1
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Mena C, Deulofeu-Capo O, Forn I, Dordal-Soriano J, Mantilla-Arias YA, Samos IP, Sebastián M, Cardelús C, Massana R, Romera-Castillo C, Mallenco-Fornies R, Gasol JM, Ruiz-González C. High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry. ISME COMMUNICATIONS 2024; 4:ycae004. [PMID: 38425478 PMCID: PMC10902890 DOI: 10.1093/ismeco/ycae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT), and we compared it with prokaryotic HPG use throughout a 9-day survey in the NW Mediterranean. BONCAT allows to fluorescently identify translationally active cells, but it has never been applied to natural eukaryotic communities. We found a large diversity of photosynthetic and heterotrophic eukaryotes incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (49 ± 25% and 52 ± 15%, respectively). Among them, pennate diatoms exhibited higher HPG incorporation in the afternoon than in the morning, whereas small (≤5 μm) photosynthetic eukaryotes and heterotrophic nanoeukaryotes showed the opposite pattern. Centric diatoms (e.g. Chaetoceros, Thalassiosira, and Lauderia spp.) dominated the eukaryotic HPG incorporation due to their high abundances and large sizes, accounting for up to 86% of the eukaryotic BONCAT signal and strongly correlating with bulk 3H-leucine uptake rates. When including prokaryotes, eukaryotes were estimated to account for 19-31% of the bulk BONCAT signal. Our results evidence a large complexity in the osmotrophic uptake of HPG, which varies over time within and across eukaryotic groups and highlights the potential of BONCAT to quantify osmotrophy and protein synthesis in complex eukaryotic communities.
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Affiliation(s)
- Catalina Mena
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Ona Deulofeu-Capo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Júlia Dordal-Soriano
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Yulieth A Mantilla-Arias
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Iván P Samos
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Clara Cardelús
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Cristina Romera-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Rebeca Mallenco-Fornies
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona 08003, Spain
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2
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S-Assimilation Influences in Carrageenan Biosynthesis Genes during Ethylene-Induced Carposporogenesis in Red Seaweed Grateloupia imbricata. Mar Drugs 2022; 20:md20070436. [PMID: 35877729 PMCID: PMC9320806 DOI: 10.3390/md20070436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
The synthesis of cell-wall sulfated galactans proceeds through UDP galactose, a major nucleotide sugar in red seaweed, whilst sulfate is transported through S-transporters into algae. Moreover, synthesis of ethylene, a volatile plant growth regulator that plays an important role in red seaweed reproduction, occurs through S-adenosyl methionine. This means that sulfur metabolism is involved in reproduction events as well as sulfated galactan synthesis of red seaweed. In this work we study the effects of methionine and MgSO4 on gene expression of polygalactan synthesis through phosphoglucomutase (PGM) and galactose 1 phosphate uridyltransferase (GALT) and of sulfate assimilation (S-transporter and sulfate adenylyltransferase, SAT) using treatment of ethylene for 15 min, which elicited cystocarp development in Grateloupia imbricata. Also, expressions of carbohydrate sulfotransferase and galactose-6-sulfurylase in charge of the addition and removal of sulfate groups to galactans backbone were examined. Outstanding results occurred in the presence of methionine, which provoked an increment in transcript number of genes encoding S-transporter and assimilation compared to controls regardless of the development stage of thalli. Otherwise, methionine diminished the transcript levels of PGM and GALT and expressions are associated with the fertilization stage of thalli of G. imbricata. As opposite, methionine and MgSO4 did not affect the transcript number of carbohydrate sulfotransferase and galactose-6-sulfurylase. Nonetheless, differential expression was obtained for sulfurylases according to the development stages of thalli of G. imbricata.
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Gade M, Tan LL, Damry AM, Sandhu M, Brock JS, Delaney A, Villar-Briones A, Jackson CJ, Laurino P. Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. JACS AU 2021; 1:2349-2360. [PMID: 34977903 PMCID: PMC8715544 DOI: 10.1021/jacsau.1c00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/14/2023]
Abstract
Protein conformational changes can facilitate the binding of noncognate substrates and underlying promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here, we analyze human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, noncognate substrates bind in a stable conformation to allow catalysis. In contrast, noncognate substrates sample stable productive binding modes less frequently in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrates likely drove the evolutionary divergence of substrate specificity in these orthologues. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated levels in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.
