1
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Riva D, Orlando M, Rabattoni V, Pollegioni L. On the quaternary structure of human D-3-phosphoglycerate dehydrogenase. Protein Sci 2024; 33:e5089. [PMID: 39012001 PMCID: PMC11250409 DOI: 10.1002/pro.5089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/27/2024] [Accepted: 06/10/2024] [Indexed: 07/17/2024]
Abstract
D-3-phosphoglycerate dehydrogenase (PHGDH) catalyzes the NAD+-dependent conversion of D-3-phospho-glycerate to 3-phosphohydroxypyruvate, the first step in the phosphorylated pathway for L-serine (L-Ser) biosynthesis. L-Ser plays different relevant metabolic roles in eukaryotic cells: alterations in L-Ser metabolism have been linked to serious neurological disorders. The human PHGDH (hPHGDH), showing a homotetrameric state in solution, is made of four domains, among which there are two regulatory domains at the C-terminus: the aspartate kinase-chorismate mutase-tyrA prephenate dehydrogenase (ACT) and allosteric substrate-binding (ASB) domains. The structure of hPHGDH was solved only for a truncated, dimeric form harboring the N-terminal end containing the substrate and the cofactor binding domains. A model ensemble of the tetrameric hPHGDH was generated using AlphaFold coupled with molecular dynamics refinement. By analyzing the inter-subunit interactions at the tetrameric interface, the residues F418, L478, P479, R454, and Y495 were selected and their role was studied by the alanine-scanning mutagenesis approach. The F418A variant modifies the putative ASB, slightly alters the activity, the fraction of protein in the tetrameric state, and the protein stability; it seems relevant in dimers' recognition to yield the tetrameric oligomer. On the contrary, the R454A, L478A, P479A, and Y495A variants (ACT domain) determine a loss of the tetrameric assembly, resulting in low stability and misfolding, triggering the aggregation and hampering the activity. The predicted tetrameric interface seems mediated by residues at the ACT domain, and the tetramer formation seems crucial for proper folding of hPHGDH, which, in turn, is essential for both stability and functionality.
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Affiliation(s)
- Daniele Riva
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Marco Orlando
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
- Present address:
Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| | - Valentina Rabattoni
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Loredano Pollegioni
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
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2
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Lee CM, Hwang Y, Kim M, Park YC, Kim H, Fang S. PHGDH: a novel therapeutic target in cancer. Exp Mol Med 2024; 56:1513-1522. [PMID: 38945960 PMCID: PMC11297271 DOI: 10.1038/s12276-024-01268-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 07/02/2024] Open
Abstract
Serine is a key contributor to the generation of one-carbon units for DNA synthesis during cellular proliferation. In addition, it plays a crucial role in the production of antioxidants that prevent abnormal proliferation and stress in cancer cells. In recent studies, the relationship between cancer metabolism and the serine biosynthesis pathway has been highlighted. In this context, 3-phosphoglycerate dehydrogenase (PHGDH) is notable as a key enzyme that functions as the primary rate-limiting enzyme in the serine biosynthesis pathway, facilitating the conversion of 3-phosphoglycerate to 3-phosphohydroxypyruvate. Elevated PHGDH activity in diverse cancer cells is mediated through genetic amplification, posttranslational modification, increased transcription, and allosteric regulation. Ultimately, these characteristics allow PHGDH to not only influence the growth and progression of cancer but also play an important role in metastasis and drug resistance. Consequently, PHGDH has emerged as a crucial focal point in cancer research. In this review, the structural aspects of PHGDH and its involvement in one-carbon metabolism are investigated, and PHGDH is proposed as a potential therapeutic target in diverse cancers. By elucidating how PHGDH expression promotes cancer growth, the goal of this review is to provide insight into innovative treatment strategies. This paper aims to reveal how PHGDH inhibitors can overcome resistance mechanisms, contributing to the development of effective cancer treatments.
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Affiliation(s)
- Chae Min Lee
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yeseong Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Minki Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ye-Chan Park
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Chronic Intractable Disease for Systems Medicine Research Center, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Severance Institute for Vascular and Metabolic Research, Yonsei University College of Medicine, Seoul, Republic of Korea.
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3
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Xu G, Zhang X, Xiao W, Shi J, Xu Z. Production of L-serine and its derivative L-cysteine from renewable feedstocks using Corynebacterium glutamicum: advances and perspectives. Crit Rev Biotechnol 2024; 44:448-461. [PMID: 36944486 DOI: 10.1080/07388551.2023.2170863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/05/2023] [Indexed: 03/23/2023]
Abstract
L-serine and its derivative L-cysteine have broad industrial applications, and their direct fermentative production from renewable biomass is gaining increasing attention. Corynebacterium glutamicum is an extensively studied and well-established industrial microorganism, which is a predominant microbial host for producing amino acids. In this review, updated information on the genetics and molecular mechanisms underlying L-serine and L-cysteine production using C. glutamicum is presented, including their synthesis and degradation pathways, and other intracellular processes related to their production, as well as the mechanisms underlying substrate import and product export are also analyzed. Furthermore, metabolic strategies for strain improvement are systematically discussed, and conclusions and future perspectives for bio-based L-serine and L-cysteine production using C. glutamicum are presented. This review can provide a thorough understanding of L-serine and L-cysteine metabolic pathways to facilitate metabolic engineering modifications of C. glutamicum and development of more efficient industrial fermentation processes for L-serine and L-cysteine production.
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Affiliation(s)
- Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, China
| | - Xiaomei Zhang
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, China
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Jiangnan University, Wuxi, China
| | - Wenhan Xiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, China
| | - Jinsong Shi
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, China
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Jiangnan University, Wuxi, China
| | - Zhenghong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, China
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4
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Marchesani F, Comani VB, Bruno S, Mozzarelli A, Carcelli M, Pollegioni L, Caldinelli L, Peracchi A, Campanini B. Effect of l-serine and magnesium ions on the functional properties of human phosphoserine phosphatase and its pathogenetic variants. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167034. [PMID: 38278334 DOI: 10.1016/j.bbadis.2024.167034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
L-Ser supply in the central nervous system of mammals mostly relies on its endogenous biosynthesis by the phosphorylated pathway (PP). Defects in any of the three enzymes operating in the pathway result in a group of neurometabolic diseases collectively known as serine deficiency disorders (SDDs). Phosphoserine phosphatase (PSP) catalyzes the last, irreversible step of the PP. Here we investigated in detail the role of physiological modulators of human PSP activity and the properties of three natural PSP variants (A35T, D32N and M52T) associated with SDDs. Our results, partially contradicting previous reports, indicate that: i. PSP is almost fully saturated with Mg2+ under physiological conditions and fluctuations in Mg2+ and Ca2+ concentrations are unlikely to play a modulatory role on PSP activity; ii. Inhibition by L-Ser, albeit at play on the isolated PSP, does not exert any effect on the flux through the PP unless the enzyme activity is severely impaired by inactivating substitutions; iii. The so-far poorly investigated A35T substitution was the most detrimental, with a 50-fold reduction in catalytic efficiency, and a reduction in thermal stability (as well as an increase in the IC50 for L-Ser). The M52T substitution had similar, but milder effects, while the D32N variant behaved like the wild-type enzyme. iv. Predictions of the structural effects of the A35T and M52T substitutions with ColabFold suggest that they might affect the structure of the flexible helix-loop region.
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Affiliation(s)
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
| | | | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Loredano Pollegioni
- The Protein Factory 2.0, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Laura Caldinelli
- The Protein Factory 2.0, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; Biopharmanet-TEC, University of Parma, 43124 Parma, Italy.
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5
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Murtas G, Zerbini E, Rabattoni V, Motta Z, Caldinelli L, Orlando M, Marchesani F, Campanini B, Sacchi S, Pollegioni L. Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels. Biofactors 2024; 50:181-200. [PMID: 37650587 DOI: 10.1002/biof.2002] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
In the brain, the non-essential amino acid L-serine is produced through the phosphorylated pathway (PP) starting from the glycolytic intermediate 3-phosphoglycerate: among the different roles played by this amino acid, it can be converted into D-serine and glycine, the two main co-agonists of NMDA receptors. In humans, the enzymes of the PP, namely phosphoglycerate dehydrogenase (hPHGDH, which catalyzes the first and rate-limiting step of this pathway), 3-phosphoserine aminotransferase, and 3-phosphoserine phosphatase are likely organized in the cytosol as a metabolic assembly (a "serinosome"). The hPHGDH deficiency is a pathological condition biochemically characterized by reduced levels of L-serine in plasma and cerebrospinal fluid and clinically identified by severe neurological impairment. Here, three single-point variants responsible for hPHGDH deficiency and Neu-Laxova syndrome have been studied. Their biochemical characterization shows that V261M, V425M, and V490M substitutions alter either the kinetic (both maximal activity and Km for 3-phosphoglycerate in the physiological direction) and the structural properties (secondary, tertiary, and quaternary structure, favoring aggregation) of hPHGDH. All the three variants have been successfully ectopically expressed in U251 cells, thus the pathological effect is not due to hindered expression level. At the cellular level, mistargeting and aggregation phenomena have been observed in cells transiently expressing the pathological protein variants, as well as a reduced L-serine cellular level. Previous studies demonstrated that the pharmacological supplementation of L-serine in hPHGDH deficiencies could ameliorate some of the related symptoms: our results now suggest the use of additional and alternative therapeutic approaches.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elena Zerbini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | | | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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6
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Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023; 22:161. [PMID: 37612753 PMCID: PMC10464499 DOI: 10.1186/s12934-023-02178-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.
