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Samsami H, Maali-Amiri R. Global insights into intermediate metabolites: Signaling, metabolic divergence and stress response modulation in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108862. [PMID: 38917735 DOI: 10.1016/j.plaphy.2024.108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
Climate change-induced environmental stresses pose significant challenges to plant survival and agricultural productivity. In response, many plants undergo genetic reprogramming, resulting in profound alterations in metabolic pathways and the production of diverse secondary metabolites. As a critical molecular junction, intermediate metabolites by targeted intensification or suppression of subpathways channel cell resources into a multifaceted array of functions such as cell signals, photosynthesis, energy metabolism, ROS homeostasis, producing defensive and protective molecules, epigenetic regulation and stress memory, phytohormones biosynthesis and cell wall architecture under stress conditions. Unlike the well-established functions of end products, intermediate metabolites are context-dependent and produce enigmatic alternatives during stress. As key components of signal transduction pathways, intermediate metabolites with relay and integration of stress signals ensure responses to stress combinations. Investigating efficient metabolic network pathways and their role in regulating unpredictable paths from upstream to downstream levels can unlock their full potential to shape the future of agriculture and ensure global food security. Here, we summarized the activity of some intermediate metabolites, from the perception step to tolerance responses to stress factors.
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Affiliation(s)
- Hanna Samsami
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran.
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2
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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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3
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Guida M, Tammaro C, Quaranta M, Salvucci B, Biava M, Poce G, Consalvi S. Amino Acid Biosynthesis Inhibitors in Tuberculosis Drug Discovery. Pharmaceutics 2024; 16:725. [PMID: 38931847 PMCID: PMC11206623 DOI: 10.3390/pharmaceutics16060725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
According to the latest World Health Organization (WHO) report, an estimated 10.6 million people were diagnosed with tuberculosis (TB) in 2022, and 1.30 million died. A major concern is the emergence of multi-drug-resistant (MDR) and extensively drug-resistant (XDR) strains, fueled by the length of anti-TB treatment and HIV comorbidity. Innovative anti-TB agents acting with new modes of action are the only solution to counteract the spread of resistant infections. To escape starvation and survive inside macrophages, Mtb has evolved to become independent of the host by synthesizing its own amino acids. Therefore, targeting amino acid biosynthesis could subvert the ability of the mycobacterium to evade the host immune system, providing innovative avenues for drug discovery. The aim of this review is to give an overview of the most recent progress in the discovery of amino acid biosynthesis inhibitors. Among the hits discovered over the past five years, tryptophan (Trp) inhibitors stand out as the most advanced and have significantly contributed to demonstrating the feasibility of this approach for future TB drug discovery. Future efforts should be directed at prioritizing the chemical optimization of these hits to enrich the TB drug pipeline with high-quality leads.
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Affiliation(s)
| | | | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
| | - Sara Consalvi
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
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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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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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Hu S, Xu J, Wu M, Yue K, Cui Y, Bai Y, You L, Guo J. Exploration of the mechanism of reinfusion of fresh autologous blood in type 2 diabetes mice to induce macrophage polarization and inhibit erythrocyte damage. J Diabetes Investig 2024; 15:70-77. [PMID: 37846170 PMCID: PMC10759728 DOI: 10.1111/jdi.14089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/02/2023] [Accepted: 09/11/2023] [Indexed: 10/18/2023] Open
Abstract
AIMS/INTRODUCTION Type 2 diabetes triggers an inflammatory response that can damage red blood cells. M2 macrophages have inhibitory effects on inflammation, and play an important role in tissue damage repair and fibrosis. Autologous blood transfusion has the potential to inhibit red blood cell damage by mediating macrophage polarization. MATERIALS AND METHODS Swiss mice were used to establish a suitable type 2 diabetes model, and autologous blood transfusion was carried out. The mice were killed, the blood of the mice was collected and CD14+ monocytes were sorted. The expression levels of phenotypic molecules CD16, CD32 and CD206 in CD14+ monocytes were analyzed by flow cytometry. The proportion of M1 and M2 macrophages were analyzed by flow cytometry. The Q value, P50 , 2,3-diphosphoglycerate and Na+ -K+ -ATPase of red blood cells were detected. The red blood cell osmotic fragility test analyzed the red blood cell osmotic fragility. Western blot analysis was used to analyze the expression changes of erythrocyte surface membrane proteins or transporters erythrocyte membrane protein band 4.1, sphingosine-1-phosphate, glycolipid transfer protein and signal peptide peptidase-like 2A. RESULTS Autologous blood transfusion induced a significant increase in the number of macrophages. The state and capacity of blood cells improved with autologous blood transfusion. Reinfusion of fresh autologous blood in type 2 diabetes mice made erythrocytes shrink. The expression of erythrocyte-related proteins proved that the erythrocyte injury in the reinfusion of fresh autologous blood + type 2 diabetes group was significantly reduced. CONCLUSION The reinfusion of fresh autologous blood into the body of patients with type 2 diabetes can induce macrophage polarization to M2, thereby inhibiting red blood cell damage.