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Affiliation(s)
- Madhuri Gade
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Li Lynn Tan
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Adam M. Damry
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Mahakaran Sandhu
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Joseph S. Brock
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Andie Delaney
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Alejandro Villar-Briones
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, ACT, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, Australian National
University, Canberra 2601, ACT, Australia
| | - Paola Laurino
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
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4
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Kleiner D, Shmulevich F, Zarivach R, Shahar A, Sharon M, Ben-Nissan G, Bershtein S. The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase. J Mol Biol 2019; 431:4796-4816. [PMID: 31520601 DOI: 10.1016/j.jmb.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/20/2019] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
Methionine S-adenosyltransferases (MATs) are predominantly homotetramers, comprised of dimers of dimers. The larger, highly conserved intradimeric interface harbors two active sites, making the dimer the obligatory functional unit. However, functionality of the smaller, more diverged, and recently evolved interdimeric interface is largely unknown. Here, we show that the interdimeric interface of Ureaplasmaurealiticum MAT has evolved to control the catalytic activity and structural integrity of the homotetramer in response to product accumulation. When all four active sites are occupied with the product, S-adenosylmethionine (SAM), binding of four additional SAM molecules to the interdimeric interface prompts a ∼45° shift in the dimer orientation and a concomitant ∼60% increase in the interface area. This rearrangement inhibits the enzymatic activity by locking the flexible active site loops in a closed state and renders the tetramer resistant to proteolytic degradation. Our findings suggest that the interdimeric interface of MATs is subject to rapid evolutionary changes that tailor the molecular properties of the entire homotetramer to the specific needs of the organism.
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Affiliation(s)
- Daniel Kleiner
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel
| | - Fannia Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel; Macromolecular Crystallography Research Center (MCRC), The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Shahar
- Macromolecular Crystallography Research Center (MCRC), The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel.
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5
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He J, Sun S, Lu M, Yuan Q, Liu Y, Liang H. Metal-nucleobase hybrid nanoparticles for enhancing the activity and stability of metal-activated enzymes. Chem Commun (Camb) 2019; 55:6293-6296. [DOI: 10.1039/c9cc03155c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel strategy for enhancing the activity and stability of metal-activated enzyme methionine adenosyltransferase (MAT) by allosteric control and confinement of metal-nulceobase hybrid coordination.
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Affiliation(s)
- Jie He
- State key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Shanshan Sun
- State key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Mingzhu Lu
- State key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Qipeng Yuan
- State key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Yanhui Liu
- State key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Hao Liang
- State key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
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6
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Lewis CA, Wolfenden R. Sulfonium Ion Condensation: The Burden Borne by SAM Synthetase. Biochemistry 2018; 57:3549-3551. [PMID: 29787240 DOI: 10.1021/acs.biochem.8b00477] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-Adenosylmethionine (SAM+) serves as the principal methylating agent in biological systems, but the thermodynamic basis of its reactivity does not seem to have been clearly established. Here, we show that methionine, methanol, and H+ combine to form S-methylmethionine (SMM+) with a temperature-independent equilibrium constant of 9.9 M-2. The corresponding group transfer potential of SMM+ (its free energy of hydrolysis at pH 7) is -8.2 kcal/mol. The "energy-rich" nature of sulfonium ions is related to the extreme acidity (p Ka -5.4) of the S-protonated thioether produced by sulfonium hydrolysis, and the large negative free energy of deprotonation of that species in neutral solution (-16.7 kcal/mol). At pH 7, SAM synthetase requires the free energy released by cleavage of two bonds of ATP to reverse that process.