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Affiliation(s)
- Sadia Naz
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Islamabad, 22060, Pakistan
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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7
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Marchesani F, Zangelmi E, Murtas G, Costanzi E, Ullah R, Peracchi A, Bruno S, Pollegioni L, Mozzarelli A, Storici P, Campanini B. L-Serine Biosynthesis in The Human Central Nervous System: Structure and Function of Phosphoserine Aminotransferase. Protein Sci 2023; 32:e4609. [PMID: 36851825 PMCID: PMC10031235 DOI: 10.1002/pro.4609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Organisms from all kingdoms of life synthesize L-serine from 3-phosphoglycerate through the phosphorylated pathway, a three-step diversion of glycolysis. Phosphoserine aminotransferase (PSAT) catalyzes the intermediate step, the pyridoxal 5'-phosphate-dependent transamination of 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and α-ketoglutarate. PSAT is particularly relevant in the central nervous system of mammals because L-serine is the metabolic precursor of D-serine, cysteine, phospholipids, and nucleotides. Several mutations in the human psat gene have been linked to serine deficiency disorders, characterized by severe neurological symptoms. Furthermore, PSAT is overexpressed in many tumors and this overexpression has been associated with poor clinical outcomes. Here, we report the detailed functional and structural characterization of the recombinant human PSAT. The reaction catalyzed by PSAT is reversible, with an equilibrium constant of about 10, and the enzyme is very efficient, with a kcat /Km of 5.9 × 106 M-1 s-1 , thus contributing in driving the pathway towards the products despite the extremely unfavorable first step catalyzed by 3-phosphoglycerate dehydrogenase. The three-dimensional X-ray crystal structure of PSAT was solved in the substrate-free as well as in the O-phosphoserine-bound forms. Both structures contain eight protein molecules in the asymmetric unit, arranged in four dimers, with a bound cofactor in each subunit. In the substrate-free form, the active site of PSAT contains a sulfate ion that, in the substrate-bound form, is replaced by the phosphate group of O-phosphoserine. Interestingly, fast crystal soaking used to produce the substrate-bound form allowed the trapping of different intermediates along the catalytic cycle. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Raheem Ullah
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
- Present address: Structural Biology Lab, NIBGE, Faisalabad, Pakistan
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Paola Storici
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
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8
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Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in Escherichia coli and Pantoea ananatis Encoded by ydiJ. Microorganisms 2022; 10:microorganisms10091766. [PMID: 36144368 PMCID: PMC9504171 DOI: 10.3390/microorganisms10091766] [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: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
In E. coli and P. ananatis, L-serine biosynthesis is initiated by the action of D-3-phosphoglycerate dehydrogenase (SerA), which converts D-3-phosphoglycerate into 3-phosphohydroxypyruvate. SerA can concomitantly catalyze the production of D-2-hydroxyglutarate (D-2-HGA) from 2-ketoglutarate by oxidizing NADH to NAD+. Several bacterial D-2-hydroxyglutarate dehydrogenases (D2HGDHs) have recently been identified, which convert D-2-HGA back to 2-ketoglutarate. However, knowledge about the enzymes that can metabolize D-2-HGA is lacking in bacteria belonging to the Enterobacteriaceae family. We found that ydiJ encodes novel D2HGDHs in P. ananatis and E. coli, which were assigned as D2HGDHPa and D2HGDHEc, respectively. Inactivation of ydiJ in P. ananatis and E. coli led to the significant accumulation of D-2-HGA. Recombinant D2HGDHEc and D2HGDHPa were purified to homogeneity and characterized. D2HGDHEc and D2HGDHPa are homotetrameric with a subunit molecular mass of 110 kDa. The pH optimum was 7.5 for D2HGDHPa and 8.0 for D2HGDHEc. The Km for D-2-HGA was 208 μM for D2HGDHPa and 83 μM for D2HGDHEc. The enzymes have strict substrate specificity towards D-2-HGA and displayed maximal activity at 45 °C. Their activity was completely inhibited by 0.5 mM Mn2+, Ni2+ or Co2+. The discovery of a novel family of D2HGDHs may provide fundamental information for the metabolic engineering of microbial chassis with desired properties.
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9
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Saez-Jimenez V, Scrima S, Lambrughi M, Papaleo E, Mapelli V, Engqvist MKM, Olsson L. Directed Evolution of ( R)-2-Hydroxyglutarate Dehydrogenase Improves 2-Oxoadipate Reduction by 2 Orders of Magnitude. ACS Synth Biol 2022; 11:2779-2790. [PMID: 35939387 PMCID: PMC9396657 DOI: 10.1021/acssynbio.2c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Pathway engineering is commonly employed to improve the
production
of various metabolites but may incur in bottlenecks due to the low
catalytic activity of a particular reaction step. The reduction of
2-oxoadipate to (R)-2-hydroxyadipate is a key reaction
in metabolic pathways that exploit 2-oxoadipate conversion via α-reduction
to produce adipic acid, an industrially important platform chemical.
Here, we engineered (R)-2-hydroxyglutarate dehydrogenase
from Acidaminococcus fermentans (Hgdh)
with the aim of improving 2-oxoadipate reduction. Using a combination
of computational analysis, saturation mutagenesis, and random mutagenesis,
three mutant variants with a 100-fold higher catalytic efficiency
were obtained. As revealed by rational analysis of the mutations found
in the variants, this improvement could be ascribed to a general synergistic
effect where mutation A206V played a key role since it boosted the
enzyme’s activity by 4.8-fold. The Hgdh variants with increased
activity toward 2-oxoadipate generated within this study pave the
way for the bio-based production of adipic acid.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Simone Scrima
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Martin K M Engqvist
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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10
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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11
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Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants. Biochem J 2021; 478:2217-2232. [PMID: 34032263 PMCID: PMC8238522 DOI: 10.1042/bcj20210191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022]
Abstract
The phosphorylated pathway of serine biosynthesis is initiated with 3-phosphoglycerate dehydrogenase (PGDH). The liverwort Marchantia polymorpha possesses an amino acid-sensitive MpPGDH which is inhibited by l-serine and activated by five proteinogenic amino acids, while the eudicot Arabidopsis thaliana has amino acid-sensitive AtPGDH1 and AtPGDH3 as well as amino acid-insensitive AtPGDH2. In this study, we analyzed PGDH isozymes of the representative land plants: the monocot Oryza sativa (OsPGDH1–3), basal angiosperm Amborella trichopoda (AmtriPGDH1–2), and moss Physcomitrium (Physcomitrella) patens (PpPGDH1–4). We demonstrated that OsPGDH1, AmtriPGDH1, PpPGDH1, and PpPGDH3 were amino acid-sensitive, whereas OsPGDH2, OsPGDH3, AmtriPGDH2, PpPGDH2, and PpPGDH4 were either sensitive to only some of the six effector amino acids or insensitive to all effectors. This indicates that PGDH sensitivity to effectors has been diversified among isozymes and that the land plant species examined, except for M. polymorpha, possess different isozyme types in terms of regulation. Phylogenetic analysis suggested that the different sensitivities convergently evolved in the bryophyte and angiosperm lineages. Site-directed mutagenesis of AtPGDH1 revealed that Asp538 and Asn556 residues in the ACT domain are involved in allosteric regulation by the effectors. These findings provide insight into the evolution of PGDH isozymes, highlighting the functional diversification of allosteric regulation in land plants.
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Murtas G, Marcone GL, Peracchi A, Zangelmi E, Pollegioni L. Biochemical and Biophysical Characterization of Recombinant Human 3-Phosphoglycerate Dehydrogenase. Int J Mol Sci 2021; 22:ijms22084231. [PMID: 33921788 PMCID: PMC8073719 DOI: 10.3390/ijms22084231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 01/18/2023] Open
Abstract
The human enzyme D-3-phosphoglycerate dehydrogenase (hPHGDH) catalyzes the reversible dehydrogenation of 3-phosphoglycerate (3PG) into 3-phosphohydroxypyruvate (PHP) using the NAD+/NADH redox cofactor, the first step in the phosphorylated pathway producing L-serine. We focused on the full-length enzyme that was produced in fairly large amounts in E. coli cells; the effect of pH, temperature and ligands on hPHGDH activity was studied. The forward reaction was investigated on 3PG and alternative carboxylic acids by employing two coupled assays, both removing the product PHP; 3PG was by far the best substrate in the forward direction. Both PHP and α-ketoglutarate were efficiently reduced by hPHGDH and NADH in the reverse direction, indicating substrate competition under physiological conditions. Notably, neither PHP nor L-serine inhibited hPHGDH, nor did glycine and D-serine, the coagonists of NMDA receptors related to L-serine metabolism. The investigation of NADH and phosphate binding highlights the presence in solution of different conformations and/or oligomeric states of the enzyme. Elucidating the biochemical properties of hPHGDH will enable the identification of novel approaches to modulate L-serine levels and thus to reduce cancer progression and treat neurological disorders.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; (G.L.M.); (L.P.)
- Correspondence:
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; (G.L.M.); (L.P.)
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (A.P.); (E.Z.)
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (A.P.); (E.Z.)
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; (G.L.M.); (L.P.)
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13
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A retrospective overview of PHGDH and its inhibitors for regulating cancer metabolism. Eur J Med Chem 2021; 217:113379. [PMID: 33756126 DOI: 10.1016/j.ejmech.2021.113379] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 11/20/2022]
Abstract
Emerging evidence suggests that cancer metabolism is closely associated to the serine biosynthesis pathway (SSP), in which glycolytic intermediate 3-phosphoglycerate is converted to serine through a three-step enzymatic transformation. As the rate-limiting enzyme in the first step of SSP, phosphoglycerate dehydrogenase (PHGDH) is overexpressed in various diseases, especially in cancer. Genetic knockdown or silencing of PHGDH exhibits obvious anti-tumor response both in vitro and in vivo, demonstrating that PHGDH is a promising drug target for cancer therapy. So far, several types of PHGDH inhibitors have been identified as a significant and newly emerging option for anticancer treatment. Herein, this comprehensive review summarizes the recent achievements of PHGDH, especially its critical role in cancer and the development of PHGDH inhibitors in drug discovery.
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14
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Yamamoto K, Mohri S, Furuya S. D-3-phosphoglycerate dehydrogenase from the silkworm Bombyx mori: Identification, functional characterization, and expression. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:e21751. [PMID: 33058282 DOI: 10.1002/arch.21751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
D-3-phosphoglycerate dehydrogenase (PHGDH) is a key enzyme involved in the synthesis of l-serine. Despite the high serine content in silk proteins and the crucial role of PHGDH in serine biosynthesis, PHGDH has not been described in silkworms to date. Here, we identified PHGDH in the silkworm Bombyx mori and evaluated its biochemical properties. On the basis of the amino acid sequence and phylogenetic tree, this PHGDH has been categorized as a new type and designated as bmPHGDH. The recombinant bmPHGDH was overexpressed and purified to homogeneity. Kinetic studies revealed that PHGDH uses NADH as a coenzyme to reduce phosphohydroxypyruvate. High expression levels of bmphgdh messenger RNA (mRNA) were observed in the middle part of the silk gland and midgut in a standard strain of silkworm. Moreover, a sericin-deficient silkworm strain displayed reduced expression of bmphgdh mRNA. These findings indicate that bmPHGDH might play a crucial role in the provision of l-serine in the larva of B. mori.