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Affiliation(s)
- She‐jun Hu
- Department of Anesthesiology, Shanghai Gongli HospitalNaval Military Medical UniversityShanghaiChina
| | - Jia‐ming Xu
- Department of Anesthesiology, Shanghai Gongli HospitalNaval Military Medical UniversityShanghaiChina
| | - Man‐di Wu
- Postgraduate training base at Shanghai Gongli HospitalNingxia Medical UniversityYinchuanChina
| | - Ke Yue
- School of MedicineShanghai UniversityShanghaiChina
| | - Ying‐hui Cui
- Department of Anesthesiology, Shanghai Gongli HospitalNaval Military Medical UniversityShanghaiChina
| | - Yu Bai
- Department of Anesthesiology, Shanghai Gongli HospitalNaval Military Medical UniversityShanghaiChina
| | - Lai‐wei You
- Department of Anesthesiology, Shanghai Gongli HospitalNaval Military Medical UniversityShanghaiChina
| | - Jian‐Rong Guo
- Department of Anesthesiology, Shanghai Gongli HospitalNaval Military Medical UniversityShanghaiChina
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Ren X, Wei Y, Zhao H, Shao J, Zeng F, Wang Z, Li L. A comprehensive review and comparison of L-tryptophan biosynthesis in Saccharomyces cerevisiae and Escherichia coli. Front Bioeng Biotechnol 2023; 11:1261832. [PMID: 38116200 PMCID: PMC10729320 DOI: 10.3389/fbioe.2023.1261832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
L-tryptophan and its derivatives are widely used in the chemical, pharmaceutical, food, and feed industries. Microbial fermentation is the most commonly used method to produce L-tryptophan, which calls for an effective cell factory. The mechanism of L-tryptophan biosynthesis in Escherichia coli, the widely used producer of L-tryptophan, is well understood. Saccharomyces cerevisiae also plays a significant role in the industrial production of biochemicals. Because of its robustness and safety, S. cerevisiae is favored for producing pharmaceuticals and food-grade biochemicals. However, the biosynthesis of L-tryptophan in S. cerevisiae has been rarely summarized. The synthetic pathways and engineering strategies of L-tryptophan in E. coli and S. cerevisiae have been reviewed and compared in this review. Furthermore, the information presented in this review pertains to the existing understanding of how L-tryptophan affects S. cerevisiae's stress fitness, which could aid in developing a novel plan to produce more resilient industrial yeast and E. coli cell factories.
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Affiliation(s)
- Xinru Ren
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Yue Wei
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Honglu Zhao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Juanjuan Shao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China
| | - Zhen Wang
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China
| | - Li Li
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
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8
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Zuo HL, Huang HY, Lin YCD, Liu KM, Lin TS, Wang YB, Huang HD. Effects of Natural Products on Enzymes Involved in Ferroptosis: Regulation and Implications. Molecules 2023; 28:7929. [PMID: 38067658 PMCID: PMC10708253 DOI: 10.3390/molecules28237929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Ferroptosis is a form of regulated cell death that is characterized by the accumulation of iron-dependent lipid peroxides. The regulation of ferroptosis involves both non-enzymatic reactions and enzymatic mechanisms. Natural products have demonstrated potential effects on various enzymes, including GPX4, HO-1, NQO1, NOX4, GCLC, and GCLM, which are mainly involved in glutathione metabolic pathway or oxidative stress regulation, and ACSL3 and ACSL4, which mainly participate in lipid metabolism, thereby influencing the regulation of ferroptosis. In this review, we have provided a comprehensive overview of the existing literature pertaining to the effects of natural products on enzymes involved in ferroptosis and discussed their potential implications for the prevention and treatment of ferroptosis-related diseases. We also highlight the potential challenge that the majority of research has concentrated on investigating the impact of natural products on the expression of enzymes involving ferroptosis while limited attention is given to the regulation of enzyme activity. This observation underscores the considerable potential and scope for exploring the influence of natural products on enzyme activity.