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Affiliation(s)
- Charles A Lewis
- From the Department of Biochemistry and Biophysics , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599-7260 , United States
| | - Richard Wolfenden
- From the Department of Biochemistry and Biophysics , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599-7260 , United States
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7
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Abstract
This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the metA gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of S-adenosylmethionine, which is an essential molecule employed in numerous biological processes. S-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In E. coli and Salmonella, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels. E. coli that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
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8
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Bromke MA, Hesse H. Phylogenetic analysis of methionine synthesis genes from Thalassiosira pseudonana. SPRINGERPLUS 2015; 4:391. [PMID: 26251775 PMCID: PMC4523565 DOI: 10.1186/s40064-015-1163-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/17/2015] [Indexed: 02/08/2023]
Abstract
Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. The sulfate assimilation and methionine synthesis pathways provide S-containing amino acids for the synthesis of proteins and a range of metabolites such as dimethylsulfoniopropionate. To obtain an insight into the localization and organization of the sulfur metabolism pathways we surveyed the genome of Thalassiosira pseudonana-a model organism for diatom research. We have identified and annotated genes for enzymes involved in respective pathways. Protein localization was predicted using similarities to known signal peptide motifs. We performed detailed phylogenetic analyses of enzymes involved in sulfate uptake/reduction and methionine metabolism. Moreover, we have found in up-stream sequences of studied diatoms methionine biosynthesis genes a conserved motif, which shows similarity to the Met31, a cis-motif regulating expression of methionine biosynthesis genes in yeast.
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Affiliation(s)
- Mariusz A Bromke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Holger Hesse
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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9
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Toney MD. Common enzymological experiments allow free energy profile determination. Biochemistry 2013; 52:5952-65. [PMID: 23906433 DOI: 10.1021/bi400696j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The determination of a complete set of rate constants [free energy profiles (FEPs)] for a complex kinetic mechanism is challenging. Enzymologists have devised a variety of informative steady-state kinetic experiments (e.g., Michaelis-Menten kinetics, viscosity dependence of kinetic parameters, kinetic isotope effects, etc.) that each provide distinct information regarding a particular kinetic system. A simple method for combining steady-state experiments in a single analysis is presented here, which allows microscopic rate constants and intrinsic kinetic isotope effects to be determined. It is first shown that Michaelis-Menten kinetic parameters (kcat and Km values), kinetic isotope efffets, solvent viscosity effects, and intermediate partitioning measurements are sufficient to define the rate constants for a reversible uni-uni mechanism with an intermediate, EZ, between the ES and EP complexes. Global optimization provides the framework for combining the independent experimental measurements, and the search for rate constants is performed using algorithms implemented in the biochemical software COPASI. This method is applied to the determination of FEPs for both alanine racemase and triosephosphate isomerase. The FEPs obtained from global optimization agree with those in the literature, with important exceptions. The method opens the door to routine and large-scale determination of FEPs for enzymes.
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Affiliation(s)
- Michael D Toney
- Department of Chemistry, University of California, Davis, California 95616, United States.
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10
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Pajares MA, Markham GD. Methionine adenosyltransferase (s-adenosylmethionine synthetase). ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 78:449-521. [PMID: 22220481 DOI: 10.1002/9781118105771.ch11] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- María A Pajares
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid Spain
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11
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Fleming RMT, Thiele I, Nasheuer HP. Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys Chem 2009; 145:47-56. [PMID: 19783351 DOI: 10.1016/j.bpc.2009.08.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 08/21/2009] [Accepted: 08/23/2009] [Indexed: 12/17/2022]
Abstract
Constraint-based modeling is an approach for quantitative prediction of net reaction flux in genome-scale biochemical networks. In vivo, the second law of thermodynamics requires that net macroscopic flux be forward, when the transformed reaction Gibbs energy is negative. We calculate the latter by using (i) group contribution estimates of metabolite species Gibbs energy, combined with (ii) experimentally measured equilibrium constants. In an application to a genome-scale stoichiometric model of Escherichia coli metabolism, iAF1260, we demonstrate that quantitative prediction of reaction directionality is increased in scope and accuracy by integration of both data sources, transformed appropriately to in vivo pH, temperature and ionic strength. Comparison of quantitative versus qualitative assignment of reaction directionality in iAF1260, assuming an accommodating reactant concentration range of 0.02-20mM, revealed that quantitative assignment leads to a low false positive, but high false negative, prediction of effectively irreversible reactions. The latter is partly due to the uncertainty associated with group contribution estimates. We also uncovered evidence that the high intracellular concentration of glutamate in E. coli may be essential to direct otherwise thermodynamically unfavorable essential reactions, such as the leucine transaminase reaction, in an anabolic direction.
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Affiliation(s)
- R M T Fleming
- Science Institute, University of Iceland, Reykjavík, Iceland.
