeny of the Candida albicans LYS1-encoded saccharopine dehydrogenase. Mol Genet Genomics 2005; 275:74-80. [PMID: 16292576 DOI: 10.1007/s00438-005-0062-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Accepted: 10/04/2005] [Indexed: 11/25/2022]
Abstract
Candida albicans LYS1-encoded saccharopine dehydrogenase (CaLys1p, SDH) catalyzes the final biosynthetic step (saccharopine to lysine + alpha-ketoglutarate) of the novel alpha-aminoadipate pathway for lysine synthesis in fungi. The reverse reaction catalyzed by lysine-alpha-ketoglutarate reductase (LKR) is used exclusively in animals and plants for the catabolism of excess lysine. The 1,146 bp C. albicans LYS1 ORF encodes a 382 amino acid SDH. In the present investigation, we have used E. coli-expressed recombinant C. albicans Lys1p for the determination of both forward and reverse SDH activities in vitro, compared the sequence identity of C. albicans Lys1p with other known SDHs and LKRs, performed extensive site-directed mutational analyses of conserved amino acid residues and analyzed the phylogenetic relationship of C. albicans Lys1p to other known SDHs and LKRs. We have identified 14 of the 68 amino acid substitutions as essential for C. albicans Lys1p SDH activity, including two highly conserved functional motifs, H93XXF96XH98 and G138XXXG142XXG145. These results provided new insight into the functional and phylogenetic characteristics of the distinct biosynthetic SDH in fungi and catabolic LKR in higher eukaryotes.
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Affiliation(s)
- Shujuan Guo
- Department of Microbiology, Miami University, Pearson Hall, Room 46, Oxford, OH 45056, USA
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16
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Yasutake Y, Yao M, Sakai N, Kirita T, Tanaka I. Crystal structure of the Pyrococcus horikoshii isopropylmalate isomerase small subunit provides insight into the dual substrate specificity of the enzyme. J Mol Biol 2004; 344:325-33. [PMID: 15522288 DOI: 10.1016/j.jmb.2004.09.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/14/2004] [Accepted: 09/15/2004] [Indexed: 10/26/2022]
Abstract
Recent studies have implied that the isopropylmalate isomerase small subunit of the hyperthermophilic archaea Pyrococcus horikoshii (PhIPMI-s) functions as isopropylmalate isomerase in the leucine biosynthesis pathway, and as homoaconitase (HACN) in the lysine biosynthesis pathway via alpha-aminoadipic acid. PhIPMI is thus considered a key to understanding the fundamental metabolism of the earliest organisms. We describe for the first time the crystal structure of PhIPMI-s, which displays dual substrate specificity. The crystal structure unexpectedly shows that four molecules create an interlocked assembly with intermolecular disulfide linkages having a skewed 222 point-group symmetry. Although the overall fold of the PhIPMI-s monomer is related closely to domain 4 of the aconitase (ACN), one alpha-helix in the ACN structure is replaced by a short loop with relatively high temperature factor values. Because this region is essential for discriminating the structurally similar substrate based on interactions with its diversified gamma-moiety, the loop structure in the PhIPMI-s must be dependent on the presence of a substrate. The flexibility of the loop region might be a structural basis for recognizing both hydrophobic and hydrophilic gamma-moieties of two distinct substrates, isopropylmalate and homocitrate.
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Affiliation(s)
- Yoshiaki Yasutake
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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17
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Miyazaki T, Miyazaki J, Yamane H, Nishiyama M. α-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus. Microbiology (Reading) 2004; 150:2327-2334. [PMID: 15256574 DOI: 10.1099/mic.0.27037-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extremely thermophilic bacteriumThermus thermophilusHB27 synthesizes lysine throughα-aminoadipate (AAA). In this study, aT. thermophilusgene encoding the enzyme that catalyses transamination of AAA was cloned as a mammalian kynurenine/AAA aminotransferase (Kat2) gene homologue. AT. thermophilusmutant with disruption of theKat2homologue required a longer lag phase for growth and showed slower growth in minimal medium. Furthermore, addition of AAA or lysine shortened the lag phase and improved the growth rate. TheKat2homologue was therefore termedlysN. LysN recognizes not only 2-oxoadipate, an intermediate of lysine biosynthesis, but also 2-oxoisocaproate, 2-oxoisovalerate and 2-oxo-3-methylvalerate, intermediates of leucine, valine and isoleucine biosyntheses, respectively, along with oxaloacetate, a compound in the TCA cycle, as an amino acceptor. These results suggest multiple roles of LysN in several cellular metabolic pathways including lysine and branched-chain amino acid biosyntheses.