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Affiliation(s)
- Kohji Yamamoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Shinya Mohri
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Shigeki Furuya
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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15
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Murtas G, Marcone GL, Sacchi S, Pollegioni L. L-serine synthesis via the phosphorylated pathway in humans. Cell Mol Life Sci 2020; 77:5131-5148. [PMID: 32594192 PMCID: PMC11105101 DOI: 10.1007/s00018-020-03574-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
L-serine is a nonessential amino acid in eukaryotic cells, used for protein synthesis and in producing phosphoglycerides, glycerides, sphingolipids, phosphatidylserine, and methylenetetrahydrofolate. Moreover, L-serine is the precursor of two relevant coagonists of NMDA receptors: glycine (through the enzyme serine hydroxymethyltransferase), which preferentially acts on extrasynaptic receptors and D-serine (through the enzyme serine racemase), dominant at synaptic receptors. The cytosolic "phosphorylated pathway" regulates de novo biosynthesis of L-serine, employing 3-phosphoglycerate generated by glycolysis and the enzymes 3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase (the latter representing the irreversible step). In the human brain, L-serine is primarily found in glial cells and is supplied to neurons for D-serine synthesis. Serine-deficient patients show severe neurological symptoms, including congenital microcephaly, psychomotor retardation, and intractable seizures, thus highlighting the relevance of de novo production of this amino acid in brain development and morphogenesis. Indeed, the phosphorylated pathway is strictly linked to cancer. Moreover, L-serine has been suggested as a ready-to-use treatment, as also recently proposed for Alzheimer's disease. Here, we present our current state of knowledge concerning the three mammalian enzymes of the phosphorylated pathway and known mutations related to pathological conditions: although the structure of these enzymes has been solved, how enzyme activity is regulated remains largely unknown. We believe that an in-depth investigation of these enzymes is crucial to identify the molecular mechanisms involved in modulating concentrations of the serine enantiomers and for studying the interplay between glial and neuronal cells and also to determine the most suitable therapeutic approach for various diseases.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy.
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16
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Maugard M, Vigneron PA, Bolaños JP, Bonvento G. l-Serine links metabolism with neurotransmission. Prog Neurobiol 2020; 197:101896. [PMID: 32798642 DOI: 10.1016/j.pneurobio.2020.101896] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/20/2020] [Accepted: 08/09/2020] [Indexed: 12/12/2022]
Abstract
Brain energy metabolism is often considered as a succession of biochemical steps that metabolize the fuel (glucose and oxygen) for the unique purpose of providing sufficient ATP to maintain the huge information processing power of the brain. However, a significant fraction (10-15 %) of glucose is shunted away from the ATP-producing pathway (oxidative phosphorylation) and may be used to support other functions. Recent studies have pointed to the marked compartmentation of energy metabolic pathways between neurons and glial cells. Here, we focused our attention on the biosynthesis of l-serine, a non-essential amino acid that is formed exclusively in glial cells (mostly astrocytes) by re-routing the metabolic fate of the glycolytic intermediate, 3-phosphoglycerate (3PG). This metabolic pathway is called the phosphorylated pathway and transforms 3PG into l-serine via three enzymatic reactions. We first compiled the available data on the mechanisms that regulate the flux through this metabolic pathway. We then reviewed the current evidence that is beginning to unravel the roles of l-serine both in the healthy and diseased brain, leading to the notion that this specific metabolic pathway connects glial metabolism with synaptic activity and plasticity. We finally suggest that restoring astrocyte-mediated l-serine homeostasis may provide new therapeutic strategies for brain disorders.
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Affiliation(s)
- Marianne Maugard
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Pierre-Antoine Vigneron
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Juan P Bolaños
- Institute of Functional Biology and Genomics (IBFG), Universidad de Salamanca, CSIC, Salamanca, Spain; Centro de Investigación Biomédica en Red sobre Fragilidad y Envejecimiento Saludable (CIBERFES), Institute of Biomedical Research of Salamanca, 37007, Salamanca, Spain
| | - Gilles Bonvento
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France.
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Li AM, Ye J. The PHGDH enigma: Do cancer cells only need serine or also a redox modulator? Cancer Lett 2020; 476:97-105. [PMID: 32032680 PMCID: PMC7092752 DOI: 10.1016/j.canlet.2020.01.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/29/2022]
Abstract
Upregulation of serine biosynthesis pathway activity is an increasingly apparent feature of many cancers. Most notably, the first rate-limiting enzyme of the pathway, phosphoglycerate dehydrogenase (PHGDH), is genomically amplified in some melanomas and breast cancers and can be transcriptionally regulated by various tumor suppressors and oncogenes. Yet emerging evidence suggests that serine-in particular, serine biosynthetic pathway activity-may promote cancer in ways beyond providing the building blocks to support cell proliferation. Here, we summarize how mammalian cells tightly control serine synthesis before discussing alternate ways in which increased serine synthetic flux through PHGDH may benefit cancer cells, such as maintenance of TCA cycle flux through alpha-ketoglutarate (αKG) and modulation of cellular redox balance. We will also provide an overview of the current landscape of therapeutics targeting serine synthesis and offer a perspective on future strategies.
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Affiliation(s)
- Albert M Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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18
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Zhao X, Fu J, Du J, Xu W. The Role of D-3-Phosphoglycerate Dehydrogenase in Cancer. Int J Biol Sci 2020; 16:1495-1506. [PMID: 32226297 PMCID: PMC7097917 DOI: 10.7150/ijbs.41051] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Serine, a non-essential amino acid, can be imported from the extracellular environment by transporters and de novo synthesized from glycolytic 3-phosphoglycerate (3-PG) in the serine biosynthetic pathway (SSP). It has been reported that active serine synthesis might be needed for the synthesis of proteins, lipids, and nucleotides and the balance of folate metabolism and redox homeostasis, which are necessary for cancer cell proliferation. Human D-3-phosphoglycerate dehydrogenase (PHGDH), the first and only rate-limiting enzyme in the de novo serine biosynthetic pathway, catalyzes the oxidation of 3-PG derived from glycolysis to 3-phosphohydroxypyruvate (3-PHP). PHGDH is highly expressed in tumors as a result of amplification, transcription, or its degradation and stability alteration, which dysregulates the serine biosynthesis pathway via metabolic enzyme activity to nourish tumors. And some recent researches reported that PHGDH promoted some tumors growth via non-metabolic way by upregulating target cancer-promoting genes. In this article, we reviewed the type, structure, expression and inhibitors of PHGDH, as well as the role it plays in cancer and tumor resistance to chemotherapy.
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Affiliation(s)
- Xiaoya Zhao
- Central Laboratory, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, China
| | - Jianfei Fu
- Department of Medical Oncology, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, China
| | - Jinlin Du
- Department of Colorectal Surgery, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, China
| | - Wenxia Xu
- Central Laboratory, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, China
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López Grueso MJ, Tarradas Valero RM, Carmona-Hidalgo B, Lagal Ruiz DJ, Peinado J, McDonagh B, Requejo Aguilar R, Bárcena Ruiz JA, Padilla Peña CA. Peroxiredoxin 6 Down-Regulation Induces Metabolic Remodeling and Cell Cycle Arrest in HepG2 Cells. Antioxidants (Basel) 2019; 8:E505. [PMID: 31652719 PMCID: PMC6912460 DOI: 10.3390/antiox8110505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/29/2022] Open
Abstract
Peroxiredoxin 6 (Prdx6) is the only member of 1-Cys subfamily of peroxiredoxins in human cells. It is the only Prdx acting on phospholipid hydroperoxides possessing two additional sites with phospholipase A2 (PLA2) and lysophosphatidylcholine-acyl transferase (LPCAT) activities. There are contrasting reports on the roles and mechanisms of multifunctional Prdx6 in several pathologies and on its sensitivity to, and influence on, the redox environment. We have down-regulated Prdx6 with specific siRNA in hepatoblastoma HepG2 cells to study its role in cell proliferation, redox homeostasis, and metabolic programming. Cell proliferation and cell number decreased while cell volume increased; import of glucose and nucleotide biosynthesis also diminished while polyamines, phospholipids, and most glycolipids increased. A proteomic quantitative analysis suggested changes in membrane arrangement and vesicle trafficking as well as redox changes in enzymes of carbon and glutathione metabolism, pentose-phosphate pathway, citrate cycle, fatty acid metabolism, biosynthesis of aminoacids, and Glycolysis/Gluconeogenesis. Specific redox changes in Hexokinase-2 (HK2), Prdx6, intracellular chloride ion channel-1 (CLIC1), PEP-carboxykinase-2 (PCK2), and 3-phosphoglycerate dehydrogenase (PHGDH) are compatible with the metabolic remodeling toward a predominant gluconeogenic flow from aminoacids with diversion at 3-phospohglycerate toward serine and other biosynthetic pathways thereon and with cell cycle arrest at G1/S transition.
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Affiliation(s)
- María José López Grueso
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
| | | | - Beatriz Carmona-Hidalgo
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
| | - Daniel José Lagal Ruiz
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
| | - José Peinado
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14004 Córdoba, Spain.
| | - Brian McDonagh
- Department of Physiology, School of Medicine, NUI Galway, H91 TK33 Galway, Ireland.
| | - Raquel Requejo Aguilar
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14004 Córdoba, Spain.
| | - José Antonio Bárcena Ruiz
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14004 Córdoba, Spain.
| | - Carmen Alicia Padilla Peña
- Department of Biochemistry and Molecular Biology, University of Córdoba, 14074 Córdoba, Spain.
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14004 Córdoba, Spain.