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12
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Markham GD, Takusagawa F, Dijulio AM, Bock CW. An investigation of the catalytic mechanism of S-adenosylmethionine synthetase by QM/MM calculations. Arch Biochem Biophys 2009; 492:82-92. [PMID: 19699176 DOI: 10.1016/j.abb.2009.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 08/14/2009] [Indexed: 12/12/2022]
Abstract
Catalysis by S-adenosylmethionine synthetase has been investigated by quantum mechanical/molecular mechanical calculations, exploiting structures of the active crystalline enzyme. The transition state energy of +19.1 kcal/mol computed for a nucleophilic attack of the methionyl sulfur on carbon-5' of the nucleotide was indistinguishable from the experimental (solution) value when the QM residues were an uncharged histidine that hydrogen bonds to the leaving oxygen-5' and an aspartate that chelates a Mg2+ ion, and was similar (+18.8 kcal/mol) when the QM region also included the active site arginine and lysines. The computed energy difference between reactant and product was also consistent with their equimolar abundance in co-crystals. The calculated geometrical changes support catalysis of a S(N)2 reaction through hydrogen bonding of the liberated oxygen-5' to the histidine, charge neutralization by the two Mg2+ ions, and stabilization of the product sulfonium cation through a close, non-bonded, contact between the sulfur and the ribose oxygen-4'.
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Affiliation(s)
- George D Markham
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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13
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Abstract
Methionine adenosyltransferases (MATs) are the family of enzymes that synthesize the main biological methyl donor, S-adenosylmethionine. The high sequence conservation among catalytic subunits from bacteria and eukarya preserves key residues that control activity and oligomerization, which is reflected in the protein structure. However, structural differences among complexes with substrates and products have led to proposals of several reaction mechanisms. In parallel, folding studies begin to explain how the three intertwined domains of the catalytic subunit are produced, and to highlight the importance of certain intermediates in attaining the active final conformation. This review analyzes the available structural data and proposes a consensus interpretation that facilitates an understanding of the pathological problems derived from impairment of MAT function. In addition, new research opportunities directed toward clarification of aspects that remain obscure are also identified.
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Affiliation(s)
- G. D. Markham
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111 USA
| | - M. A. Pajares
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
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14
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Abstract
Amoebae of the xD strain of Amoeba proteus that arose from the D strain by spontaneous infection of Legionella-like X-bacteria are now dependent on their symbionts for survival. Each xD amoeba contains about 42,000 symbionts within symbiosomes, and established xD amoebae die if their symbionts are removed. Thus, harmful infective bacteria changed into necessary cell components. As a result of harboring X-bacteria. xD amoebae exhibit various physiological and genetic characteristics that are different from those of symbiont-free D amoebae. One of the recent findings is that bacterial symbionts control the expression of a host's house-keeping gene. Thus, the expression of the normal amoeba sams gene (sams1) encoding one form of S-adenosylmethionine synthetase is switched to that of sams2 by endosymbiotic X-bacteria. Possible mechanisms for the switching of sams genes brought about by endosymbionts and its significance are discussed.
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Affiliation(s)
- Kwang W Jeon
- Department of Biochemistry, University of Tennessee, Knoxville, TN 37996, USA.
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15
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Spies MA, Woodward JJ, Watnik MR, Toney MD. Alanine Racemase Free Energy Profiles from Global Analyses of Progress Curves. J Am Chem Soc 2004; 126:7464-75. [PMID: 15198593 DOI: 10.1021/ja049579h] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1). steady-state kinetic constants, (2). solvent viscosity dependence, (3). spectral analysis of reaction intermediates, (4). equilibrium overshoots for progress curves measured in D(2)O, and (5). the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.
