1
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Gu Y, Alam S, Oliferenko S. Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size. Nat Commun 2023; 14:5544. [PMID: 37684233 PMCID: PMC10491753 DOI: 10.1038/s41467-023-41347-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| | - Sara Alam
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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2
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Bai Y, Jiao W, Vörster J, Parker EJ. Conformational interdomain flexibility in a bacterial α-isopropylmalate synthase is necessary for leucine biosynthesis. J Biol Chem 2022; 299:102789. [PMID: 36509144 PMCID: PMC9860122 DOI: 10.1016/j.jbc.2022.102789] [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: 09/29/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
α-Isopropylmalate synthase (IPMS) catalyzes the first step in leucine (Leu) biosynthesis and is allosterically regulated by the pathway end product, Leu. IPMS is a dimeric enzyme with each chain consisting of catalytic, accessory, and regulatory domains, with the accessory and regulatory domains of each chain sitting adjacent to the catalytic domain of the other chain. The IPMS crystal structure shows significant asymmetry because of different relative domain conformations in each chain. Owing to the challenges posed by the dynamic and asymmetric structures of IPMS enzymes, the molecular details of their catalytic and allosteric mechanisms are not fully understood. In this study, we have investigated the allosteric feedback mechanism of the IPMS enzyme from the bacterium that causes meningitis, Neisseria meningitidis (NmeIPMS). By combining molecular dynamics simulations with small-angle X-ray scattering, mutagenesis, and heterodimer generation, we demonstrate that Leu-bound NmeIPMS is in a rigid conformational state stabilized by asymmetric interdomain polar interactions. Furthermore, we found removing these polar interactions by mutagenesis impaired the allosteric response without compromising Leu binding. Our results suggest that the allosteric inhibition of NmeIPMS is achieved by restricting the flexibility of the accessory and regulatory domains, demonstrating that significant conformational flexibility is required for catalysis.
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Affiliation(s)
- Yu Bai
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Jan Vörster
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand,For correspondence: Emily J. Parker
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3
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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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4
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Isogai S, Matsushita T, Imanishi H, Koonthongkaew J, Toyokawa Y, Nishimura A, Yi X, Kazlauskas R, Takagi H. High-Level Production of Lysine in the Yeast Saccharomyces cerevisiae by Rational Design of Homocitrate Synthase. Appl Environ Microbiol 2021; 87:e0060021. [PMID: 33990312 PMCID: PMC8276798 DOI: 10.1128/aem.00600-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes the aldol condensation of 2-oxoglutarate (2-OG) and acetyl coenzyme A (AcCoA) to form homocitrate, which is the first enzyme of the lysine biosynthetic pathway in the yeast Saccharomyces cerevisiae. The HCS activity is tightly regulated via feedback inhibition by the end product lysine. Here, we designed a feedback inhibition-insensitive HCS of S. cerevisiae (ScLys20) for high-level production of lysine in yeast cells. In silico docking of the substrate 2-OG and the inhibitor lysine to ScLys20 predicted that the substitution of serine with glutamate at position 385 would be more suitable for desensitization of the lysine feedback inhibition than the substitution from serine to phenylalanine in the already known Ser385Phe variant. Enzymatic analysis revealed that the Ser385Glu variant is far more insensitive to feedback inhibition than the Ser385Phe variant. We also found that the lysine contents in yeast cells expressing the Ser385Glu variant were 4.62- and 1.47-fold higher than those of cells expressing the wild-type HCS and Ser385Phe variant, respectively, due to the extreme desensitization to feedback inhibition. In this study, we obtained highly feedback inhibition-insensitive HCS using in silico docking and enzymatic analysis. Our results indicate that the rational engineering of HCS for feedback inhibition desensitization by lysine could be useful for constructing new yeast strains with higher lysine productivity. IMPORTANCE A traditional method for screening toxic analogue-resistant mutants has been established for the breeding of microbes that produce high levels of amino acids, including lysine. However, another efficient strategy is required to further improve their productivity. Homocitrate synthase (HCS) catalyzes the first step of lysine biosynthesis in the yeast Saccharomyces cerevisiae, and its activity is subject to feedback inhibition by lysine. Here, in silico design of a key enzyme that regulates the biosynthesis of lysine was utilized to increase the productivity of lysine. We designed HCS for the high-level production of lysine in yeast cells by in silico docking simulation. The engineered HCS exhibited much less sensitivity to lysine and conferred higher production of lysine than the already known variant obtained by traditional breeding. The combination of in silico design and experimental analysis of a key enzyme will contribute to advances in metabolic engineering for the construction of industrial microorganisms.