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20
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Xu XL, Grant GA. Determinants of substrate specificity in D-3-phosphoglycerate dehydrogenase. Conversion of the M. tuberculosis enzyme from one that does not use α-ketoglutarate as a substrate to one that does. Arch Biochem Biophys 2019; 671:218-224. [PMID: 31344342 DOI: 10.1016/j.abb.2019.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/09/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
Abstract
d-3-Phosphoglycerate dehydrogenase (PGDH) converts d-3-phosphoglycerate (PGA) to phosphohydroxypyruvate (PHP) in the first step of l-serine biosynthesis. This reaction is reversible, and some PGDHs are capable of using α-ketoglutarate (αKG) instead of PHP in the reverse direction to produce α-hydroxyglutarate. The enzymes so far shown to have this ability are Type II PGDHs, suggesting that this may be a common feature of the Type II enzymes. Type I PGDHs examined so far do not share this feature. Inspection of PGDH sequences shows that a GCFCI … WXKX motif is commonly found in Type II PGDHs while a GRAGT … WXRX motif is commonly associated with Type I PGDHs. The removal of the cationic side chain at the first position shown above in the Type I PGDH from Mycobacterium tuberculosis converts it to an enzyme capable of using αKG where the native enzyme is not. It also produces an enzyme that regenerates NAD+ in the forward reaction when coupled to phosphoserine aminotransferase, as was previously shown for E. coli PGDH. Substitution of an arginyl residue for a lysyl residue at the second position of ecPGDH, decreases the kcat/Km of the enzyme by approximately 50-fold when using αKG, but only approximately 3-fold when using PHP. This suggests that a PGDH dependent cycle that conserves NAD+ in E. coli may be operative in many other organisms expressing the GCFCI … WXKX motif.
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Affiliation(s)
- Xiao Lan Xu
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, 63110, MO, United States
| | - Gregory A Grant
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, 63110, MO, United States; Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, 63110, MO, United States.
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21
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Okuda J, Nagata S, Yasuda M, Suezawa C. Validating the inhibitory effects of d- and l-serine on the enzyme activity of d-3-phosphoglycerate dehydrogenases that are purified from Pseudomonas aeruginosa, Escherichia coli and human colon. Gut Pathog 2019; 11:35. [PMID: 31303896 PMCID: PMC6600881 DOI: 10.1186/s13099-019-0315-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/21/2019] [Indexed: 11/10/2022] Open
Abstract
Background We previously demonstrated that the serA gene is associated with bacterial pathogenicity, including bacterial penetration through the Caco-2 cell monolayers, bacterial motility, bacterial adherence, and fly mortality. l-Serine is known to inhibit the d-3-phosphoglycerate dehydrogenase (PGDH) activity of the SerA protein, and it significantly reduced the bacterial pathogenicity as described above. We also demonstrated that in a PGDH assay using crude extracts isolated from overnight cultures of E. coli overexpressing the P. aeruginosa serA gene, l-serine inhibited the PGDH activity of the SerA protein. The basal PGDH activity of the negative control strain was high, presumably due to contamination of unknown proteins in the crude extracts. Therefore, to further confirm the direct inhibition of PGDH activity of P. aeruginosa SerA by l-serine, we purified and characterized the PGDH from P. aeruginosa and compared it with the previously characterized PGDHs from E. coli, and the human colon as controls. Results Optimum pH and ionic strength of the purified PGDHs were different depending on the three species; optimal activity of P. aeruginosa PGDH was at pH 7.5 with 50-100 mM Tris-HCl, E. coli PGDH was at pH 8.5 with 100-200 mM Tris-HCl, and human PGDH was at pH 9.0 with 100-200 mM Tris-HCl. The addition of l-serine reduced the activity of PGDH from P. aeruginosa and E. coli, but not the PGDH from human colon. The median inhibitory concentration (IC50) of l-serine was 630 μM for P. aeruginosa and 250 μM for E. coli, while IC50 of d-serine was much higher than that of l-serine; 76 mM in P. aeruginosa PGDH and 45 mM in E. coli PGDH. Conclusions These results suggest that l-serine significantly repressed P. aeruginosa pathogenicity through direct inhibition of the PGDH activity, but was not able to inhibit the human PGDH activity. Oral administration of l-serine to compromised hosts might interfere with bacterial translocation and prevent gut-derived sepsis caused by P. aeruginosa through inhibition of the function of the serA gene product.
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Affiliation(s)
- Jun Okuda
- Division of Microbiology, Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, Japan
| | - Syouya Nagata
- Division of Microbiology, Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, Japan
| | - Masashi Yasuda
- Division of Microbiology, Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, Japan
| | - Chigusa Suezawa
- Division of Microbiology, Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, Japan
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22
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Mullarky E, Xu J, Robin AD, Huggins DJ, Jennings A, Noguchi N, Olland A, Lakshminarasimhan D, Miller M, Tomita D, Michino M, Su T, Zhang G, Stamford AW, Meinke PT, Kargman S, Cantley LC. Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells. Bioorg Med Chem Lett 2019; 29:2503-2510. [PMID: 31327531 DOI: 10.1016/j.bmcl.2019.07.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 12/11/2022]
Abstract
Cancer cells reprogram their metabolism to support growth and to mitigate cellular stressors. The serine synthesis pathway has been identified as a metabolic pathway frequently altered in cancers and there has been considerable interest in developing pharmacological agents to target this pathway. Here, we report a series of indole amides that inhibit human 3-phosphoglycerate dehydrogenase (PHGDH), the enzyme that catalyzes the first committed step of the serine synthesis pathway. Using X-ray crystallography, we show that the indole amides bind the NAD+ pocket of PHGDH. Through structure-based optimization we were able to develop compounds with low nanomolar affinities for PHGDH in an enzymatic IC50 assay. In cellular assays, the most potent compounds inhibited de novo serine synthesis with low micromolar to sub-micromolar activities and these compounds successfully abrogated the proliferation of cancer cells in serine free media. The indole amide series reported here represent an important improvement over previously published PHGDH inhibitors as they are markedly more potent and their mechanism of action is better defined.
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Affiliation(s)
- Edouard Mullarky
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, United States; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, United States.
| | - Jiayi Xu
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States
| | - Anita D Robin
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, United States; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, United States
| | - David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States
| | | | - Naoyoshi Noguchi
- Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd., Shonan Research Center, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Andrea Olland
- Xtal Biostructures, 12 Michigan Drive, Natick, MA 01760, United States
| | | | - Michael Miller
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States
| | - Daisuke Tomita
- Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd., Shonan Research Center, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States
| | - Taojunfeng Su
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY 10021, United States
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY 10021, United States
| | - Andrew W Stamford
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States
| | - Peter T Meinke
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States
| | - Stacia Kargman
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, NY 10021, United States
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, United States; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, United States.
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23
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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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24
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Haufroid M, Mirgaux M, Leherte L, Wouters J. Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:592-604. [DOI: 10.1107/s2059798319006867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/13/2019] [Indexed: 11/10/2022]
Abstract
The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine. It is directly involved in the biosynthesis of other important metabolites such as glycine and D-serine (a neuromodulator). hPSP is involved in the survival mechanism of cancer cells and has recently been found to be an essential biomarker. Here, three new high-resolution crystal structures of hPSP (1.5–2.0 Å) in complexes with phosphoserine and with serine, which are the substrate and the product of the reaction, respectively, and in complex with a noncleavable substrate analogue (homocysteic acid) are presented. New types of interactions take place between the enzyme and its ligands. Moreover, the loop involved in the open/closed state of the enzyme is fully refined in a totally unfolded conformation. This loop is further studied through molecular-dynamics simulations. Finally, all of these analyses allow a more complete reaction mechanism for this enzyme to be proposed which is consistent with previous publications on the subject.
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25
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Haufroid M, Wouters J. Targeting the Serine Pathway: A Promising Approach against Tuberculosis? Pharmaceuticals (Basel) 2019; 12:E66. [PMID: 31052291 PMCID: PMC6630544 DOI: 10.3390/ph12020066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis is still the leading cause of death by a single infectious agent. Effective chemotherapy has been used and improved since the 1950s, but strains resistant to this therapy and most antibacterial drugs on the market are emerging. Only 10 new drugs are in clinical trials, and two of them have already demonstrated resistance. This paper gives an overview of current treatment options against tuberculosis and points out a promising approach of discovering new effective drugs. The serine production pathway is composed of three enzymes (SerA1, SerC and SerB2), which are considered essential for bacterial growth, and all of them are considered as a therapeutic drug target. Their crystal structure are described and essential regulatory domains pointed out. Sequence alignment with similar enzymes in other host would help to identify key residues to target in order to achieve selective inhibition. Currently, only inhibitors of SerB2 are described in the literature. However, inhibitors of human enzymes are discussed, and could be used as a good starting point for a drug discovery program. The aim of this paper is to give some guidance for the design of new hits for every enzyme in this pathway.
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Affiliation(s)
- Marie Haufroid
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Medicine and Drug Innovation Center (Namedic), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), B-5000 Namur, Belgium.
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Medicine and Drug Innovation Center (Namedic), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), B-5000 Namur, Belgium.
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26
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Opoku-Temeng C, Onyedibe KI, Aryal UK, Sintim HO. Proteomic analysis of bacterial response to a 4-hydroxybenzylidene indolinone compound, which re-sensitizes bacteria to traditional antibiotics. J Proteomics 2019; 202:103368. [PMID: 31028946 DOI: 10.1016/j.jprot.2019.04.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/21/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023]
Abstract
Halogenated 4-hydroxybenzylidene indolinones have been shown to re-sensitize methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE) to methicillin and vancomycin respectively. The mechanism of antibiotic re-sensitization was however not previously studied. Here, we probe the scope of antibiotic re-sensitization and present the global proteomics analysis of S. aureus treated with GW5074, a 4-hydroxybenzylidene indolinone compound. With a minimum inhibitory concentration (MIC) of 8 μg/mL against S. aureus, GW5074 synergized with beta-lactam antibiotics like ampicillin, carbenicillin and cloxacillin, the DNA synthesis inhibitor, ciprofloxacin, the protein synthesis inhibitor, gentamicin and the folate acid synthesis inhibitor, trimethoprim. Global proteomics analysis revealed that GW5074 treatment resulted in significant downregulation of enzymes involved in the purine biosynthesis. S. aureus proteins involved in amino acid metabolism and peptide transport were also observed to be downregulated. Interestingly, anti-virulence targets such as AgrC (a quorum sensing-related histidine kinase), AgrA (a quorum sensing-related response regulator) as well as downstream targets, such as hemolysins, lipases and proteases in S. aureus were also downregulated by GW5074. We observed that the peptidoglycan hydrolase, SceD was significantly upregulated. The activity of GW5074 on S. aureus suggests that the compound primes bacteria for the antibacterial action of ineffective antibiotics. SIGNIFICANCE: Antibiotic resistance continues to present significant challenges to the treatment of bacterial infections. Given that antibiotic resistance is a natural phenomenon and that it has become increasingly difficult to discover novel antibiotics, efforts to improve the activity of existing agents are worth pursuing. A few small molecules that re-sensitize resistant bacteria to traditional antibiotics have been described but the molecular details that underpin how these compounds work to re-sensitize bacteria remain largely unknown. In this report, global label-free quantitative proteomics was used to identify changes in the proteome that occurs when GW5074, a compound that re-sensitize MRSA to methicillin, is administered to S. aureus. The identification of pathways that are impacted by GW5074 could help identify novel targets for antibiotic re-sensitization.