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Affiliation(s)
- M Ashley Spies
- Department of Chemistry and Statistical Laboratory, University of California, One Shields Avenue, Davis, California 95616, USA
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16
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Abstract
The expression of genes for S-adenosylmethionine synthetase (SAMS), which catalyzes the synthesis of S-adenosylmethionine (AdoMet), a major methyl donor in cells, was studied in symbiont-free (D) and symbiont-bearing (xD) amoeba strains to determine the effect of bacterial endosymbionts. The symbionts suppressed the expression of the gene in host xD amoebae, but amoebae still exhibited about half the enzyme activity found in symbiont-free D amoebae. The study was aimed at elucidating mechanisms of the suppression of the amoeba's gene and determining the alternative source for the gene product. Unexpectedly, we found a second sams (sams2) gene in amoebae, which encoded 390 amino acids. Results of experiments measuring SAMS activities and amounts of AdoMet in D and xD amoebae showed that the half SAMS activity found in xD amoebae came from the amoeba's SAMS2 and not from their endosymbionts. The expression of amoeba sams genes was switched from sams1 to sams2 as a result of infection with X-bacteria, raising the possibility that the switch in the expression of sams genes by bacteria plays a role in the development of symbiosis and the host-pathogen interactions. This is the first report showing such a switch in the expression of host sams genes by infecting bacteria.
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Affiliation(s)
- Taeck J Jeon
- Department of Biochemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
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17
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Taylor JC, Markham GD. Conformational dynamics of the active site loop of S-adenosylmethionine synthetase illuminated by site-directed spin labeling. Arch Biochem Biophys 2003; 415:164-71. [PMID: 12831838 DOI: 10.1016/s0003-9861(03)00277-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
S-adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase, methionine adenosyltransferase, a.k.a. MAT) is one of numerous enzymes that have a flexible polypeptide loop that moves to gate access to the active site in a motion that is closely coupled to catalysis. Crystallographic studies of this tetrameric enzyme have shown that the loop is closed in the absence of bound substrates. However, the loop must open to allow substrate binding and a variety of data indicate that the loop is closed during the catalytic steps. Previous kinetic studies indicate that during turnover loop motion occurs on a time scale of 10(-2)s, ca. 10-fold faster than chemical transformations and turnover. Site-directed spin labeling has been used to introduce nitroxide groups at two positions in the loop to illuminate how the motion of the loop is affected by substrate binding. The two loop mutants constructed, G105C and D107C, retain wild type levels of MAT activity; attachment of a methanethiosulfonate spin label to convert the cysteine to the "R1" residue reduced the k(cat) only for the labeled D107R1 form (7-fold). The K(m) value for methionine increased 2- to 4-fold for the cysteine mutants and 2- to 7-fold for the labeled proteins, whereas the K(m) for ATP was changed by at most 2-fold. EPR spectra for both labeled proteins are nearly identical and show the presence of two major spin label environments with rotational diffusion rates differing by approximately 10-fold; the slower rate is ca. 4-fold faster than the estimated protein rotational rate. The spectra are not altered by addition of substrates or products. At both positions the less mobile conformation constitutes ca. 65% of the total species, indicating an equilibrium that only slightly favors one form, that in which the label is more immobilized. The equilibrium constant that relates the two forms is comparable to the equilibrium constant of 1.5 for a conformational change that was previously deduced from the viscosity dependence of the rate of AdoMet formation. The results suggest that the motion of the loop may be an intrinsic property of the protein and not be strictly ligand modulated.
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Affiliation(s)
- John C Taylor
- Fox Chase Cancer Center, Institute for Cancer Research, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
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Abstract
As a result of harboring obligatory bacterial endosymbionts, the xD strain of Amoeba proteus no longer produces its own S-adenosylmethionine synthetase (SAMS). When symbiont-free D amoebae are infected with symbionts (X-bacteria), the amount of amoeba SAMS decreases to a negligible level within four weeks, but about 47% of the SAMS activity, which apparently comes from another source, is still detected. Complete nucleotide sequences of sams genes of D and xD amoebae are presented and show that there are no differences between the two. Long-established xD amoebae contain an intact sams gene and thus the loss of xD amoeba's SAMS is not due to the loss of the gene itself. The open reading frame of the amoeba's sams gene has 1,281 nucleotides, encoding SAMS of 426 amino acids with a mass of 48 kDa and pI of 6.5. The amino acid sequence of amoeba SAMS is longer than the SAMS of other organisms by having an extra internal stretch of 28 amino acids. The 5'-flanking region of amoeba sams contains consensus-binding sites for several transcription factors that are related to the regulation of sams genes in E. coli and yeast. The complete nucleotide sequence of the symbiont's sams gene is also presented. The open reading frame of X-bacteria sams is 1,146 nucleotides long, encoding SAMS of 381 amino acids with a mass of 41 kDa and pI of 6.0. The X-bacteria SAMS has 45% sequence identity with that of A. proteus.