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Affiliation(s)
- Shota Isogai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tomonori Matsushita
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroyuki Imanishi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Jirasin Koonthongkaew
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yoichi Toyokawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Xiao Yi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- The BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- The BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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5
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Vishnivetskaya TA, Almatari AL, Spirina EV, Wu X, Williams DE, Pfiffner SM, Rivkina EM. Insights into community of photosynthetic microorganisms from permafrost. FEMS Microbiol Ecol 2021; 96:5979775. [PMID: 33181853 DOI: 10.1093/femsec/fiaa229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
This work integrates cultivation studies of Siberian permafrost and analyses of metagenomes from different locations in the Arctic with the aim of obtaining insights into the community of photosynthetic microorganisms in perennially frozen deposits. Cyanobacteria and microalgae have been described in Arctic aquatic and surface soil environments, but their diversity and ability to withstand harsh conditions within the permafrost are still largely unknown. Community structure of photosynthetic organisms in permafrost sediments was explored using Arctic metagenomes available through the MG-RAST. Sequences affiliated with cyanobacteria represented from 0.25 to 3.03% of total sequences, followed by sequences affiliated with Streptophyta (algae and vascular plants) 0.01-0.45% and Chlorophyta (green algae) 0.01-0.1%. Enrichment and cultivation approaches revealed that cyanobacteria and green algae survive in permafrost and they could be revived during prolonged incubation at low light intensity. Among photosynthetic microorganisms isolated from permafrost, the filamentous Oscillatoria-like cyanobacteria and unicellular green algae of the genus Chlorella were dominant. Our findings suggest that permafrost cyanobacteria and green algae are expected to be effective members of the re-assembled community after permafrost thawing and soil collapse.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA.,Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
| | - Abraham L Almatari
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Elena V Spirina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
| | - Xiaofen Wu
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Daniel E Williams
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Elizaveta M Rivkina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
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6
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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7
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Dose B, Ross C, Niehs SP, Scherlach K, Bauer JP, Hertweck C. Food‐Poisoning Bacteria Employ a Citrate Synthase and a Type II NRPS To Synthesize Bolaamphiphilic Lipopeptide Antibiotics**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Benjamin Dose
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Claudia Ross
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Sarah P. Niehs
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Johanna P. Bauer
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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8
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Dose B, Ross C, Niehs SP, Scherlach K, Bauer JP, Hertweck C. Food-Poisoning Bacteria Employ a Citrate Synthase and a Type II NRPS To Synthesize Bolaamphiphilic Lipopeptide Antibiotics*. Angew Chem Int Ed Engl 2020; 59:21535-21540. [PMID: 32780428 PMCID: PMC7756705 DOI: 10.1002/anie.202009107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 12/21/2022]
Abstract
Mining the genome of the food-spoiling bacterium Burkholderia gladioli pv. cocovenenans revealed five nonribosomal peptide synthetase (NRPS) gene clusters, including an orphan gene locus (bol). Gene inactivation and metabolic profiling linked the bol gene cluster to novel bolaamphiphilic lipopeptides with antimycobacterial activity. A combination of chemical analysis and bioinformatics elucidated the structures of bolagladin A and B, lipocyclopeptides featuring an unusual dehydro-β-alanine enamide linker fused to an unprecedented tricarboxylic fatty acid tail. Through a series of targeted gene deletions, we proved the involvement of a designated citrate synthase (CS), priming ketosynthases III (KS III), a type II NRPS, including a novel desaturase for enamide formation, and a multimodular NRPS in generating the cyclopeptide. Network analyses revealed the evolutionary origin of the CS and identified cryptic CS/NRPS gene loci in various bacterial genomes.
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Affiliation(s)
- Benjamin Dose
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Claudia Ross
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Sarah P. Niehs
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Johanna P. Bauer
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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9
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Biochemical characterization of 2-phosphinomethylmalate synthase from Streptomyces hygroscopicus: A member of the DRE-TIM metallolyase superfamily. Arch Biochem Biophys 2020; 691:108489. [PMID: 32697946 DOI: 10.1016/j.abb.2020.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/23/2022]
Abstract
2-Phosphinomethylmalate synthase (PMMS) from Streptomyces hygroscopicus catalyzes the first step in the biosynthesis of the herbicide bialophos using 3-phosphinopyruvic acid and acetyl coenzyme A as substrates to form 2-phosphinomethylmalic acid and coenzyme A. PMMS belongs to the Claisen condensation-like (CC-like) subgroup of the DRE-TIM metallolyase superfamily, which uses conserved active site architecture to catalyze a functionally-diverse set of reactions. Analysis of a sequence similarity network for the CC-like subgroup identified PMMS and the related R-citrate synthase in an early-diverging cluster suggesting that this group of sequences are more distinct in relation to other Claisen-condensation subgroup members. To better understand the structure/function landscape of the CC-like subgroup PMMS was recombinantly expressed in Escherichia coli, purified, and characterized with respect to its enzymatic properties. Using oxaloacetate as a substrate analog, the recombinantly-produced enzyme exhibited improved Michaelis constants relative to the previously reported natively-produced enzyme. Results from pH rate profiles and kinetic isotope effects were consistent with results from other members of the CC-like subgroup supporting acid-base chemistry and hydrolysis of the direct Claisen-condensation product as the rate-determining step. Results of site-directed mutagenesis experiments indicate that PMMS uses an active-site architecture similar to homocitrate synthase to select for a dicarboxylic acid substrate.