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Affiliation(s)
- Hua-Li Zuo
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China; (H.-Y.H.); (Y.-C.-D.L.); (T.-S.L.); (Y.-B.W.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China; (H.-Y.H.); (Y.-C.-D.L.); (T.-S.L.); (Y.-B.W.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China; (H.-Y.H.); (Y.-C.-D.L.); (T.-S.L.); (Y.-B.W.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Kun-Meng Liu
- Center for Medical Artificial Intelligence, Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China;
| | - Ting-Syuan Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China; (H.-Y.H.); (Y.-C.-D.L.); (T.-S.L.); (Y.-B.W.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Yi-Bing Wang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China; (H.-Y.H.); (Y.-C.-D.L.); (T.-S.L.); (Y.-B.W.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China; (H.-Y.H.); (Y.-C.-D.L.); (T.-S.L.); (Y.-B.W.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
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9
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Ratz-Mitchem ML, Leary G, Grindeland A, Silvius D, Guter J, Kavanaugh MP, Gunn TM. Generation and characterization of a knock-in mouse model for spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM). Mamm Genome 2023; 34:572-585. [PMID: 37642681 PMCID: PMC10680402 DOI: 10.1007/s00335-023-10013-4] [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: 04/20/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
Solute carrier family 1 member 4 (SLC1A4), also referred to as Alanine/Serine/Cysteine/Threonine-preferring Transporter 1 (ASCT1), is a sodium-dependent neutral amino acid transporter. It is expressed in many tissues, including the brain, where it is expressed primarily on astrocytes and plays key roles in neuronal differentiation and development, maintaining neurotransmitter homeostasis, and N-methyl-D-aspartate neurotransmission, through regulation of L- and D-serine. Mutations in SLC1A4 are associated with the rare autosomal recessive neurodevelopmental disorder spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM, OMIM 616657). Psychomotor development and speech are significantly impaired in these patients, and many develop seizures. We generated and characterized a knock-in mouse model for the most common mutant allele, which results in a single amino acid change (p.Glu256Lys, or E256K). Homozygous mutants had increased D-serine uptake in the brain, microcephaly, and thin corpus callosum and cortex layer 1. While p.E256K homozygotes showed some significant differences in exploratory behavior relative to wildtype mice, their performance in assays for motor coordination, endurance, learning, and memory was normal, and they showed no significant differences in long-term potentiation. Taken together, these results indicate that the impact of the p.E256K mutation on cognition and motor function is minimal in mice, but other aspects of SLC1A4 function in the brain are conserved. Mice homozygous for p.E256K may be a good model for understanding the developmental basis of the corpus callosum and microcephaly phenotypes observed in SPATCCM patients and assessing whether they are rescued by serine supplementation.
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Affiliation(s)
| | - Greg Leary
- The McLaughlin Research Institute, 1520 23Rd St. S, Great Falls, MT, 59405, USA
- The Division of Biological Sciences, The University of Montana, Missoula, MT, USA
| | - Andrea Grindeland
- The McLaughlin Research Institute, 1520 23Rd St. S, Great Falls, MT, 59405, USA
| | - Derek Silvius
- The McLaughlin Research Institute, 1520 23Rd St. S, Great Falls, MT, 59405, USA
| | - Joseph Guter
- The McLaughlin Research Institute, 1520 23Rd St. S, Great Falls, MT, 59405, USA
| | - Michael P Kavanaugh
- The McLaughlin Research Institute, 1520 23Rd St. S, Great Falls, MT, 59405, USA.
- The Division of Biological Sciences, The University of Montana, Missoula, MT, USA.