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Affiliation(s)
- Clement Opoku-Temeng
- Graduate Program in Biochemistry, University of Maryland, College Park, MD 20742, USA; Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Kenneth Ikenna Onyedibe
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Herman O Sintim
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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27
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Paczia N, Becker-Kettern J, Conrotte JF, Cifuente JO, Guerin ME, Linster CL. 3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis. Biochemistry 2019; 58:259-275. [PMID: 30668112 DOI: 10.1021/acs.biochem.8b00990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic mechanism of 3-phosphoglycerate to 3-phosphohydroxypyruvate oxidation, which forms the first step of the main conserved de novo serine synthesis pathway, has been revisited recently in certain microorganisms. While this step is classically considered to be catalyzed by an NAD-dependent dehydrogenase (e.g., PHGDH in mammals), evidence has shown that in Pseudomonas, Escherichia coli, and Saccharomyces cerevisiae, the PHGDH homologues act as transhydrogenases. As such, they use α-ketoglutarate, rather than NAD+, as the final electron acceptor, thereby producing D-2-hydroxyglutarate in addition to 3-phosphohydroxypyruvate during 3-phosphoglycerate oxidation. Here, we provide a detailed biochemical and sequence-structure relationship characterization of the yeast PHGDH homologues, encoded by the paralogous SER3 and SER33 genes, in comparison to the human and other PHGDH enzymes. Using in vitro assays with purified recombinant enzymes as well as in vivo growth phenotyping and metabolome analyses of yeast strains engineered to depend on either Ser3, Ser33, or human PHGDH for serine synthesis, we confirmed that both yeast enzymes act as transhydrogenases, while the human enzyme is a dehydrogenase. In addition, we show that the yeast paralogs differ from the human enzyme in their sensitivity to inhibition by serine as well as hydrated NADH derivatives. Importantly, our in vivo data support the idea that a 3PGA transhydrogenase instead of dehydrogenase activity confers a growth advantage under conditions where the NAD+:NADH ratio is low. The results will help to elucidate why different species evolved different reaction mechanisms to carry out a widely conserved metabolic step in central carbon metabolism.
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Affiliation(s)
- Nicole Paczia
- Luxembourg Centre for Systems Biomedicine , University of Luxembourg , L-4367 Belvaux , Luxembourg
| | - Julia Becker-Kettern
- Luxembourg Centre for Systems Biomedicine , University of Luxembourg , L-4367 Belvaux , Luxembourg
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine , University of Luxembourg , L-4367 Belvaux , Luxembourg
| | - Javier O Cifuente
- Structural Biology Unit , CIC bioGUNE Technological Park of Bizkaia , 48160 Derio , Vizcaya , Spain
| | - Marcelo E Guerin
- Structural Biology Unit , CIC bioGUNE Technological Park of Bizkaia , 48160 Derio , Vizcaya , Spain.,IKERBASQUE , Basque Foundation for Science , 48013 Bilbao , Spain
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine , University of Luxembourg , L-4367 Belvaux , Luxembourg
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28
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Ghiraldi-Lopes LD, Campanerut-Sá PAZ, Evaristo GPC, Meneguello JE, Fiorini A, Baldin VP, de Souza EM, de Lima Scodro RB, Siqueira VLD, Cardoso RF. New insights on Ethambutol Targets in Mycobacterium tuberculosis. Infect Disord Drug Targets 2019; 19:73-80. [PMID: 29366429 DOI: 10.2174/1871526518666180124140840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND In recent years, very few effective drugs against Mycobacterium tuberculosis have emerged, which motivates the research with drugs already used in the treatment of tuberculosis. Ethambutol is a bacteriostatic drug that affects cell wall integrity, but the effects of this drug on bacilli are not fully exploited. OBJECTIVE Based on the need to better investigate the complex mechanism of action of ethambutol, our study presented the proteome profile of M. tuberculosis after different times of ethambutol exposure, aiming to comprehend the dynamics of bacilli response to its effects. M. tuberculosis was exposed to ½ MIC of ethambutol at 24 and 48 hours. The proteins were identified by MALDI-TOF/TOF. RESULTS The main protein changes occurred in metabolic proteins as dihydrolipoyl dehydrogenase (Rv0462), glutamine synthetase1 (Rv2220), electron transfer flavoprotein subunit beta (Rv3029c) and adenosylhomocysteinase (Rv3248c). CONCLUSION Considering the functions of these proteins, our results support that the intermediary metabolism and respiration were affected by ethambutol and this disturbance provided proteins that could be explored as additional targets for this drug.
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Affiliation(s)
- Luciana D Ghiraldi-Lopes
- Universidade Estadual de Maringa - Departamento de Analises Clinicas e Biomedicina, Maringa, Parana, Brazil
| | | | - Geisa P Caprini Evaristo
- Laboratorio de Apoio ao Desenvolvimento Tecnologico - Instituto de Quimica, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jean E Meneguello
- Universidade Estadual de Maringa - Departamento de Analises Clinicas e Biomedicina, Maringa, Parana, Brazil
| | - Adriana Fiorini
- Universidade Estadual de Maringa - Departamento de Analises Clinicas e Biomedicina, Maringa, Parana, Brazil
| | - Vanessa P Baldin
- Universidade Estadual de Maringa - Departamento de Analises Clinicas e Biomedicina, Maringa, Parana, Brazil
| | | | | | - Vera L D Siqueira
- Universidade Estadual de Maringa - Departamento de Analises Clinicas e Biomedicina, Maringa, Parana, Brazil
| | - Rosilene F Cardoso
- Universidade Estadual de Maringa - Departamento de Analises Clinicas e Biomedicina, Maringa, Parana, Brazil
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29
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Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W. Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. BMC Evol Biol 2018; 18:199. [PMID: 30577795 PMCID: PMC6303947 DOI: 10.1186/s12862-018-1309-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/27/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. RESULTS We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. CONCLUSIONS The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
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Affiliation(s)
- Dorota Matelska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA
| | - Jagoda Jabłońska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Marcin J Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA
| | - Jan Kutner
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA. .,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA. .,Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland.
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30
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Abstract
l-Serine is the immediate precursor of d-serine, a major agonist of the N-methyl-d-aspartate (NMDA) receptor. l-Serine is a pivotal amino acid since it serves as a precursor to a large number of essential metabolites besides d-serine. In all non-photosynthetic organisms, including mammals, a major source of l-serine is the phosphorylated pathway of l-serine biosynthesis. The pathway consists of three enzymes, d-3-phosphoglycerate dehydrogenase (PGDH), phosphoserine amino transferase (PSAT), and l-phosphoserine phosphatase (PSP). PGDH catalyzes the first step in the pathway by converting d-3-phosphoglycerate (PGA), an intermediate in glycolysis, to phosphohydroxypyruvate (PHP) concomitant with the reduction of NAD+. In some, but not all organisms, the catalytic activity of PGDH can be regulated by feedback inhibition by l-serine. Three types of PGDH can be distinguished based on their domain structure. Type III PGDHs contain only a nucleotide binding and substrate binding domain. Type II PGDHs contain an additional regulatory domain (ACT domain), and Type I PGDHs contain a fourth domain, termed the ASB domain. There is no consistent pattern of domain content that correlates with organism type, and even when additional domains are present, they are not always functional. PGDH deficiency results in metabolic defects of the nervous system whose systems range from microcephaly at birth, seizures, and psychomotor retardation. Although deficiency of any of the pathway enzymes have similar outcomes, PGDH deficiency is predominant. Dietary or intravenous supplementation with l-serine is effective in controlling seizures but has little effect on psychomotor development. An increase in PGDH levels, due to overexpression, is also associated with a wide array of cancers. In culture, PGDH is required for tumor cell proliferation, but extracellular l-serine is not able to support cell proliferation. This has led to the hypothesis that the pathway is performing some function related to tumor growth other than supplying l-serine. The most well-studied PGDHs are bacterial, primarily from Escherichia coli and Mycobacterium tuberculosis, perhaps because they have been of most interest mechanistically. However, the relatively recent association of PGDH with neuronal defects and human cancers has provoked renewed interest in human PGDH.
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Affiliation(s)
- Gregory A Grant
- Departments of Developmental Biology and Medicine, Washington University School of Medicine, St. Louis, MO, United States.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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31
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Furukawa N, Miyanaga A, Nakajima M, Taguchi H. Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria. Biochemistry 2018; 57:5388-5406. [PMID: 30149697 DOI: 10.1021/acs.biochem.8b00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
d-Lactate dehydrogenases (d-LDHs) from Fusobacterium nucleatum (FnLDH) and Escherichia coli (EcLDH) exhibit positive cooperativity in substrate binding, and the Pseudomonas aeruginosa enzyme (PaLDH) shows negatively cooperative substrate binding. The apo and ternary complex structures of FnLDH and PaLDH have been determined together with the apo-EcLDH structure. The three enzymes consistently form homotetrameric structures with three symmetric axes, the P-, Q-, and R-axes, unlike Lactobacillus d-LDHs, P-axis-related dimeric enzymes, although apo-FnLDH and EcLDH form asymmetric and distorted quaternary structures. The tetrameric structure allows apo-FnLDH and EcLDH to form wide intersubunit contact surfaces between the opened catalytic domains of the two Q-axis-related subunits in coordination with their asymmetric and distorted quaternary structures. These contact surfaces comprise intersubunit hydrogen bonds and hydrophobic interactions and likely prevent the domain closure motion during initial substrate binding. In contrast, apo-PaLDH possesses a highly symmetrical quaternary structure and partially closed catalytic domains that are favorable for initial substrate binding and forms virtually no intersubunit contact surface between the catalytic domains, which present their negatively charged surfaces to each other at the subunit interface. Complex FnLDH and PaLDH possess highly symmetrical quaternary structures with closed forms of the catalytic domains, which are separate from each other at the subunit interface. Structure-based mutations successfully converted the three enzymes to their dimeric forms, which exhibited no significant cooperativity in substrate binding. These observations indicate that the three enzymes undergo typical sequential allosteric transitions to exhibit their distinctive allosteric functions through the tetrameric structures.