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Affiliation(s)
- Taeck J Jeon
- Department of Biochemistry, University of Tennessee, Knoxville, Tennessee 37996, USA.
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Pérez-Pertejo Y, Reguera RM, Villa H, García-Estrada C, Balaña-Fouce R, Pajares MA, Ordóñez D. Leishmania donovani methionine adenosyltransferase. Role of cysteine residues in the recombinant enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:28-35. [PMID: 12492472 DOI: 10.1046/j.1432-1033.2003.03355.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Methionine adenosyltransferase (MAT, EC 2.5.1.6)-mediated synthesis of S-adenosylmethionine (AdoMet) is a two-step process consisting of the formation of AdoMet and the subsequent cleavage of the tripolyphosphate (PPPi) molecule, a reaction induced, in turn, by AdoMet. The fact that the two activities, AdoMet synthesis and tripolyphosphate hydrolysis, can be measured separately is particularly useful when the site-directed mutagenesis approach is used to determine the functional role of the amino acid residues involved in each. The present report describes the cloning and subsequent functional refolding, using a bacterial expression system, of the MAT gene (GenBank accession number AF179714) from Leishmania donovani, the etiological agent of visceral leishmaniasis. The absolute need to include a sulfhydryl-protection reagent in the refolding buffer for this protein, in conjunction with the rapid inactivation of the functionally refolded protein by N-ethylmaleimide, suggests the presence of crucial cysteine residues in the primary structure of the MAT protein. The seven cysteines in L. donovani MAT were mutated to their isosterical amino acid, serine. The C22S, C44S, C92S and C305S mutants showed a drastic loss of AdoMet synthesis activity compared to the wild type, and the C33S and C47S mutants retained a mere 12% of wild-type MAT activity. C106S mutant activity and kinetics remained unchanged with respect to the wild-type. Cysteine substitutions also modified PPPi cleavage and AdoMet induction. The C22S, C44S and C305S mutants lacked in tripolyphosphatase activity altogether, whereas C33S, C47S and C92S retained low but detectable activity. The behavior of the C92S mutant was notable: its inability to synthesize AdoMet combined with its retention of tripolyphosphatase activity appear to be indicative of the specific involvement of the respective residue in the first step of the MAT reaction.
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Affiliation(s)
- Yolanda Pérez-Pertejo
- Departamento de Farmacología y Toxicología (INTOXCAL), Universidad de León, León, Spain
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Peters GH, Bywater RP. Essential motions in a fungal lipase with bound substrate, covalently attached inhibitor and product. J Mol Recognit 2002; 15:393-404. [PMID: 12501159 DOI: 10.1002/jmr.579] [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: 11/06/2022]
Abstract
As an aid to understanding the influence of dynamic fluctuations during esterolytic catalysis, we follow protein flexibility at three different steps along the catalytic pathway from substrate binding to product clearance via a covalently attached inhibitor, which represents a transition-state mimic. We have applied a classical approach, using molecular dynamics simulations to monitor protein dynamics in the nanosecond regime. We filter out small amplitude fluctuations and focus on the anharmonic contributions to the overall dynamics. This 'essential dynamics' analysis reveals different modes of response along the pathway suggesting that binding, catalysis and product clearance occur along different energy surfaces. Motions in the enzyme with a covalently attached ligand are more complex and occur along several eigenvectors. The magnitudes of the fluctuations in these individual subspaces are significantly smaller than those observed for the substrate and product molecules, indicating that the energy surface is shallow and that a relatively large number of conformational substates are accessible. On the other hand, substrate binding and product release occur at distinct modes of the protein flexibility suggesting that these processes occur along rough energy surfaces with only a few minima. Detailed energetic analyses along the trajectories indicated that in all cases binding is dominated by van der Waals interactions. The carboxylate form of the product is stabilized by a tight hydrogen bond network involving in particular Ser82, which may be a potential cause of product inhibition. Considerations such as these should aid the understanding of mechanisms of substrate, inhibitor or product recognition and could become of importance in the design of new substrates or inhibitors for enzymes.