- Neuroscience Program, University of Montana, 32 Campus Drive, Missoula, MT, 59803, USA.
| | - Teresa M Gunn
- The McLaughlin Research Institute, 1520 23Rd St. S, Great Falls, MT, 59405, USA.
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10
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Yang X, Mao Z, Huang J, Wang R, Dong H, Zhang Y, Ma H. Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. Synth Syst Biotechnol 2023; 8:597-605. [PMID: 37743907 PMCID: PMC10514394 DOI: 10.1016/j.synbio.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/12/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Metabolic network models have become increasingly precise and accurate as the most widespread and practical digital representations of living cells. The prediction functions were significantly expanded by integrating cellular resources and abiotic constraints in recent years. However, if unreasonable modeling methods were adopted due to a lack of consideration of biological knowledge, the conflicts between stoichiometric and other constraints, such as thermodynamic feasibility and enzyme resource availability, would lead to distorted predictions. In this work, we investigated a prediction anomaly of EcoETM, a constraints-based metabolic network model, and introduced the idea of enzyme compartmentalization into the analysis process. Through rational combination of reactions, we avoid the false prediction of pathway feasibility caused by the unrealistic assumption of free intermediate metabolites. This allowed us to correct the pathway structures of l-serine and l-tryptophan. A specific analysis explains the application method of the EcoETM-like model and demonstrates its potential and value in correcting the prediction results in pathway structure by resolving the conflict between different constraints and incorporating the evolved roles of enzymes as reaction compartments. Notably, this work also reveals the trade-off between product yield and thermodynamic feasibility. Our work is of great value for the structural improvement of constraints-based models.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhitao Mao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Ruoyu Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Huaming Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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11
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Yang H, Zhang B, Wu ZD, Chen LF, Pan JY, Xiu XL, Cai X, Liu ZQ, Zheng YG. Combinatorial Metabolic Engineering of Escherichia coli for Enhanced L-Cysteine Production: Insights into Crucial Regulatory Modes and Optimization of Carbon-Sulfur Metabolism and Cofactor Availability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13409-13418. [PMID: 37639615 DOI: 10.1021/acs.jafc.3c03709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Microbial production of valuable compounds can be enhanced by various metabolic strategies. This study proposed combinatorial metabolic engineering to develop an effective Escherichia coli cell factory dedicated to L-cysteine production. First, the crucial regulatory modes that control L-cysteine levels were investigated to guide metabolic modifications. A two-stage fermentation was achieved by employing multi-copy gene expression, improving the balance between production and growth. Subsequently, carbon flux distribution was further optimized by modifying the C1 unit metabolism and the glycolytic pathway. The modifications of sulfur assimilation demonstrated superior performance of thiosulfate utilization pathways in enhancing L-cysteine titer. Furthermore, the studies focusing on cofactor availability and preference emphasized the vital role of synergistic enhancement of sulfur-carbon metabolism in L-cysteine overproduction. In a 5 L bioreactor, the strain BW15-3/pED accumulated 12.6 g/L of L-cysteine. This work presented an effective metabolic engineering strategy for the development of L-cysteine-producing strains.
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Affiliation(s)
- Hui Yang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Zi-Dan Wu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Li-Feng Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Jia-Yuan Pan
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Xiao-Ling Xiu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
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Qing X, Wang Q, Xu H, Liu P, Lai L. Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase. Molecules 2023; 28:6430. [PMID: 37687259 PMCID: PMC10563079 DOI: 10.3390/molecules28176430] [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: 08/05/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Although loop epitopes at protein-protein binding interfaces often play key roles in mediating oligomer formation and interaction specificity, their binding sites are underexplored as drug targets owing to their high flexibility, relatively few hot spots, and solvent accessibility. Prior attempts to develop molecules that mimic loop epitopes to disrupt protein oligomers have had limited success. In this study, we used structure-based approaches to design and optimize cyclic-constrained peptides based on loop epitopes at the human phosphoglycerate dehydrogenase (PHGDH) dimer interface, which is an obligate homo-dimer with activity strongly dependent on the oligomeric state. The experimental validations showed that these cyclic peptides inhibit PHGDH activity by directly binding to the dimer interface and disrupting the obligate homo-oligomer formation. Our results demonstrate that loop epitope derived cyclic peptides with rationally designed affinity-enhancing substitutions can modulate obligate protein homo-oligomers, which can be used to design peptide inhibitors for other seemingly intractable oligomeric proteins.