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Affiliation(s)
- Nayuta Furukawa
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan.,Department of Applied Life Sciences , Niigata University of Pharmacy and Applied Life Sciences , 265-1 Higashijima , Akiha-ku, Niigata 956-8603 , Japan
| | - Akimasa Miyanaga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
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32
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Akashi H, Okamura E, Nishihama R, Kohchi T, Hirai MY. Identification and Biochemical Characterization of the Serine Biosynthetic Enzyme 3-Phosphoglycerate Dehydrogenase in Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2018; 9:956. [PMID: 30061906 PMCID: PMC6054995 DOI: 10.3389/fpls.2018.00956] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/13/2018] [Indexed: 05/29/2023]
Abstract
L-serine is an important molecule in all living organisms, and thus its biosynthesis is considered to be regulated according to demand. 3-Phosphoglycerate dehydrogenase (PGDH), the first committed enzyme of the phosphorylated pathway of L-serine biosynthesis, is regulated by negative feedback from L-serine in bacteria. In the case of the vascular plant Arabidopsis thaliana, two PGDH isozymes out of three are inhibited by L-serine and activated by L-alanine, L-valine, L-methionine, L-homoserine, and L-homocysteine, suggesting a more complicated regulatory mechanism of L-serine biosynthesis in A. thaliana than in bacteria. However, it remains to be clarified whether the activation mechanism of PGDH by amino acids is conserved in land plants. In this study, we identified the sole isozyme of PGDH in the liverwort Marchantia polymorpha (MpPGDH) and elucidated its biochemical characteristics. MpPGDH cDNA encodes a 65.6 kDa protein that contains a putative transit peptide for chloroplast localization. MpPGDH shares 75-80% identity with A. thaliana isozymes and forms a homotetramer in vitro. Recombinant MpPGDH exhibited an optimal pH of 9.0, apparent Michaelis constants of 0.49 ± 0.04 and 0.096 ± 0.010 mM for 3-PGA and NAD+, respectively, and apparent maximum velocity of 5.65 ± 0.10 μmol⋅min-1⋅mg-1, similar to those of A. thaliana isozymes. Phosphate ions were found to stabilize MpPGDH, suggesting that phosphate ions are also a crucial factor in the regulation of serine biosynthesis via the phosphorylated pathway in Marchantia polymorpha. MpPGDH was inhibited by L-serine in a cooperative manner and was activated by L-alanine, L-valine, L-methionine, L-homoserine, and L-homocysteine to a lesser extent than it is in A. thaliana. The results suggest that an ancestral PGDH of land plants was inhibited byL-serine and slightly activated by five other amino acids.
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Affiliation(s)
- Hiromichi Akashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Eiji Okamura
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masami Y. Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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33
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Unterlass JE, Wood RJ, Baslé A, Tucker J, Cano C, Noble MM, Curtin NJ. Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH). Oncotarget 2017; 8:104478-104491. [PMID: 29262655 PMCID: PMC5732821 DOI: 10.18632/oncotarget.22327] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/16/2017] [Indexed: 11/25/2022] Open
Abstract
Cancer cells reprogram their metabolism and energy production to sustain increased growth, enable metastasis and overcome resistance to cancer treatments. Although primary roles for many metabolic proteins have been identified, some are promiscuous in regards to the reaction they catalyze. To efficiently target these enzymes, a good understanding of their enzymatic function and structure, as well as knowledge regarding any substrate or catalytic promiscuity is required. Here we focus on the characterization of human 3-phosphoglycerate dehydrogenase (PHGDH). PHGDH catalyzes the NAD+-dependent conversion of 3-phosphoglycerate to phosphohydroxypyruvate, which is the first step in the de novo synthesis pathway of serine, a critical amino acid for protein and nucleic acid biosynthesis. We have investigated substrate analogues to assess whether PHGDH might possess other enzymatic roles that could explain its occasional over-expression in cancer, as well as to help with the design of specific inhibitors. We also report the crystal structure of the catalytic subunit of human PHGDH, a dimer, solved with bound cofactor in one monomer and both cofactor and L-tartrate in the second monomer. In vitro enzyme activity measurements show that the catalytic subunit of PHGDH is still active and that PHGDH activity could be significantly inhibited with adenosine 5'-diphosphoribose.
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Affiliation(s)
- Judith E. Unterlass
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
- Present address: Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robert J. Wood
- Cancer Research Technology, Discovery Laboratories, Babraham Research Campus, Cambridge, UK
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Julie Tucker
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Céline Cano
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Martin M.E. Noble
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Nicola J. Curtin
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
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Grant GA. Regulatory Mechanism of Mycobacterium tuberculosis Phosphoserine Phosphatase SerB2. Biochemistry 2017; 56:6481-6490. [PMID: 29140686 DOI: 10.1021/acs.biochem.7b01082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Almost all organisms contain the same biosynthetic pathway for the synthesis of l-serine from the glycolytic intermediate, d-3-phosphoglycerate. However, regulation of this pathway varies from organism to organism. Many organisms control the activity of the first enzyme in the pathway, d-3-phosphoglycerate dehydrogenase (PGDH), by feedback inhibition through the interaction of l-serine with the ACT domains within the enzyme. The last enzyme in the pathway, phosphoserine phosphatase (PSP), has also been reported to be inhibited by l-serine. The high degree of sequence homology between Mycobacterium tuberculosis PSP (mtPSP) and Mycobacterium avium PSP (maPSP), which has recently been shown to contain ACT domains, suggested that the mtPSP also contained ACT domains. This raised the question of whether the ACT domains in mtPSP played a functional role similar to that of the ACT domains in PGDH. This investigation reveals that l-serine allosterically inhibits mtPSP by a mechanism of partial competitive inhibition by binding to the ACT domains. Therefore, in mtPSP, l-serine is an allosteric feedback inhibitor that acts by decreasing the affinity of the substrate for the enzyme. mtPGDH is also feedback inhibited by l-serine, but only in the presence of millimolar concentrations of phosphate. Therefore, the inhibition of mtPSP by l-serine would act as a secondary control point for the regulation of the l-serine biosynthetic pathway under physiological conditions where the level of phosphate would be below that needed for l-serine feedback inhibition of mtPGDH.
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Affiliation(s)
- Gregory A Grant
- Departments of Developmental Biology and Medicine, Washington University School of Medicine , 660 South Euclid Avenue, Box 8103, St. Louis, Missouri 63110, United States
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Coupling between d-3-phosphoglycerate dehydrogenase and d-2-hydroxyglutarate dehydrogenase drives bacterial l-serine synthesis. Proc Natl Acad Sci U S A 2017; 114:E7574-E7582. [PMID: 28827360 DOI: 10.1073/pnas.1619034114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
l-Serine biosynthesis, a crucial metabolic process in most domains of life, is initiated by d-3-phosphoglycerate (d-3-PG) dehydrogenation, a thermodynamically unfavorable reaction catalyzed by d-3-PG dehydrogenase (SerA). d-2-Hydroxyglutarate (d-2-HG) is traditionally viewed as an abnormal metabolite associated with cancer and neurometabolic disorders. Here, we reveal that bacterial anabolism and catabolism of d-2-HG are involved in l-serine biosynthesis in Pseudomonas stutzeri A1501 and Pseudomonas aeruginosa PAO1. SerA catalyzes the stereospecific reduction of 2-ketoglutarate (2-KG) to d-2-HG, responsible for the major production of d-2-HG in vivo. SerA combines the energetically favorable reaction of d-2-HG production to overcome the thermodynamic barrier of d-3-PG dehydrogenation. We identified a bacterial d-2-HG dehydrogenase (D2HGDH), a flavin adenine dinucleotide (FAD)-dependent enzyme, that converts d-2-HG back to 2-KG. Electron transfer flavoprotein (ETF) and ETF-ubiquinone oxidoreductase (ETFQO) are also essential in d-2-HG metabolism through their capacity to transfer electrons from D2HGDH. Furthermore, while the mutant with D2HGDH deletion displayed decreased growth, the defect was rescued by adding l-serine, suggesting that the D2HGDH is functionally tied to l-serine synthesis. Substantial flux flows through d-2-HG, being produced by SerA and removed by D2HGDH, ETF, and ETFQO, maintaining d-2-HG homeostasis. Overall, our results uncover that d-2-HG-mediated coupling between SerA and D2HGDH drives bacterial l-serine synthesis.
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Integration of flux measurements to resolve changes in anabolic and catabolic metabolism in cardiac myocytes. Biochem J 2017; 474:2785-2801. [PMID: 28706006 PMCID: PMC5545928 DOI: 10.1042/bcj20170474] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 12/18/2022]
Abstract
Although ancillary pathways of glucose metabolism are critical for synthesizing cellular building blocks and modulating stress responses, how they are regulated remains unclear. In the present study, we used radiometric glycolysis assays, [13C6]-glucose isotope tracing, and extracellular flux analysis to understand how phosphofructokinase (PFK)-mediated changes in glycolysis regulate glucose carbon partitioning into catabolic and anabolic pathways. Expression of kinase-deficient or phosphatase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in rat neonatal cardiomyocytes co-ordinately regulated glycolytic rate and lactate production. Nevertheless, in all groups, >40% of glucose consumed by the cells was unaccounted for via catabolism to pyruvate, which suggests entry of glucose carbons into ancillary pathways branching from metabolites formed in the preparatory phase of glycolysis. Analysis of 13C fractional enrichment patterns suggests that PFK activity regulates glucose carbon incorporation directly into the ribose and the glycerol moieties of purines and phospholipids, respectively. Pyrimidines, UDP-N-acetylhexosamine, and the fatty acyl chains of phosphatidylinositol and triglycerides showed lower 13C incorporation under conditions of high PFK activity; the isotopologue 13C enrichment pattern of each metabolite indicated limitations in mitochondria-engendered aspartate, acetyl CoA and fatty acids. Consistent with this notion, high glycolytic rate diminished mitochondrial activity and the coupling of glycolysis to glucose oxidation. These findings suggest that a major portion of intracellular glucose in cardiac myocytes is apportioned for ancillary biosynthetic reactions and that PFK co-ordinates the activities of the pentose phosphate, hexosamine biosynthetic, and glycerolipid synthesis pathways by directly modulating glycolytic intermediate entry into auxiliary glucose metabolism pathways and by indirectly regulating mitochondrial cataplerosis.