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Affiliation(s)
- Günther H Peters
- Department of Chemistry, MEMPHYS Center for Biomembrane Physics Technical University of Denmark, Building 206, DK-2800, Lyngby, Denmark
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Lu ZJ, Markham GD. Enzymatic properties of S-adenosylmethionine synthetase from the archaeon Methanococcus jannaschii. J Biol Chem 2002; 277:16624-31. [PMID: 11872742 DOI: 10.1074/jbc.m110456200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
S-Adenosylmethionine synthetase (ATP:l-methionine S-adenosyltransferase, MAT) catalyzes a unique enzymatic reaction that leads to formation of the primary biological alkylating agent. MAT from the hyperthermophilic archaeon Methanococcus jannaschii (MjMAT) is a prototype of the newly discovered archaeal class of MAT proteins that are nearly unrecognizable in sequence when compared with the class that encompasses both the eucaryal and bacterial enzymes. In this study the functional properties of purified recombinant MjMAT have been evaluated. The products of the reaction are AdoMet, PP(i), and P(i); >90% of the P(i) originates from the gamma-phosphoryl group of ATP. The circular dichroism spectrum of the dimeric MjMAT indicates that the secondary structure is more helical than the Escherichia coli counterpart (EcMAT), suggesting a different protein topology. The steady state kinetic mechanism is sequential, with random addition of ATP and methionine; AdoMet is the first product released, followed by release of PP(i) and P(i). The substrate specificity differs remarkably from the previously characterized MATs; the nucleotide binding site has a very broad tolerance of alterations in the adenosine moiety. MjMAT has activity at 70 degrees C comparable with that of EcMAT at 37 degrees C, consistent with the higher temperature habitat of M. jannaschii. The activation energy for AdoMet formation is larger than that for the E. coli MAT-catalyzed reaction, in accord with the notion that enzymes from thermophilic organisms are often more rigid than their mesophilic counterparts. The broad substrate tolerance of this enzyme proffers routes to preparation of novel AdoMet analogs.
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Affiliation(s)
- Zichun J Lu
- Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, Pennsylvania 19111, USA
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Pérez Mato I, Sanchez del Pino MM, Chamberlin ME, Mudd SH, Mato JM, Corrales FJ. Biochemical basis for the dominant inheritance of hypermethioninemia associated with the R264H mutation of the MAT1A gene. A monomeric methionine adenosyltransferase with tripolyphosphatase activity. J Biol Chem 2001; 276:13803-9. [PMID: 11278456 DOI: 10.1074/jbc.m009017200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (AdoMet), the main alkylating agent in living cells. Additionally, in the liver, MAT is also responsible for up to 50% of methionine catabolism. Humans with mutations in the gene MAT1A, the gene that encodes the catalytic subunit of MAT I and III, have decreased MAT activity in liver, which results in a persistent hypermethioninemia without homocystinuria. The hypermethioninemic phenotype associated with these mutations is inherited as an autosomal recessive trait. The only exception is the dominant mild hypermethioninemia associated with a G-A transition at nucleotide 791 of exon VII. This change yields a MAT1A-encoded subunit in which arginine 264 is replaced by histidine. Our results indicate that in the homologous rat enzyme, replacement of the equivalent arginine 265 by histidine (R265H) results in a monomeric MAT with only 0.37% of the AdoMet synthetic activity. However the tripolyphosphatase activity is similar to that found in the wild type (WT) MAT and is inhibited by PP(i). Our in vivo studies demonstrate that the R265H MAT I/III mutant associates with the WT subunit resulting in a dimeric R265H-WT MAT unable to synthesize AdoMet. Tripolyphosphatase activity is maintained in the hybrid MAT, but is not stimulated by methionine and ATP, indicating a deficient binding of the substrates. Our data indicate that the active site for tripolyphosphatase activity is functionally active in the monomeric R265H MAT I/III mutant. Moreover, our results provide a molecular mechanism that might explain the dominant inheritance of the hypermethioninemia associated with the R264H mutation of human MAT I/III.
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Affiliation(s)
- I Pérez Mato
- Division of Hepatology and Gene Therapy, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain
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Metzler DE, Metzler CM, Sauke DJ. The Metabolism of Nitrogen and Amino Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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