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Affiliation(s)
- Takashi Miyazaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Junichi Miyazaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hisakazu Yamane
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Wallace MA, Liou LL, Martins J, Clement MHS, Bailey S, Longo VD, Valentine JS, Gralla EB. Superoxide inhibits 4Fe-4S cluster enzymes involved in amino acid biosynthesis. Cross-compartment protection by CuZn-superoxide dismutase. J Biol Chem 2004; 279:32055-62. [PMID: 15166213 DOI: 10.1074/jbc.m403590200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Among the phenotypes of Saccharomyces cerevisiae mutants lacking CuZn-superoxide dismutase (Sod1p) is an aerobic lysine auxotrophy; in the current work we show an additional leaky auxotrophy for leucine. The lysine and leucine biosynthetic pathways each contain a 4Fe-4S cluster enzyme homologous to aconitase and likely to be superoxide-sensitive, homoaconitase (Lys4p) and isopropylmalate dehydratase (Leu1p), respectively. We present evidence that direct aerobic inactivation of these enzymes in sod1 Delta yeast results in the auxotrophies. Located in the cytosol and intermembrane space of the mitochondria, Sod1p likely provides direct protection of the cytosolic enzyme Leu1p. Surprisingly, Lys4p does not share a compartment with Sod1p but is located in the mitochondrial matrix. The activity of a second matrix protein, the tricarboxylic acid cycle enzyme aconitase, was similarly lowered in sod1 Delta mutants. We measured only slight changes in total mitochondrial iron and found no detectable difference in mitochondrial "free" (EPR-detectable) iron making it unlikely that a gross defect in mitochondrial iron metabolism is the cause of the decreased enzyme activities. Thus, we conclude that when Sod1p is absent a lysine auxotrophy is induced because Lys4p is inactivated in the matrix by superoxide that originates in the intermembrane space and diffuses across the inner membrane.
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Affiliation(s)
- Matthew Alan Wallace
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095-1569, USA
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19
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Lombo T, Takaya N, Miyazaki J, Gotoh K, Nishiyama M, Kosuge T, Nakamura A, Hoshino T. Functional analysis of the small subunit of the putative homoaconitase fromPyrococcus horikoshiiin theThermuslysine biosynthetic pathway. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09498.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Uhrigshardt H, Walden M, John H, Anemüller S. Purification and characterization of the first archaeal aconitase from the thermoacidophilicSulfolobus acidocaldarius. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1432-1327.2001.02049.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Sakai H, Vassylyeva MN, Matsuura T, Sekine SI, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S. Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8. J Mol Biol 2003; 332:729-40. [PMID: 12963379 DOI: 10.1016/s0022-2836(03)00946-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The thermophilic bacterium Thermus thermophilus synthesizes lysine through the alpha-aminoadipate pathway, which uses alpha-aminoadipate as a biosynthetic intermediate of lysine. LysX is the essential enzyme in this pathway, and is believed to catalyze the acylation of alpha-aminoadipate. We have determined the crystal structures of LysX and its complex with ADP at 2.0A and 2.38A resolutions, respectively. LysX is composed of three alpha+beta domains, each composed of a four to five-stranded beta-sheet core flanked by alpha-helices. The C-terminal and central domains form an ATP-grasp fold, which is responsible for ATP binding. LysX has two flexible loop regions, which are expected to play an important role in substrate binding and protection. In spite of the low level of sequence identity, the overall fold of LysX is surprisingly similar to that of other ATP-grasp fold proteins, such as D-Ala:D-Ala ligase, PurT-encoded glycinamide ribonucleotide transformylase, glutathione synthetase, and synapsin I. In particular, they share a similar spatial arrangement of the amino acid residues around the ATP-binding site. This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity.