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10
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Suzuki T, Tomita T, Hirayama K, Suzuki M, Kuzuyama T, Nishiyama M. Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius. FEBS J 2020; 288:1975-1988. [PMID: 32897601 DOI: 10.1111/febs.15527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 11/26/2022]
Abstract
Homocitrate synthase (HCS) catalyzes the aldol condensation of α-ketoglutarate and acetyl coenzyme A to form homocitrate, which is the first committed step of lysine biosynthesis through the α-aminoadipate pathway in yeast, fungi, and some prokaryotes. We determined the crystal structure of a truncated form of HCS from a hyperthermophilic acidophilic archaeon, Sulfolobus acidocaldarius, which lacks the RAM (Regulation of amino acid metabolism) domain at the C terminus serving as the regulatory domain for the feedback inhibition by lysine, in complex with α-ketoglutarate, Mg2+ , and CoA. This structure coupled with mutational analysis revealed that a subdomain, subdomain II, connecting the N-terminal catalytic domain and C-terminal RAM domain is involved in the recognition of acetyl-CoA. This is the first structural evidence of the function of subdomain II in the related enzyme family, which will lead to a better understanding of the catalytic mechanism of HCS. DATABASES: Structural data are available in the RCSB PDB database under the accession number 6KTQ.
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Affiliation(s)
- Tomohiro Suzuki
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Kenta Hirayama
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
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11
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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12
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New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. Sci Rep 2020; 10:4860. [PMID: 32184419 PMCID: PMC7078309 DOI: 10.1038/s41598-020-61729-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/24/2020] [Indexed: 11/26/2022] Open
Abstract
The opportunistic pathogen Malassezia pachydermatis causes bloodstream infections in preterm infants or individuals with immunodeficiency disorders and has been associated with a broad spectrum of diseases in animals such as seborrheic dermatitis, external otitis and fungemia. The current approaches to treat these infections are failing as a consequence of their adverse effects, changes in susceptibility and antifungal resistance. Thus, the identification of novel therapeutic targets against M. pachydermatis infections are highly relevant. Here, Gene Essentiality Analysis and Flux Variability Analysis was applied to a previously reported M. pachydermatis metabolic network to identify enzymes that, when absent, negatively affect biomass production. Three novel therapeutic targets (i.e., homoserine dehydrogenase (MpHSD), homocitrate synthase (MpHCS) and saccharopine dehydrogenase (MpSDH)) were identified that are absent in humans. Notably, L-lysine was shown to be an inhibitor of the enzymatic activity of MpHCS and MpSDH at concentrations of 1 mM and 75 mM, respectively, while L-threonine (1 mM) inhibited MpHSD. Interestingly, L- lysine was also shown to inhibit M. pachydermatis growth during in vitro assays with reference strains and canine isolates, while it had a negligible cytotoxic activity on HEKa cells. Together, our findings form the bases for the development of novel treatments against M. pachydermatis infections.
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13
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Abstract
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Nitrogenase harbors three distinct
metal prosthetic groups that
are required for its activity. The simplest one is a [4Fe-4S] cluster
located at the Fe protein nitrogenase component. The MoFe protein
component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase
metalloclusters requires the participation of the structural nitrogenase
components and many accessory proteins, and occurs both in
situ, for the P-cluster, and in external assembly sites for
FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves
molecular scaffolds, metallochaperones, radical chemistry, and novel
and unique biosynthetic intermediates. This review provides a critical
overview of discoveries on nitrogenase cofactor structure, function,
and activity over the last four decades.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Emilio Jiménez-Vicente
- Department of Biochemistry, Virginia Polytechnic Institute, Blacksburg, Virginia 24061, United States
| | - Carlos Echavarri-Erasun
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
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14
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Suzuki T, Akiyama N, Yoshida A, Tomita T, Lassak K, Haurat MF, Okada T, Takahashi K, Albers S, Kuzuyama T, Nishiyama M. Biochemical characterization of archaeal homocitrate synthase from
Sulfolobus acidocaldarius. FEBS Lett 2019; 594:126-134. [DOI: 10.1002/1873-3468.13550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Nagisa Akiyama
- Biotechnology Research Center The University of Tokyo Japan
| | - Ayako Yoshida
- Biotechnology Research Center The University of Tokyo Japan
| | - Takeo Tomita
- Biotechnology Research Center The University of Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Japan
| | - Kerstin Lassak
- Molecular Biology of Archaea Institute of Biology University of Freiburg Germany
| | | | - Takuya Okada
- Biotechnology Research Center The University of Tokyo Japan
| | | | - Sonja‐Verena Albers
- Molecular Biology of Archaea Institute of Biology University of Freiburg Germany
| | - Tomohisa Kuzuyama
- Biotechnology Research Center The University of Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Japan
| | - Makoto Nishiyama