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Affiliation(s)
- Xiaoyu Qing
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China;
| | - Hanyu Xu
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Pei Liu
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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Serra M, Di Maio A, Bassareo V, Nuzzo T, Errico F, Servillo F, Capasso M, Parekh P, Li Q, Thiolat ML, Bezard E, Calabresi P, Sulzer D, Carta M, Morelli M, Usiello A. Perturbation of serine enantiomers homeostasis in the striatum of MPTP-lesioned monkeys and mice reflects the extent of dopaminergic midbrain degeneration. Neurobiol Dis 2023:106226. [PMID: 37451474 DOI: 10.1016/j.nbd.2023.106226] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Loss of dopaminergic midbrain neurons perturbs l-serine and d-serine homeostasis in the post-mortem caudate putamen (CPu) of Parkinson's disease (PD) patients. However, it is unclear whether the severity of dopaminergic nigrostriatal degeneration plays a role in deregulating serine enantiomers' metabolism. Here, through high-performance liquid chromatography (HPLC), we measured the levels of these amino acids in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated monkeys and MPTP-plus-probenecid (MPTPp)-treated mice to determine whether and how dopaminergic midbrain degeneration affects the levels of serine enantiomers in various basal ganglia subregions. In addition, in the same brain regions, we measured the levels of key neuroactive amino acids modulating glutamatergic neurotransmission, including L-glutamate, glycine, l-aspartate, d-aspartate, and their precursors l-glutamine, L-asparagine. In monkeys, MPTP treatment produced severe denervation of nigrostriatal dopaminergic fibers (⁓75%) and increased the levels of serine enantiomers in the rostral putamen (rPut), but not in the subthalamic nucleus, and the lateral and medial portion of the globus pallidus. Moreover, this neurotoxin significantly reduced the protein expression of the astrocytic serine transporter ASCT1 and the glycolytic enzyme GAPDH in the rPut of monkeys. Conversely, concentrations of d-serine and l-serine, as well as ASCT1 and GAPDH expression were unaffected in the striatum of MPTPp-treated mice, which showed only mild dopaminergic degeneration (⁓30%). These findings unveil a link between the severity of dopaminergic nigrostriatal degeneration and striatal serine enantiomers concentration, ASCT1 and GAPDH expression. We hypothesize that the up-regulation of d-serine and l-serine levels occurs as a secondary response within a homeostatic loop to support the metabolic and neurotransmission demands imposed by the degeneration of dopaminergic neurons.
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Affiliation(s)
- Marcello Serra
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Anna Di Maio
- Laboratory of Translational Neuroscience, CEINGE Biotecnologie Avanzate Francesco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Science and Technologies, Università Degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Valentina Bassareo
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Tommaso Nuzzo
- Laboratory of Translational Neuroscience, CEINGE Biotecnologie Avanzate Francesco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Science and Technologies, Università Degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Francesco Errico
- Laboratory of Translational Neuroscience, CEINGE Biotecnologie Avanzate Francesco Salvatore, Naples, Italy; Department of Agricultural Sciences, University of Naples "Federico II", Naples, Italy
| | - Federica Servillo
- Department of Neuroscience, Cattolica Sacro Cuore University, Rome, Italy
| | - Mario Capasso
- Laboratory of Translational Neuroscience, CEINGE Biotecnologie Avanzate Francesco Salvatore, Naples, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Pansini, 5, Napoli 80131, Italy
| | - Pathik Parekh
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Qin Li
- Motac Neuroscience, UKM15 6WE, Manchester, United Kingdom; Institute of Lab Animal Sciences, China Academy of Medical Sciences, Beijing, China
| | - Marie-Laure Thiolat
- Université de Bordeaux, Institut des Maladies Neurodégénératives, Bordeaux, France; Centre National de la Recherche Scientifique Unité Mixte de Recherche 5293, Institut des Maladies Neurodégénératives, Bordeaux, France
| | - Erwan Bezard
- Motac Neuroscience, UKM15 6WE, Manchester, United Kingdom; Institute of Lab Animal Sciences, China Academy of Medical Sciences, Beijing, China; Université de Bordeaux, Institut des Maladies Neurodégénératives, Bordeaux, France; Centre National de la Recherche Scientifique Unité Mixte de Recherche 5293, Institut des Maladies Neurodégénératives, Bordeaux, France
| | - Paolo Calabresi
- Department of Neuroscience, Cattolica Sacro Cuore University, Rome, Italy; Neurologia, Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - David Sulzer
- Departments of Psychiatry, Neurology, Pharmacology, Columbia University Irving Medical Center, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Manolo Carta
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Micaela Morelli
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy; National Research Council of Italy, Institute of Neuroscience, Cagliari, Italy
| | - Alessandro Usiello
- Laboratory of Translational Neuroscience, CEINGE Biotecnologie Avanzate Francesco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Science and Technologies, Università Degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.