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Affiliation(s)
- Hiroaki Sakai
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
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22
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Heinzelmann E, Berger S, Puk O, Reichenstein B, Wohlleben W, Schwartz D. A glutamate mutase is involved in the biosynthesis of the lipopeptide antibiotic friulimicin in Actinoplanes friuliensis. Antimicrob Agents Chemother 2003; 47:447-57. [PMID: 12543643 PMCID: PMC151761 DOI: 10.1128/aac.47.2.447-457.2003] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actinoplanes friuliensis produces the lipopeptide antibiotic friulimicin. This antibiotic is active against gram-positive bacteria such as multiresistant Enterococcus and Staphylococcus strains. It consists of 10 amino acids that form a ring structure and 1 exocyclic amino acid to which an acyl residue is attached. By a reverse genetic approach, biosynthetic genes were identified that are required for the nonribosomal synthesis of the antibiotic. In close proximity two genes (glmA and glmB) were found which are involved in the production of methylaspartate, one of the amino acids of the peptide core. Methylaspartate is synthesized by a glutamate mutase mechanism, which was up to now only described for glutamate fermentation in Clostridium sp. or members of the family ENTEROBACTERIACEAE: The active enzyme consists of two subunits, and the corresponding genes overlap each other. To demonstrate enzyme activity in a heterologous host, it was necessary to genetically fuse glmA and glmB. The resulting gene was overexpressed in Streptomyces lividans, and the fusion protein was purified in an active form. For gene disruption mutagenesis, a host-vector system was established which enables genetic manipulation of Actinoplanes spp. for the first time. Thus, targeted inactivation of biosynthetic genes was possible, and their involvement in friulimicin biosynthesis was demonstrated.
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Affiliation(s)
- E Heinzelmann
- Hans-Knöll-Institut für Naturstoff-Forschung, 07745 Jena, Germany
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23
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Miyazaki J, Kobashi N, Nishiyama M, Yamane H. Characterization of homoisocitrate dehydrogenase involved in lysine biosynthesis of an extremely thermophilic bacterium, Thermus thermophilus HB27, and evolutionary implication of beta-decarboxylating dehydrogenase. J Biol Chem 2003; 278:1864-71. [PMID: 12427751 DOI: 10.1074/jbc.m205133200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the presence of an enzyme that catalyzes beta-decarboxylating dehydrogenation of homoisocitrate to synthesize 2-oxoadipate has been postulated in the lysine biosynthesis pathway through alpha-aminoadipate (AAA), the enzyme has not yet been analyzed at all, because no gene encoding the enzyme has been identified until recently. A gene encoding a protein with a significant amino acid sequence identity to both isocitrate dehydrogenase and 3-isopropylmalate dehydrogenase was cloned from Thermus thermophilus HB27. The gene product produced in recombinant Escherichia coli cells demonstrated homoisocitrate dehydrogenase (HICDH) activity. A knockout mutant of the gene showed an AAA-auxotrophic phenotype, indicating that the gene product is involved in lysine biosynthesis through AAA. We therefore named this gene hicdh. HICDH, the gene product, did not catalyze the conversion of 3-isopropylmalate to 2-oxoisocaproate, a leucine biosynthetic reaction, but it did recognize isocitrate, a related compound in the tricarboxylic acid cycle, as well as homoisocitrate as a substrate. It is of interest that HICDH catalyzes the reaction with isocitrate about 20 times more efficiently than the reaction with the putative native substrate, homoisocitrate. The broad specificity and possible dual function suggest that this enzyme represents a key link in the evolution of the pathways utilizing citrate derivatives. Site-directed mutagenesis study reveals that replacement of Arg(85) with Val in HICDH causes complete loss of activity with isocitrate but significant activity with 3-isopropylmalate and retains activity with homoisocitrate. These results indicate that Arg(85) is a key residue for both substrate specificity and evolution of beta-decarboxylating dehydrogenases.
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Affiliation(s)
- Junichi Miyazaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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24
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Wulandari AP, Miyazaki J, Kobashi N, Nishiyama M, Hoshino T, Yamane H. Characterization of bacterial homocitrate synthase involved in lysine biosynthesis. FEBS Lett 2002; 522:35-40. [PMID: 12095615 DOI: 10.1016/s0014-5793(02)02877-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In Thermus thermophilus homocitrate synthase (HCS) catalyzes the initial reaction of lysine biosynthesis through alpha-aminoadipic acid, synthesis of homocitrate from 2-oxoglutarate and acetyl-CoA. HCS is strongly inhibited by lysine, indicating that the biosynthesis is regulated by the endproduct at the initial reaction in the pathway. HCS also catalyzes the reaction using oxaloacetate in place of 2-oxoglutarate as a substrate, similar to citrate synthase in the tricarboxylic acid cycle. Several other properties of Thermus HCS and an evolutionary relationship of the biosynthetic pathway in the bacterium to other metabolic pathways are also described.