- Biotechnology Research Center The University of Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Japan
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15
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Gionco B, Tavares ER, de Oliveira AG, Yamada-Ogatta SF, do Carmo AO, Pereira UDP, Chideroli RT, Simionato AS, Navarro MOP, Chryssafidis AL, Andrade G. New Insights about Antibiotic Production by Pseudomonas aeruginosa: A Gene Expression Analysis. Front Chem 2017; 5:66. [PMID: 28966922 PMCID: PMC5605626 DOI: 10.3389/fchem.2017.00066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/31/2017] [Indexed: 12/22/2022] Open
Abstract
The bacterial resistance for antibiotics is one of the most important problems in public health and only a small number of new products are in development. Antagonistic microorganisms from soil are a promising source of new candidate molecules. Products of secondary metabolism confer adaptive advantages for their producer, in the competition for nutrients in the microbial community. The biosynthesis process of compounds with antibiotic activity is the key to optimize their production and the transcriptomic study of microorganisms is of great benefit for the discovery of these metabolic pathways. Pseudomonas aeruginosa LV strain growing in the presence of copper chloride produces a bioactive organometallic compound, which has a potent antimicrobial activity against various microorganisms. The objective of this study was to verify overexpressed genes and evaluate their relation to the organometallic biosynthesis in this microorganism. P. aeruginosa LV strain was cultured in presence and absence of copper chloride. Two methods were used for transcriptomic analysis, genome reference-guided assembly and de novo assembly. The genome referenced analysis identified nine upregulated genes when bacteria were exposed to copper chloride, while the De Novo Assembly identified 12 upregulated genes. Nineteen genes can be related to an increased microbial metabolism for the extrusion process of exceeding intracellular copper. Two important genes are related to the biosynthesis of phenazine and tetrapyrroles compounds, which can be involved in the bioremediation of intracellular copper and we suggesting that may involve in the biosynthesis of the organometallic compound. Additional studies are being carried out to further prove the function of the described genes and relate them to the biosynthetic pathway of the organometallic compound.
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Affiliation(s)
- Bárbara Gionco
- Microbial Ecology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
| | - Eliandro R Tavares
- Molecular Biology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
| | - Admilton G de Oliveira
- Microbial Ecology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
| | - Sueli F Yamada-Ogatta
- Molecular Biology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
| | - Anderson O do Carmo
- Department of General Biology, Institute of Biologic Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Ulisses de Pádua Pereira
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, Universidade Estadual de LondrinaLondrina, Brazil
| | - Roberta T Chideroli
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, Universidade Estadual de LondrinaLondrina, Brazil
| | - Ane S Simionato
- Microbial Ecology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
| | - Miguel O P Navarro
- Microbial Ecology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
| | - Andreas L Chryssafidis
- Laboratory of Veterinary Toxicology, Department of Preventive Veterinary Medicine, Universidade Estadual de LondrinaLondrina, Brazil
| | - Galdino Andrade
- Microbial Ecology Laboratory, Department of Microbiology, Universidade Estadual de LondrinaLondrina, Brazil
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16
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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17
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Gabriel I, Milewski S. Characterization of recombinant homocitrate synthase from Candida albicans. Protein Expr Purif 2015; 125:7-18. [PMID: 26363118 DOI: 10.1016/j.pep.2015.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 10/23/2022]
Abstract
LYS21 and LYS22 genes from Candida albicans encoding isoforms of homocitrate synthase (HCS), an enzyme catalyzing the first committed step in the l-lysine biosynthetic pathway, were cloned and expressed as N-oligoHistagged fusion proteins in Escherichia coli. The purified gene products revealed HCS activity, i.e. catalyzed the condensation of α-ketoglutarate with acetyl-coenzyme A to yield homocitrate. The recombinant enzymes were purified to homogeneity and characterized for their physical properties and substrate specificities. As determined by size-exclusion chromatography (SEC) and native page electrophoresis, both isoenzymes adopt multiple quaternary structures, with the homotetrameric one being the most abundant. The KM (acetyl-CoA)=0.8±0.15mM and KM (α-ketoglutarate)=0.113±0.02mM for His6CaLys21p and KM (acetyl-CoA)=0.48±0.09mM and KM (α-ketoglutarate)=0.152±0.03mM values for His6CaLys22p were determined. Both enzyme versions were inhibited by l-Lys, i.e. the end product of the α-aminoadipate pathway but Lys22p was more sensitive than Lys21p, with Ki (L-Lys)=128±8μM for His6CaLys21p and Ki (L-Lys)=4.37±0.68μM for His6CaLys22p. The isoforms of C. albicans HCS exhibited differential sensitivity to several l-Lys analogues. Most notably, dl-α-difluoromethyllysine strongly inhibited His6CaLys22p (IC50 32±3μM) but was not inhibitory at all towards His6CaLys21p. Differential sensitivity of recombinant C. albicans Δlys21/LYS22, LYS21/Δlys22 and Δlys21/Δlys22 mutant strains to lysine analog, 2-aminoethyl-l-cysteine and biochemical properties of homocitrate synthase isoforms suggest different roles of two HCS isoenzymes in α-aminoadipate pathway.