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Ghiraldi-Lopes LD, Campanerut-Sá PAZ, Meneguello JE, Seixas FAV, Lopes-Ortiz MA, Scodro RBL, Pires CTA, da Silva RZ, Siqueira VLD, Nakamura CV, Cardoso RF. Proteomic profile of Mycobacterium tuberculosis after eupomatenoid-5 induction reveals potential drug targets. Future Microbiol 2017; 12:867-879. [DOI: 10.2217/fmb-2017-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: We investigated a proteome profile, protein–protein interaction and morphological changes of Mycobacterium tuberculosis after different times of eupomatenoid-5 (EUP-5) induction to evaluate the cellular response to the drug-induced damages. Methods: The bacillus was induced to sub-minimal inhibitory concentration of EUP-5 at 12 h, 24 h and 48 h. The proteins were separated by 2D gel electrophoresis, identified by LC/MS-MS. Scanning electron microscopy and Search Tool for the Retrieval of Interacting Genes/Proteins analyses were performed. Results: EUP-5 impacts mainly in M. tuberculosis proteins of intermediary metabolism and interactome suggests a multisite disturbance that contributes to bacilli death. Scanning electron microscopy revealed the loss of bacillary form. Conclusion: Some of the differentially expressed proteins have the potential to be drug targets such as citrate synthase (Rv0896), phosphoglycerate kinase (Rv1437), ketol-acid reductoisomerase (Rv3001c) and ATP synthase alpha chain (Rv1308).
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Affiliation(s)
- Luciana D Ghiraldi-Lopes
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Paula AZ Campanerut-Sá
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Jean E Meneguello
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Flávio AV Seixas
- Department of Biochemistry, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Mariana A Lopes-Ortiz
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Uningá University Center, Rod PR 317, 6114, 87035-510, Maringá, Paraná, Brazil
| | - Regiane BL Scodro
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Claudia TA Pires
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Rosi Z da Silva
- State University of Ponta Grossa, Avenida General Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Paraná, Brazil
| | - Vera LD Siqueira
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Celso V Nakamura
- Postgraduate Program in Pharmaceutical Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Rosilene F Cardoso
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
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Carlson GM, Fenton AW. What Mutagenesis Can and Cannot Reveal About Allostery. Biophys J 2017; 110:1912-23. [PMID: 27166800 DOI: 10.1016/j.bpj.2016.03.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/24/2016] [Accepted: 03/14/2016] [Indexed: 10/21/2022] Open
Abstract
Allosteric regulation of protein function is recognized to be widespread throughout biology; however, knowledge of allosteric mechanisms, the molecular changes within a protein that couple one binding site to another, is limited. Although mutagenesis is often used to probe allosteric mechanisms, we consider herein what the outcome of a mutagenesis study truly reveals about an allosteric mechanism. Arguably, the best way to evaluate the effects of a mutation on allostery is to monitor the allosteric coupling constant (Qax), a ratio of the substrate binding constants in the absence versus presence of an allosteric effector. A range of substitutions at a given residue position in a protein can reveal when a particular substitution causes gain-of-function, which addresses a key challenge in interpreting mutation-dependent changes in the magnitude of Qax. Thus, whole-protein mutagenesis studies offer an acceptable means of identifying residues that contribute to an allosteric mechanism. With this focus on monitoring Qax, and keeping in mind the equilibrium nature of allostery, we consider alternative possibilities for what an allosteric mechanism might be. We conclude that different possible mechanisms (rotation-of-solid-domains, movement of secondary structure, side-chain repacking, changes in dynamics, etc.) will result in different findings in whole-protein mutagenesis studies.
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Affiliation(s)
- Gerald M Carlson
- Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Aron W Fenton
- Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.
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Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana. Sci Rep 2017; 7:3533. [PMID: 28615699 PMCID: PMC5471267 DOI: 10.1038/s41598-017-03807-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/17/2017] [Indexed: 12/25/2022] Open
Abstract
The proteinogenic amino acid l-serine is a precursor for various essential biomolecules in all organisms. 3-Phosphoglycerate dehydrogenase (PGDH) is the first committed enzyme of the phosphorylated pathway of l-serine biosynthesis, and is regulated by negative feedback from l-serine in bacteria and plants. In the present study, two Arabidopsis PGDH isoforms were inhibited by l-serine but were activated by l-amino acids such as l-homocysteine in vitro. Activation and inhibition by these amino acids was cooperative, suggesting an allosteric mechanism. Moreover, the half maximal effective concentration of l-homocysteine was 2 orders of magnitude lower than that of l-serine, suggesting greater regulatory potency. These are the first data to show that PGDH is activated by various biomolecules and indicate that serine biosynthesis is regulated by multiple pathways.
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Mishra V, Kumar A, Ali V, Zhang KYJ, Nozaki T. Characterization of pH-induced transitions of Entamoeba histolytica D-phosphoglycerate dehydrogenase. Int J Biol Macromol 2015; 79:284-9. [PMID: 25944370 DOI: 10.1016/j.ijbiomac.2015.04.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/16/2015] [Accepted: 04/22/2015] [Indexed: 11/30/2022]
Abstract
Entamoeba histolytica D-phosphoglycerate dehydrogenase (EhPGDH) exists as a functionally active homodimer at pH 7. Our earlier studies have shown that ionic interactions are essentially required for the oligomeric status and activity of the protein. Present study focuses on pH associated structural modulations of EhPGDH. Far-UV CD spectra showed loss in the secondary structure of the protein as a function of low pH, however, the protein was not completely unfolded even at pH 2. Energy minimized average simulated models of EhPGDH at different pH show stable secondary structure elements in the nucleotide binding domain (NBD) however, the substrate binding domain (SBD) was more sensitive toward acidic pH and completely unfolds at pH 2. The data suggest presence of partially folded/unfolded intermediate state at pH 2. Size exclusion chromatography shows that this intermediate has larger hydrodynamic radius compared with dimer (pH 7) or monomer (pH 5). The intermediate has poor tertiary organization with significantly exposed hydrophobic patches monitored by pH-dependent fluorescence spectroscopy and molecular dynamic simulations. Collectively, the results suggest that the two domains (NBD and SBD) of EhPGDH have independent pH-dependent structural transitions with stabilization of an intermediate state at pH 2.
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Affiliation(s)
- Vibhor Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Lucknow 226031, India.
| | - Ashutosh Kumar
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohamo 2300045, Kanagawa, Japan
| | - Vahab Ali
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohamo 2300045, Kanagawa, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious diseases, 1-23-1 Toyama, Shinjuku-Ku, Tokyo 162-8640, Japan
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Mattaini KR, Brignole EJ, Kini M, Davidson SM, Fiske BP, Drennan CL, Vander Heiden MG. An epitope tag alters phosphoglycerate dehydrogenase structure and impairs ability to support cell proliferation. Cancer Metab 2015; 3:5. [PMID: 25926973 PMCID: PMC4414297 DOI: 10.1186/s40170-015-0131-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/31/2015] [Indexed: 11/22/2022] Open
Abstract
Background The gene encoding the serine biosynthesis pathway enzyme PHGDH is located in a region of focal genomic copy number gain in human cancers. Cells with PHGDH amplification are dependent on enzyme expression for proliferation. However, dependence on increased PHGDH expression extends beyond production of serine alone, and further studies of PHGDH function are necessary to elucidate its role in cancer cells. These studies will require a physiologically relevant form of the enzyme for experiments using engineered cell lines and recombinant protein. Results The addition of an N-terminal epitope tag to PHGDH abolished the ability to support proliferation of PHGDH-amplified cells despite retention of some activity to convert 3-PG to PHP. Introducing an R236E mutation into PHGDH eliminates enzyme activity, and this catalytically inactive enzyme cannot support proliferation of PHGDH-dependent cells, arguing that canonical enzyme activity is required. Tagged and untagged PHGDH exhibit the same intracellular localization and ability to produce D-2-hydroxyglutarate (D-2HG), an error product of PHGDH, arguing that neither mislocalization nor loss of D-2HG production explains the inability of epitope-tagged PHGDH to support proliferation. To enable studies of PHGDH function, we report a method to purify recombinant PHGDH and found that untagged enzyme activity was greater than N-terminally tagged enzyme. Analysis of tagged and untagged PHGDH using size exclusion chromatography and electron microscopy found that an N-terminal epitope tag alters enzyme structure. Conclusions Purification of untagged recombinant PHGDH eliminates the need to use an epitope tag for enzyme studies. Furthermore, while tagged PHGDH retains some ability to convert 3PG to PHP, the structural alterations caused by including an epitope tag disrupts the ability of PHGDH to sustain cancer cell proliferation. Electronic supplementary material The online version of this article (doi:10.1186/s40170-015-0131-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine R Mattaini
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Edward J Brignole
- Department of Chemistry Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Howard Hughes Medical Institute Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Mitali Kini
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Brian P Fiske
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Department of Chemistry Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Howard Hughes Medical Institute Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ; Dana-Farber Cancer Institute, Boston, MA 02215 USA ; Broad Institute, Cambridge, MA 02139 USA
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Xu XL, Chen S, Salinas ND, Tolia NH, Grant GA. Comparison of Type 1 D-3-phosphoglycerate dehydrogenases reveals unique regulation in pathogenic Mycobacteria. Arch Biochem Biophys 2015; 570:32-9. [PMID: 25698123 DOI: 10.1016/j.abb.2015.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
D-3-phosphoglycerate dehydrogenases (PGDH) from all organisms catalyze the conversion of D-3-phosphoglycerate to phosphohydroxypyruvate as the first step in the biosynthesis of l-serine. This investigation compares the properties of Type 1 PGDHs from seven different species and demonstrates that conserved residues in the ACT and ASB domains of some allow l-serine to act as a feedback inhibitor at low micromolar concentrations. In addition, the serine sensitivity is dependent on the presence of phosphate ions. These residues are most highly conserved among PGDHs from the actinomycetales family, but only certain pathogenic mycobacteria appear to have the full complement of residues required for high sensitivity to serine. These basic residues are also responsible for the presence of dual pH optima in the acidic region that is also phosphate dependent. Analytical ultracentrifugation analysis demonstrates that the dual pH optima do not require changes in oligomeric state. This study also demonstrates that substrate inhibition is a common feature of Type 1 PGDHs and that it is suppressed by phosphate, indicating that phosphate likely interacts at both the catalytic and regulatory sites. The unique features resulting from the complement of basic residues conserved in pathogenic mycobacteria may impart important metabolic advantages to these organisms.
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Affiliation(s)
- Xiao Lan Xu
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, United States
| | - Shawei Chen
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, United States
| | - Nichole D Salinas
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, United States
| | - Niraj H Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, United States
| | - Gregory A Grant
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, United States; Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, United States.