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Affiliation(s)
- Asri Peni Wulandari
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan
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25
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Sturtz LA, Culotta VC. Superoxide dismutase null mutants of baker's yeast, Saccharomyces cerevisiae. Methods Enzymol 2002; 349:167-72. [PMID: 11912906 DOI: 10.1016/s0076-6879(02)49332-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Lori A Sturtz
- Division of Toxicological Sciences, Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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26
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Miyazaki J, Kobashi N, Fujii T, Nishiyama M, Yamane H. Characterization of a lysK gene as an argE homolog in Thermus thermophilus HB27. FEBS Lett 2002; 512:269-74. [PMID: 11852094 DOI: 10.1016/s0014-5793(02)02290-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We conducted a chromosome walk to obtain a DNA fragment downstream of lysJ and found an argE homolog in a putative operon composed of lysJ-orfC-orfD-argE homologs. A knockout mutant of the argE homolog showed significantly slow growth on a minimal medium, and the growth was markedly improved by addition of lysine. We therefore termed this gene lysK. Purified LysK protein has deacetylating activities for both N(2)-acetyllysine and N(2)-acetylornithine at almost equal efficiency. These results suggest that lysK which may share an ancestor with argE functions not only for the lysine biosynthesis, but also for arginine biosynthesis in Thermus thermophilus.
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Affiliation(s)
- Junichi Miyazaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
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27
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Miyazaki J, Kobashi N, Nishiyama M, Yamane H. Functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through alpha-aminoadipate. J Bacteriol 2001; 183:5067-73. [PMID: 11489859 PMCID: PMC95382 DOI: 10.1128/jb.183.17.5067-5073.2001] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our previous studies revealed that lysine is synthesized through alpha-aminoadipate in an extremely thermophilic bacterium, Thermus thermophilus HB27. Sequence analysis of a gene cluster involved in the lysine biosynthesis of this microorganism suggested that the conversion from alpha-aminoadipate to lysine proceeds in a way similar to that of arginine biosynthesis. In the present study, we cloned an argD homolog of T. thermophilus HB27 which was not included in the previously cloned lysine biosynthetic gene cluster and determined the nucleotide sequence. A knockout of the argD-like gene, now termed lysJ, in T. thermophilus HB27 showed that this gene is essential for lysine biosynthesis in this bacterium. The lysJ gene was cloned into a plasmid and overexpressed in Escherichia coli, and the LysJ protein was purified to homogeneity. When the catalytic activity of LysJ was analyzed in a reverse reaction in the putative pathway, LysJ was found to transfer the epsilon-amino group of N(2)-acetyllysine, a putative intermediate in lysine biosynthesis, to 2-oxoglutarate. When N(2)-acetylornithine, a substrate for arginine biosynthesis, was used as the substrate for the reaction, LysJ transferred the delta-amino group of N(2)-acetylornithine to 2-oxoglutarate 16 times more efficiently than when N(2)-acetyllysine was the amino donor. All these results suggest that lysine biosynthesis in T. thermophilus HB27 is functionally and evolutionarily related to arginine biosynthesis.
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Affiliation(s)
- J Miyazaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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28
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Abstract
The budding yeast Saccharomyces cerevisiae contains two homologues of bacterial IscA proteins, designated Isa1p and Isa2p. Bacterial IscA is a product of the isc (iron-sulfur cluster) operon and has been suggested to participate in Fe-S cluster formation or repair. To test the function of yeast Isa1p and Isa2p, single or combinatorial disruptions were introduced in ISA1 and ISA2. The resultant isaDelta mutants were viable but exhibited a dependency on lysine and glutamate for growth and a respiratory deficiency due to an accumulation of mutations in mitochondrial DNA. As with other yeast genes proposed to function in Fe-S cluster assembly, mitochondrial iron concentration was significantly elevated in the isa mutants, and the activities of the Fe-S cluster-containing enzymes aconitase and succinate dehydrogenase were dramatically reduced. An inspection of Isa-like proteins from bacteria to mammals revealed three invariant cysteine residues, which in the case of Isa1p and Isa2p are essential for function and may be involved in iron binding. As predicted, Isa1p is targeted to the mitochondrial matrix. However, Isa2p is present within the intermembrane space of the mitochondria. Our deletion analyses revealed that Isa2p harbors a bipartite N-terminal leader sequence containing a mitochondrial import signal linked to a second sequence that targets Isa2p to the intermembrane space. Both signals are needed for Isa2p function. A model for the nonredundant roles of Isa1p and Isa2p in delivering iron to sites of the Fe-S cluster assembly is discussed.