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Affiliation(s)
- Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, 11/12 Narutowicza Str., 80-233 Gdansk, Poland.
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, 11/12 Narutowicza Str., 80-233 Gdansk, Poland
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18
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Torres-Machorro AL, Aris JP, Pillus L. A moonlighting metabolic protein influences repair at DNA double-stranded breaks. Nucleic Acids Res 2015; 43:1646-58. [PMID: 25628362 PMCID: PMC4330366 DOI: 10.1093/nar/gku1405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Catalytically active proteins with divergent dual functions are often described as ‘moonlighting’. In this work we characterize a new, chromatin-based function of Lys20, a moonlighting protein that is well known for its role in metabolism. Lys20 was initially described as homocitrate synthase (HCS), the first enzyme in the lysine biosynthetic pathway in yeast. Its nuclear localization led to the discovery of a key role for Lys20 in DNA damage repair through its interaction with the MYST family histone acetyltransferase Esa1. Overexpression of Lys20 promotes suppression of DNA damage sensitivity of esa1 mutants. In this work, by taking advantage of LYS20 mutants that are active in repair but not in lysine biosynthesis, the mechanism of suppression of esa1 was characterized. First we analyzed the chromatin landscape of esa1 cells, finding impaired histone acetylation and eviction. Lys20 was recruited to sites of DNA damage, and its overexpression promoted enhanced recruitment of the INO80 remodeling complex to restore normal histone eviction at the damage sites. This study improves understanding of the evolutionary, structural and biological relevance of independent activities in a moonlighting protein and links metabolism to DNA damage repair.
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Affiliation(s)
- Ana Lilia Torres-Machorro
- Section of Molecular Biology, Division of Biological Sciences, UC San Diego Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0347, USA
| | - John P Aris
- Department of Anatomy and Cell Biology, Health Science Center, University of Florida, Gainesville, FL 32610-0235, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, UC San Diego Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0347, USA
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19
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Zhang Z, Wu J, Lin W, Wang J, Yan H, Zhao W, Ma J, Ding J, Zhang P, Zhao GP. Subdomain II of α-isopropylmalate synthase is essential for activity: inferring a mechanism of feedback inhibition. J Biol Chem 2014; 289:27966-78. [PMID: 25128527 DOI: 10.1074/jbc.m114.559716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The committed step of leucine biosynthesis, converting acetyl-CoA and α-ketoisovalerate into α-isopropylmalate, is catalyzed by α-isopropylmalate synthase (IPMS), an allosteric enzyme subjected to feedback inhibition by the end product L-leucine. We characterized the short form IPMS from Leptospira biflexa (LbIPMS2), which exhibits a catalytic activity comparable with that of the long form IPMS (LbIPMS1) and has a similar N-terminal domain followed by subdomain I and subdomain II but lacks the whole C-terminal regulatory domain. We found that partial deletion of the regulatory domain of LbIPMS1 resulted in a loss of about 50% of the catalytic activity; however, when the regulatory domain was deleted up to Arg-385, producing a protein that is almost equivalent to the intact LbIPMS2, about 90% of the activity was maintained. Moreover, in LbIPMS2 or LbIPMS1, further deletion of several residues from the C terminus of subdomain II significantly impaired or completely abolished the catalytic activity, respectively. These results define a complete and independently functional catalytic module of IPMS consisting of both the N-terminal domain and the two subdomains. Structural comparison of LbIPMS2 and the Mycobacterium tuberculosis IPMS revealed two different conformations of subdomain II that likely represent two substrate-binding states related to cooperative catalysis. The biochemical and structural analyses together with the previously published hydrogen-deuterium exchange data led us to propose a conformation transition mechanism for feedback inhibition mediated by subdomains I and II that might associated with alteration of the binding affinity toward acetyl-CoA.