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Di Maio A, Nuzzo T, Gilio L, Serra M, Buttari F, Errico F, De Rosa A, Bassi MS, Morelli M, Sasabe J, Sulzer D, Carta M, Centonze D, Usiello A. Homeostasis of serine enantiomers is disrupted in the post-mortem caudate putamen and cerebrospinal fluid of living Parkinson's disease patients. Neurobiol Dis 2023:106203. [PMID: 37336364 DOI: 10.1016/j.nbd.2023.106203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023] Open
Abstract
L-serine generated in astrocytes plays a pivotal role in modulating essential neurometabolic processes, while its enantiomer, D-serine, specifically regulates NMDA receptor (NMDAR) signalling. Despite their physiological relevance in modulating cerebral activity, serine enantiomers metabolism in Parkinson's disease (PD) remains elusive. Using High-Performance Liquid Chromatography (HPLC), we measured D- and L-serine levels along with other amino acids known to modulate NMDAR function, such as L-glutamate, L-aspartate, D-aspartate, and glycine, in the post-mortem caudate putamen (CPu) and superior frontal gyrus (SFG) of PD patients. Moreover, we examined these amino acids in the cerebrospinal fluid (CSF) of de novo living PD, Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS) patients versus subjects with other neurological disorders (OND), used as control. We found higher D-serine and L-serine levels in the CPu of PD patients but not in the SFG, a cerebral region that, in contrast to the CPu, is not innervated by nigral dopaminergic terminals. We also highlighted a significant elevation of both serine enantiomers in the CSF samples from PD but not in those of AD and ALS patients, compared with control subjects. By contrast, none or only minor changes were found in the amount of other neuroactive amino acids mentioned above. Our findings identify D-serine and L-serine level upregulation as a biochemical signature associated with nigrostriatal dopaminergic degeneration in PD.
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Affiliation(s)
- Anna Di Maio
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Tommaso Nuzzo
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Luana Gilio
- Unit of Neurology, IRCCS Neuromed, Pozzilli (IS), Italy; Faculty of Psychology, Uninettuno Telematic International University, Rome, Italy; Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Marcello Serra
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Fabio Buttari
- Unit of Neurology, IRCCS Neuromed, Pozzilli (IS), Italy
| | - Francesco Errico
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Arianna De Rosa
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Micaela Morelli
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy; National Research Council of Italy, Institute of Neuroscience, Cagliari, Italy
| | - Jumpei Sasabe
- Department of Pharmacology, Keio University School of Medicine, Tokyo, Japan
| | - David Sulzer
- Departments of Psychiatry, Neurology, Pharmacology, Columbia University Irving Medical Center, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Manolo Carta
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Diego Centonze
- Unit of Neurology, IRCCS Neuromed, Pozzilli (IS), Italy; Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Alessandro Usiello
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.