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Affiliation(s)
- L T Jensen
- Department of Environmental Health Sciences, Johns Hopkins University School of Public Health, Baltimore, Maryland 21205, USA
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29
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Saas J, Ziegelbauer K, von Haeseler A, Fast B, Boshart M. A developmentally regulated aconitase related to iron-regulatory protein-1 is localized in the cytoplasm and in the mitochondrion of Trypanosoma brucei. J Biol Chem 2000; 275:2745-55. [PMID: 10644738 DOI: 10.1074/jbc.275.4.2745] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial energy metabolism and Krebs cycle activities are developmentally regulated in the life cycle of the protozoan parasite Trypanosoma brucei. Here we report cloning of a T. brucei aconitase gene that is closely related to mammalian iron-regulatory protein 1 (IRP-1) and plant aconitases. Kinetic analysis of purified recombinant TbACO expressed in Escherichia coli resulted in a K(m) (isocitrate) of 3 +/- 0.4 mM, similar to aconitases of other organisms. This was unexpected since an arginine conserved in the aconitase protein family and crucial for substrate positioning in the catalytic center and for activity of pig mitochondrial aconitase (Zheng, L., Kennedy, M. C., Beinert, H., and Zalkin, H. (1992) J. Biol. Chem. 267, 7895-7903) is substituted by leucine in the TbACO sequence. Expression of the 98-kDa TbACO was shown to be lowest in the slender bloodstream stage of the parasite, 8-fold elevated in the stumpy stage, and increased a further 4-fold in the procyclic stage. The differential expression of TbACO protein contrasted with only minor changes in TbACO mRNA, indicating translational or post-translational mechanisms of regulation. Whereas animal cells express two distinct compartmentalized aconitases, mitochondrial aconitase and cytoplasmic aconitase/IRP-1, TbACO accounts for total aconitase activity in trypanosomes. By cell fractionation and immunofluorescence microscopy, we show that native as well as a transfected epitope-tagged TbACO localizes in both the mitochondrion (30%) and in the cytoplasm (70%). Together with phylogenetic reconstructions of the aconitase family, this suggests that animal IRPs have evolved from a multicompartmentalized ancestral aconitase. The possible functions of a cytoplasmic aconitase in trypanosomes are discussed.
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Affiliation(s)
- J Saas
- Arbeitsgruppe Molekulare Zellbiologie, Institut für Molekularbiologie und Biochemie und Institut für Infektionsmedizin, Freie Universität, Berlin, Germany
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Nishida H, Nishiyama M, Kobashi N, Kosuge T, Hoshino T, Yamane H. A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Genome Res 1999; 9:1175-83. [PMID: 10613839 DOI: 10.1101/gr.9.12.1175] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In previous studies we determined the nucleotide sequence of the gene cluster containing lys20, hacA (lys4A), hacB (lys4B), orfE, orfF, rimK, argC, and argB of Thermus thermophilus, an extremely thermophilic bacterium. In this study, we characterized the role of each gene in the cluster by gene disruption and examined auxotrophy in the disruptants. All disruptants except for the orfE disruption showed a lysine auxotrophic phenotype. This was surprising because this cluster consists of genes coding for unrelated proteins based on their names, which had been tentatively designated by homology analysis. Although the newly found pathway contains alpha-aminoadipic acid as a lysine biosynthetic intermediate, this pathway is not the same as the eukaryotic one. When each of the gene products was phylogenetically analyzed, we found that genes evolutionarily-related to the lysine biosynthetic genes in T. thermophilus were all present in a hyperthermophilic and anaerobic archaeon, Pyrococcus horikoshii, and formed a gene cluster in a manner similar to that in T. thermophilus. Furthermore, this gene cluster was analogous in part to the present leucine and arginine biosyntheses pathways. This lysine biosynthesis cluster is assumed to be one of the origins of lysine biosynthesis and could therefore become a key to the evolution of amino acid biosynthesis.
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Affiliation(s)
- H Nishida
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
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