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Gusyatiner MM, Ziyatdinov MK. 2-Hydroxyglutarate production is necessary for the reaction catalyzed by 3-phosphoglycerate dehydrogenase in Escherichia coli. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s2079978015010021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Khodayari A, Chowdhury A, Maranas CD. Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model. Front Bioeng Biotechnol 2015; 2:76. [PMID: 25601910 PMCID: PMC4283520 DOI: 10.3389/fbioe.2014.00076] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/05/2014] [Indexed: 01/25/2023] Open
Abstract
Computational strain-design prediction accuracy has been the focus for many recent efforts through the selective integration of kinetic information into metabolic models. In general, kinetic model prediction quality is determined by the range and scope of genetic and/or environmental perturbations used during parameterization. In this effort, we apply the k-OptForce procedure on a kinetic model of E. coli core metabolism constructed using the Ensemble Modeling (EM) method and parameterized using multiple mutant strains data under aerobic respiration with glucose as the carbon source. Minimal interventions are identified that improve succinate yield under both aerobic and anaerobic conditions to test the fidelity of model predictions under both genetic and environmental perturbations. Under aerobic condition, k-OptForce identifies interventions that match existing experimental strategies while pointing at a number of unexplored flux re-directions such as routing glyoxylate flux through the glycerate metabolism to improve succinate yield. Many of the identified interventions rely on the kinetic descriptions that would not be discoverable by a purely stoichiometric description. In contrast, under fermentative (anaerobic) condition, k-OptForce fails to identify key interventions including up-regulation of anaplerotic reactions and elimination of competitive fermentative products. This is due to the fact that the pathways activated under anaerobic condition were not properly parameterized as only aerobic flux data were used in the model construction. This study shed light on the importance of condition-specific model parameterization and provides insight on how to augment kinetic models so as to correctly respond to multiple environmental perturbations.
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Affiliation(s)
- Ali Khodayari
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Anupam Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
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Lang EJM, Cross PJ, Mittelstädt G, Jameson GB, Parker EJ. Allosteric ACTion: the varied ACT domains regulating enzymes of amino-acid metabolism. Curr Opin Struct Biol 2014; 29:102-11. [PMID: 25543886 DOI: 10.1016/j.sbi.2014.10.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/28/2014] [Indexed: 11/29/2022]
Abstract
Allosteric regulation of enzyme activity plays important metabolic roles. Here we review the allostery of enzymes of amino-acid metabolism conferred by a discrete domain known as the ACT domain. This domain of 60-70 residues has a βαββαβ topology leading to a four-stranded β4β1β3β2 antiparallel sheet with two antiparallel helices on one face. Extensive sequence variation requires a combined sequence/structure/function analysis for identification of the ACT domain. Common features include highly varied modes of self-association of ACT domains, ligand binding at domain interfaces, and transmittal of allosteric signals through conformational changes and/or the manipulation of quaternary equilibria. A recent example illustrates the relatively facile adoption of this versatile module of allostery by gene fusion.
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Affiliation(s)
- Eric J M Lang
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Penelope J Cross
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Gerd Mittelstädt
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Singh RK, Raj I, Pujari R, Gourinath S. Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine. FEBS J 2014; 281:5498-512. [PMID: 25294608 DOI: 10.1111/febs.13091] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/11/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Abstract
D-Phosphoglycerate dehydrogenase (PGDH) catalyzes the first committed step of the phosphorylated serine biosynthesis pathway. Here, we report for the first time, the crystal structures of Type IIIK PGDH from Entamoeba histolytica in the apo form, as well as in complexes with substrate (3-phosphoglyceric acid) and cofactor (NAD(+) ) to 2.45, 1.8 and 2.2 Å resolution, respectively. Comparison of the apo structure with the substrate-bound structure shows that the substrate-binding domain is rotated by ~ 20° to close the active-site cleft. The cofactor-bound structure also shows a closed-cleft conformation, in which NAD(+) is bound to the nucleotide-binding domain and a formate ion occupies the substrate-binding site. Superposition of the substrate- and cofactor-bound structures represents a snapshot of the enzyme in the active form, where C2 of the substrate and C4N of the cofactor are 2.2 Å apart, and the amino group of Lys263 is close enough to the substrate to remove the proton from the hydroxyl group of PGA, indicating the role of Lys in the catalysis. Mutation of Lys263 to Ala yields just 0.8% of the specific activity of the wild-type enzyme, revealing that Lys263 indeed plays an integral role in the catalytic activity. The detectable activity of the mutant, however, indicates that after 20° rotation of the substrate-binding domain, the resulting positions of the substrate and cofactor are sufficiently close to make a productive reaction.
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Affiliation(s)
- Rohit K Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Furukawa N, Miyanaga A, Togawa M, Nakajima M, Taguchi H. Diverse allosteric and catalytic functions of tetrameric d-lactate dehydrogenases from three Gram-negative bacteria. AMB Express 2014; 4:76. [PMID: 25401076 PMCID: PMC4230899 DOI: 10.1186/s13568-014-0076-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
NAD-dependent d-lactate dehydrogenases (d-LDHs) reduce pyruvate into d-lactate with oxidation of NADH into NAD+. Although non-allosteric d-LDHs from Lactobacilli have been extensively studied, the catalytic properties of allosteric d-LDHs from Gram-negative bacteria except for Escherichia coli remain unknown. We characterized the catalytic properties of d-LDHs from three Gram-negative bacteria, Fusobacterium nucleatum (FNLDH), Pseudomonas aeruginosa (PALDH), and E. coli (ECLDH) to gain an insight into allosteric mechanism of d-LDHs. While PALDH and ECLDH exhibited narrow substrate specificities toward pyruvate like usual d-LDHs, FNLDH exhibited a broad substrate specificity toward hydrophobic 2-ketoacids such as 2-ketobutyrate and 2-ketovalerate, the former of which gave a 2-fold higher kcat/S0.5 value than pyruvate. Whereas the three enzymes consistently showed hyperbolic shaped pyruvate saturation curves below pH 6.5, FNLDH and ECLDH, and PALDH showed marked positive and negative cooperativity, respectively, in the pyruvate saturation curves above pH 7.5. Oxamate inhibited the catalytic reactions of FNLDH competitively with pyruvate, and the PALDH reaction in a mixed manner at pH 7.0, but markedly enhanced the reactions of the two enzymes at low concentration through canceling of the apparent homotropic cooperativity at pH 8.0, although it constantly inhibited the ECLDH reaction. Fructose 1,6-bisphosphate and certain divalent metal ions such as Mg2+ also markedly enhanced the reactions of FNLDH and PALDH, but none of them enhanced the reaction of ECLDH. Thus, our study demonstrates that bacterial d-LDHs have highly divergent allosteric and catalytic properties.
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48
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Kumar SM, Pampa KJ, Manjula M, Hemantha Kumar G, Kunishima N, Lokanath NK. Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles. Biochem Biophys Res Commun 2014; 451:126-30. [PMID: 25065739 DOI: 10.1016/j.bbrc.2014.07.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 10/25/2022]
Abstract
In the L-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77Å and 1.95Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type IIIH and such PGDHs structures having this type are reported for the first time.
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Affiliation(s)
- S M Kumar
- Department of Studies in Physics, University of Mysore, Mysore 570 006, India
| | - K J Pampa
- Department of Studies in Microbiology, University of Mysore, Mysore 570 006, India
| | - M Manjula
- Department of Studies in Physics, University of Mysore, Mysore 570 006, India
| | - G Hemantha Kumar
- Department of Studies in Computer Science, University of Mysore, Mysore 570 006, India
| | - Naoki Kunishima
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - N K Lokanath
- Department of Studies in Physics, University of Mysore, Mysore 570 006, India.
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Xu XL, Grant GA. Regulation of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase by phosphate-modulated quaternary structure dynamics and a potential role for polyphosphate in enzyme regulation. Biochemistry 2014; 53:4239-49. [PMID: 24956108 DOI: 10.1021/bi500469d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the first reaction in the "phosphorylated" pathway of l-serine biosynthesis. In Mycobacterium tuberculosis, it is a type 1 enzyme (mtPGDH) in that it contains both an ACT domain and an ASB domain in addition to a catalytic domain. The published crystal structures (Protein Data Bank entries 1YGY and 3DC2) show a tartrate molecule interacting with cationic residues at the ASB-ACT domain interfaces and a serine molecule bound at the ACT domain interface. These sites have previously been shown to be involved in the mechanism of serine and substrate inhibition of catalytic activity. This investigation has revealed a mechanism of allosteric quaternary structure dynamics in mtPGDH that is modulated by physiologically relevant molecules, phosphate and polyphosphate. In the absence of phosphate and polyphosphate, the enzyme exists in equilibrium between an inactive dimer and an active tetramer that is insensitive to inhibition of catalytic activity by L-serine. Phosphate induces a conversion to an active tetramer and octamer that are sensitive to inhibition of catalytic activity by L-serine. Small polyphosphates (pyrophosphate and triphosphate) induce a conversion to an active dimer that is insensitive to L-serine inhibition. The difference in the tendency of each respective dimer to form a tetramer as well as slightly altered elution positions on size exclusion chromatography indicates that there is likely a conformational difference between the serine sensitive and insensitive states. This appears to constitute a unique mechanism in type 1 PGDHs that may be unique in pathogenic Mycobacterium species and may provide the organisms with a unique metabolic advantage.
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Affiliation(s)
- Xiao Lan Xu
- Department of Developmental Biology and ‡Department of Medicine, Washington University School of Medicine , 660 South Euclid Avenue, Box 8103, St. Louis, Missouri 63110, United States
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Eoh H, Rhee KY. Allostery and compartmentalization: old but not forgotten. Curr Opin Microbiol 2014; 18:23-9. [PMID: 24607642 PMCID: PMC5228163 DOI: 10.1016/j.mib.2014.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 11/16/2022]
Abstract
Homeostasis is an essential capability of all cells mediated by complex and diverse regulatory networks. Despite this complexity, many of the fundamental regulatory mechanisms used by cells have been evolutionarily conserved. It is thus somewhat surprising that the apparent physiologic significance of these mechanisms has been experimentally neglected. Here, we review 2 widely recognized regulatory mechanisms, allostery and compartmentalization, which exemplify this dissociation in our current understanding of the microbial pathogen, Mycobacterium tuberculosis.
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Affiliation(s)
- Hyungjin Eoh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
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