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Ratz ML, Leary G, Grindeland A, Silvius D, Guter J, Kavanaugh MP, Gunn TM. Generation and characterization of a knock-in mouse model for Spastic Tetraplegia, Thin Corpus Callosum, and Progressive Microcephaly (SPATCCM). RESEARCH SQUARE 2023:rs.3.rs-2839029. [PMID: 37162879 PMCID: PMC10168478 DOI: 10.21203/rs.3.rs-2839029/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
SLC1A4 (solute carrier family 1 member 4, also referred to as ASCT1, Alanine/Serine/Cysteine/Threonine-preferring Transporter 1) is a sodium-dependent neutral amino acid transporter. It is highly expressed in many tissues, including the brain, where it is expressed primarily on astrocytes and plays key roles in neuronal differentiation and development, maintaining neurotransmitter homeostasis, and N-methyl-D-aspartate (NMDA) neurotransmission, through regulation of L- and D-serine. Mutations in SLC1A4 are associated with the rare autosomal recessive neurodevelopmental disorder spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM, OMIM 616657). Psychomotor development and speech are significantly impaired in these patients, and many develop seizures. We generated and characterized a knock-in mouse model for the most common mutant allele, which results in a single amino acid change (p.Glu256Lys, or E256K). Homozygous mutants had increased D-serine uptake in the brain, microcephaly, and thin corpus callosum and cortex layer 1. While p.E256K homozygotes showed some significant differences in exploratory behavior relative to wildtype mice, their performance in assays for motor coordination, endurance, learning, and memory was normal, and they showed no significant differences in long-term potentiation. Taken together, these results indicate that some aspects of SLC1A4 function in brain development are conserved between mice and humans, but the impact of the p.E256K mutation on cognition and motor function is minimal in mice.
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Fu J, Chen L, Su T, Xu S, Liu Y. Mild phenotypes of phosphoglycerate dehydrogenase deficiency by a novel mutation of PHGDH gene: Case report and literature review. Int J Dev Neurosci 2023; 83:44-52. [PMID: 36308023 DOI: 10.1002/jdn.10236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 02/04/2023] Open
Abstract
Phosphoglycerate dehydrogenase (PHGDH) deficiency is a rare autosomal recessive genetic disease of serine biosynthesis. Its typical features are congenital microcephaly, epileptic seizures, and psychomotor developmental delay. Here, we reported the first Chinese familial cases with genetically confirmed PHGDH deficiency and reviewed several previous reports. Two siblings in this family presented with microcephaly, psychomotor retardation, and epilepsy in early juvenile. Brain magnetic resonance imaging (MRI) showed only a slight change of enlarged ventricle. Biochemical investigations revealed low serum serine and glycine concentrations. The whole-exome sequencing (WES) results identified a missense variant in the PHGDH gene (NM_006623.4: exon11: c.1211T>A, p. Val404Asp). Although two patients in this Chinese family carried the same pathogenic mutation in the PHGDH, their symptoms and responses to treatment were not exactly the same. We found a novel variant in the PHGDH gene and expanded the genotypic and phenotypic spectrum of serine biosynthesis disorders.
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Affiliation(s)
- Junyi Fu
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liqing Chen
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tangfeng Su
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sanqing Xu
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Liu
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Pinto AT, Machado AB, Osório H, Pinto ML, Vitorino R, Justino G, Santa C, Castro F, Cruz T, Rodrigues C, Lima J, Sousa JLR, Cardoso AP, Figueira R, Monteiro A, Marques M, Manadas B, Pauwels J, Gevaert K, Mareel M, Rocha S, Duarte T, Oliveira MJ. Macrophage Resistance to Ionizing Radiation Exposure Is Accompanied by Decreased Cathepsin D and Increased Transferrin Receptor 1 Expression. Cancers (Basel) 2022; 15:270. [PMID: 36612268 PMCID: PMC9818572 DOI: 10.3390/cancers15010270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/06/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
PURPOSE To identify a molecular signature of macrophages exposed to clinically relevant ionizing radiation (IR) doses, mirroring radiotherapy sessions. METHODS Human monocyte-derived macrophages were exposed to 2 Gy/ fraction/ day for 5 days, mimicking one week of cancer patient's radiotherapy. Protein expression profile by proteomics was performed. RESULTS A gene ontology analysis revealed that radiation-induced protein changes are associated with metabolic alterations, which were further supported by a reduction of both cellular ATP levels and glucose uptake. Most of the radiation-induced deregulated targets exhibited a decreased expression, as was the case of cathepsin D, a lysosomal protease associated with cell death, which was validated by Western blot. We also found that irradiated macrophages exhibited an increased expression of the transferrin receptor 1 (TfR1), which is responsible for the uptake of transferrin-bound iron. TfR1 upregulation was also found in tumor-associated mouse macrophages upon tumor irradiation. In vitro irradiated macrophages also presented a trend for increased divalent metal transporter 1 (DMT1), which transports iron from the endosome to the cytosol, and a significant increase in iron release. CONCLUSIONS Irradiated macrophages present lower ATP levels and glucose uptake, and exhibit decreased cathepsin D expression, while increasing TfR1 expression and altering iron metabolism.