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Affiliation(s)
- Zilong Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and Shanghai International Travel Healthcare Center, Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200335, China
| | - Jian Wu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Lin
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Jin Wang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Han Yan
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Wei Zhao
- Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College, and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jun Ma
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China,
| | - Peng Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China,
| | - Guo-Ping Zhao
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College, and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China, Shanghai-Ministry of Science and Technology Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China, Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region 999077, China, and
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20
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Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA. Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. Biochemistry 2014; 53:2915-25. [PMID: 24720347 PMCID: PMC4025573 DOI: 10.1021/bi500246z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The characterization of functionally diverse enzyme superfamilies provides the opportunity to identify evolutionarily conserved catalytic strategies, as well as amino acid substitutions responsible for the evolution of new functions or specificities. Isopropylmalate synthase (IPMS) belongs to the DRE-TIM metallolyase superfamily. Members of this superfamily share common active site elements, including a conserved active site helix and an HXH divalent metal binding motif, associated with stabilization of a common enolate anion intermediate. These common elements are overlaid by variations in active site architecture resulting in the evolution of a diverse set of reactions that include condensation, lyase/aldolase, and carboxyl transfer activities. Here, using IPMS, an integrated biochemical and bioinformatics approach has been utilized to investigate the catalytic role of residues on an active site helix that is conserved across the superfamily. The construction of a sequence similarity network for the DRE-TIM metallolyase superfamily allows for the biochemical results obtained with IPMS variants to be compared across superfamily members and within other condensation-catalyzing enzymes related to IPMS. A comparison of our results with previous biochemical data indicates an active site arginine residue (R80 in IPMS) is strictly required for activity across the superfamily, suggesting that it plays a key role in catalysis, most likely through enolate stabilization. In contrast, differential results obtained from substitution of the C-terminal residue of the helix (Q84 in IPMS) suggest that this residue plays a role in reaction specificity within the superfamily.
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Affiliation(s)
- Ashley K Casey
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35406, United States
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21
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Bulfer SL, Brunzelle JS, Trievel RC. Crystal structure of Saccharomyces cerevisiae Aro8, a putative α-aminoadipate aminotransferase. Protein Sci 2013; 22:1417-24. [PMID: 23893908 PMCID: PMC3795499 DOI: 10.1002/pro.2315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/06/2022]
Abstract
α-Aminoadipate aminotransferase (AAA-AT) catalyzes the amination of 2-oxoadipate to α-aminoadipate in the fourth step of the α-aminoadipate pathway of lysine biosynthesis in fungi. The aromatic aminotransferase Aro8 has recently been identified as an AAA-AT in Saccharomyces cerevisiae. This enzyme displays broad substrate selectivity, utilizing several amino acids and 2-oxo acids as substrates. Here we report the 1.91Å resolution crystal structure of Aro8 and compare it to AAA-AT LysN from Thermus thermophilus and human kynurenine aminotransferase II. Inspection of the active site of Aro8 reveals asymmetric cofactor binding with lysine-pyridoxal-5-phosphate bound within the active site of one subunit in the Aro8 homodimer and pyridoxamine phosphate and a HEPES molecule bound to the other subunit. The HEPES buffer molecule binds within the substrate-binding site of Aro8, yielding insights into the mechanism by which it recognizes multiple substrates and how this recognition differs from other AAA-AT/kynurenine aminotransferases.
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Affiliation(s)
- Stacie L Bulfer
- Department of Biological Chemistry, University of MichiganAnn Arbor, Michigan, 48109
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University Center for Synchrotron ResearchArgonne, Illinois, 60439
| | - Raymond C Trievel
- Department of Biological Chemistry, University of MichiganAnn Arbor, Michigan, 48109
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22
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Identification and characterization of re-citrate synthase in Syntrophus aciditrophicus. J Bacteriol 2013; 195:1689-96. [PMID: 23378508 DOI: 10.1128/jb.02185-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Glutamate is usually synthesized from acetyl coenzyme A (acetyl-CoA) via citrate, isocitrate, and 2-oxoglutarate. Genome analysis revealed that in Syntrophus aciditrophicus, the gene for Si-citrate synthase is lacking. An alternative pathway starting from the catabolic intermediate glutaconyl-CoA via 2-hydroxyglutarate could be excluded by genomic analysis. On the other hand, a putative gene (SYN_02536; NCBI gene accession no. CP000252.1) annotated as coding for isopropylmalate/citramalate/homocitrate synthase has been shown to share 49% deduced amino acid sequence identity with the gene encoding Re-citrate synthase of Clostridium kluyveri. We cloned and overexpressed this gene in Escherichia coli together with the genes encoding the chaperone GroEL. The recombinant homotetrameric enzyme with a C-terminal Strep-tag (4 × 72,892 Da) was separated from GroEL on a Strep-Tactin column by incubation with ATP, K(+), and Mg(2+). The pure Re-citrate synthase used only acetyl-CoA and oxaloacetate as the substrates. As isolated, the enzyme contained stoichiometric amounts of Ca(2+) (0.9 Ca/73 kDa) but achieved higher specific activities in the presence of Mn(2+) (1.2 U/mg) or Co(2+) (2.0 U/mg). To determine the stereospecificity of the enzyme, [(14)C]citrate was enzymatically synthesized from oxaloacetate and [1-(14)C]acetyl-CoA; the subsequent cleavage by Si-citrate lyase yielded unlabeled acetate and labeled oxaloacetate, demonstrating that the enzyme is a Re-citrate synthase. The production of Re-citrate synthase by S. aciditrophicus grown axenically on crotonate was revealed by synthesis of [(14)C]citrate in a cell extract followed by stereochemical analysis. This result was supported by detection of transcripts of the Re-citrate synthase gene in axenic as well as in syntrophic cultures using quantitative reverse transcriptase PCR (qRT-PCR).
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23
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24
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Crystal structure and functional analysis of JMJD5 indicate an alternate specificity and function. Mol Cell Biol 2012; 32:4044-52. [PMID: 22851697 DOI: 10.1128/mcb.00513-12] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
JMJD5 is a Jumonji C (JmjC) protein that has been implicated in breast cancer tumorigenesis, circadian rhythm regulation, embryological development, and osteoclastogenesis. Recently, JMJD5 (also called KDM8) has been reported to demethylate dimethylated Lys-36 in histone H3 (H3K36me2), regulating genes that control cell cycle progression. Here, we report high-resolution crystal structures of the human JMJD5 catalytic domain in complex with the substrate 2-oxoglutarate (2-OG) and the inhibitor N-oxalylglycine (NOG). The structures reveal a β-barrel fold that is conserved in the JmjC family and a long shallow cleft that opens into the enzyme's active site. A comparison with other JmjC enzymes illustrates that JMJD5 shares sequence and structural homology with the asparaginyl and histidinyl hydroxylase FIH-1 (factor inhibiting hypoxia-inducible factor 1 [HIF-1]), the lysyl hydroxylase JMJD6, and the RNA hydroxylase TYW5 but displays limited homology to JmjC lysine demethylases (KDMs). Contrary to previous findings, biochemical assays indicate that JMJD5 does not display demethylase activity toward methylated H3K36 nor toward the other methyllysines in the N-terminal tails of histones H3 and H4. Together, these results imply that JMJD5 participates in roles independent of histone demethylation and may function as a protein hydroxylase given its structural homology with FIH-1 and JMJD6.
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25
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Kumar VP, West AH, Cook PF. Kinetic and chemical mechanisms of homocitrate synthase from Thermus thermophilus. J Biol Chem 2011; 286:29428-29439. [PMID: 21733842 DOI: 10.1074/jbc.m111.246355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The homocitrate synthase from Thermus thermophilus (TtHCS) is a metal-activated enzyme with either Mg(2+) or Mn(2+) capable of serving as the divalent cation. The enzyme exhibits a sequential kinetic mechanism. The mechanism is steady state ordered with α-ketoglutarate (α-Kg) binding prior to acetyl-CoA (AcCoA) with Mn(2+), whereas it is steady state random with Mg(2+), suggesting a difference in the competence of the E·Mn·α-Kg·AcCoA and E·Mg·α-Kg·AcCoA complexes. The mechanism is supported by product and dead-end inhibition studies. The primary isotope effect obtained with deuterioacetylCoA (AcCoA-d(3)) in the presence of Mg(2+) is unity (value 1.0) at low concentrations of AcCoA, whereas it is 2 at high concentrations of AcCoA. Data suggest the presence of a slow conformational change induced by binding of AcCoA that accompanies deprotonation of the methyl group of AcCoA. The solvent kinetic deuterium isotope effect is also unity at low AcCoA, but is 1.7 at high AcCoA, consistent with the proposed slow conformational change. The maximum rate is pH independent with either Mg(2+) or Mn(2+) as the divalent metal ion, whereas V/K(α-Kg) (with Mn(2+)) decreases at low and high pH giving pK values of about 6.5 and 8.0. Lysine is a competitive inhibitor that binds to the active site of TtHCS, and shares some of the same binding determinants as α-Kg. Lysine binding exhibits negative cooperativity, indicating cross-talk between the two monomers of the TtHCS dimer. Data are discussed in terms of the overall mechanism of TtHCS.
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Affiliation(s)
- Vidya Prasanna Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Paul F Cook
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019.
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26
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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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27
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Bulfer SL, McQuade TJ, Larsen MJ, Trievel RC. Application of a high-throughput fluorescent acetyltransferase assay to identify inhibitors of homocitrate synthase. Anal Biochem 2011; 410:133-40. [PMID: 21073853 PMCID: PMC3115995 DOI: 10.1016/j.ab.2010.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 01/06/2023]
Abstract
Homocitrate synthase (HCS) catalyzes the first step of l-lysine biosynthesis in fungi by condensing acetyl-coenzyme A and 2-oxoglutarate to form 3R-homocitrate and coenzyme A. Due to its conservation in pathogenic fungi, HCS has been proposed as a candidate for antifungal drug design. Here we report the development and validation of a robust fluorescent assay for HCS that is amenable to high-throughput screening for inhibitors in vitro. Using this assay, Schizosaccharomyces pombe HCS was screened against a diverse library of approximately 41,000 small molecules. Following confirmation, counter screens, and dose-response analysis, we prioritized more than 100 compounds for further in vitro and in vivo analysis. This assay can be readily adapted to screen for small molecule modulators of other acyl-CoA-dependent acyltransferases or enzymes that generate a product with a free sulfhydryl group, including histone acetyltransferases, aminoglycoside N-acetyltransferases, thioesterases, and enzymes involved in lipid metabolism.
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Affiliation(s)
- Stacie L Bulfer
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Scott EM, Pillus L. Homocitrate synthase connects amino acid metabolism to chromatin functions through Esa1 and DNA damage. Genes Dev 2010; 24:1903-13. [PMID: 20810648 DOI: 10.1101/gad.1935910] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The enzyme homocitrate synthase (HCS) catalyzes the first step in lysine biosynthesis, and early biochemical data placed it in the cytoplasm or mitochondria, where most amino acid synthesis occurs. It was therefore surprising when refined fractionation techniques and specific immunoreagents clearly demonstrated its localization to the nucleus. These observations raised the question of whether HCS had a function within the nucleus independent of lysine synthesis. We demonstrate that HCS encoded by LYS20 in yeast is linked to the key process of DNA damage repair through the essential MYST family histone acetyltransferase Esa1 and the H2A.Z histone variant. This discovery indicates that HCS has a role in addition to amino acid synthesis, and that it functions in nuclear activities involving chromatin regulation that are distinct from its previously established role in lysine biosynthesis. The chromatin-linked roles are dependent on nuclear localization of Lys20, but are independent of HCS catalytic activity. Thus, Lys20 appears to have evolved as a bifunctional protein that connects cellular metabolism with chromatin functions.
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Affiliation(s)
- Erin M Scott
- Division of Biological Sciences, Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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Bulfer SL, Scott EM, Pillus L, Trievel RC. Structural basis for L-lysine feedback inhibition of homocitrate synthase. J Biol Chem 2010; 285:10446-53. [PMID: 20089861 PMCID: PMC2856251 DOI: 10.1074/jbc.m109.094383] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 01/12/2010] [Indexed: 11/06/2022] Open
Abstract
The alpha-aminoadipate pathway of lysine biosynthesis is modulated at the transcriptional and biochemical levels by feedback inhibition. The first enzyme in the alpha-aminoadipate pathway, homocitrate synthase (HCS), is the target of the feedback regulation and is strongly inhibited by l-lysine. Here we report the structure of Schizosaccharomyces pombe HCS (SpHCS) in complex with l-lysine. The structure illustrates that the amino acid directly competes with the substrate 2-oxoglutarate for binding within the active site of HCS. Differential recognition of the substrate and inhibitor is achieved via a switch position within the (alpha/beta)(8) TIM barrel of the enzyme that can distinguish between the C5-carboxylate group of 2-oxoglutarate and the epsilon-ammonium group of l-lysine. In vitro and in vivo assays demonstrate that mutations of the switch residues, which interact with the l-lysine epsilon-ammonium group, abrogate feedback inhibition, as do substitutions of residues within the C-terminal domain that were identified in a previous study of l-lysine-insensitive HCS mutants in Saccharomyces cerevisiae. Together, these results yield new insights into the mechanism of feedback regulation of an enzyme central to lysine biosynthesis.
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Affiliation(s)
- Stacie L. Bulfer
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Erin M. Scott
- the Division of Biological Sciences and Moores UCSD Cancer Center, University of California San Diego, La Jolla, California 92093-0347
| | - Lorraine Pillus
- the Division of Biological Sciences and Moores UCSD Cancer Center, University of California San Diego, La Jolla, California 92093-0347
| | - Raymond C. Trievel
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
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Okada T, Tomita T, Wulandari AP, Kuzuyama T, Nishiyama M. Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus. J Biol Chem 2010; 285:4195-4205. [PMID: 19996101 PMCID: PMC2823558 DOI: 10.1074/jbc.m109.086330] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Indexed: 11/06/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes aldol-type condensation of acetyl coenzyme A (acetyl-CoA) and alpha-ketoglutarate (alpha-KG) to synthesize homocitrate (HC), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. As known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, HCS is regulated via feedback inhibition by the end product, lysine. Here, we determined the crystal structures of HCS from Thermus thermophilus complexed with alpha-KG, HC, or lysine. In the HC complex, the C1-carboxyl group of HC, which is derived from acetyl-CoA, is hydrogen-bonded with His-292* from another subunit (indicated by the asterisk), indicating direct involvement of this residue in the catalytic mechanism of HCS. The crystal structure of HCS complexed with lysine showed that lysine is bound to the active site with rearrangement of amino acid residues in the substrate-binding site, which accounts for the competitive inhibition by lysine with alpha-KG. Comparison between the structures suggests that His-72, which is conserved in lysine-sensitive HCSs and binds the C5-carboxyl group of alpha-KG, serves as a switch for the conformational change. Replacement of His-72 by leucine made HCS resistant to lysine inhibition, demonstrating the regulatory role of this conserved residue.
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Affiliation(s)
- Takuya Okada
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Takeo Tomita
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Asri P Wulandari
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Makoto Nishiyama
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and; the RIKEN SPring-8 Center, Hyogo 679-5148, Japan.
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