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Affiliation(s)
- Ana Teresa Pinto
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Ana Beatriz Machado
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- Champalimaud Centre for the Unknown, Fundação Champalimaud, 1400-038 Lisboa, Portugal
| | - Hugo Osório
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Departament of Pathology, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Marta Laranjeiro Pinto
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Gonçalo Justino
- Centro de Química Estrutural–Institute of Molecular Sciences, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001 Lisboa, Portugal
| | - Cátia Santa
- CNC–Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), Universidade de Coimbra, 3030-789 Coimbra, Portugal
| | - Flávia Castro
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Tânia Cruz
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Carla Rodrigues
- REQUIMTE–LAQV, Chemistry Department, NOVA School of Science and Technology, Universidade de Lisboa, 2829-516 Caparica, Portugal
| | - Jorge Lima
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - José Luís R. Sousa
- Personal Health Data Science Group, Sano-Centre for Computational Personalised Medicine, 30-054 Krakow, Poland
| | - Ana Patrícia Cardoso
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Rita Figueira
- Radiotherapy Service, Centro Hospitalar Universitário São João (CHUSJ), EPE, 4200-319 Porto, Portugal
| | - Armanda Monteiro
- Radiotherapy Service, Centro Hospitalar Universitário São João (CHUSJ), EPE, 4200-319 Porto, Portugal
| | - Margarida Marques
- Radiotherapy Service, Centro Hospitalar Universitário São João (CHUSJ), EPE, 4200-319 Porto, Portugal
| | - Bruno Manadas
- Institute for Interdisciplinary Research (III), Universidade de Coimbra, 3030-789 Coimbra, Portugal
| | - Jarne Pauwels
- VIB-UGent Center for Medical Biotechnology, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
| | - Marc Mareel
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, 9000 Ghent, Belgium
| | - Sónia Rocha
- Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3 GE, UK
| | - Tiago Duarte
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Maria José Oliveira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB–Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- Departament of Pathology, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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Bioprocess Engineering, Transcriptome, and Intermediate Metabolite Analysis of L-Serine High-Yielding Escherichia coli W3110. Microorganisms 2022; 10:microorganisms10101927. [PMID: 36296205 PMCID: PMC9612172 DOI: 10.3390/microorganisms10101927] [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: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
L-serine is widely used in the food, cosmetic, and pharmaceutical industries. However, the complicated metabolic network and regulatory mechanism of L-serine production lead to the suboptimal productivity of the direct fermentation of L-serine and limits its large-scale industrial production. In this study, a high-yield L-serine production Escherichia coli strain was constructed by a series of defined genetic modification methodologies. First, L-serine-mediated feedback inhibition was removed and L-serine biosynthetic pathway genes (serAfr, serC, and serB) associated with phosphoglycerate kinase (pgk) were overexpressed. Second, the L-serine conversion pathway was further examined by introducing a glyA mutation (K229G) and deleting other degrading enzymes based on the deletion of initial sdaA. Finally, the L-serine transport system was rationally engineered to reduce uptake and accelerate L-serine export. The optimally engineered strain produced 35 g/L L-serine with a productivity of 0.98 g/L/h and a yield of 0.42 g/g glucose in a 5-L fermenter, the highest productivity and yield of L-serine from glucose reported to date. Furthermore, transcriptome and intermediate metabolite of the high-yield L-serine production Escherichia coli strain were analyzed. The results demonstrated the regulatory mechanism of L-serine production is delicate, and that combined metabolic and bioprocess engineering strategies for L-serine producing strains can improve the productivity and yield.
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Liu Y, Wang R, Liu J, Lu H, Li H, Wang Y, Ni X, Li J, Guo Y, Ma H, Liao X, Wang M. Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum. SCIENCE ADVANCES 2022; 8:eabq2157. [PMID: 36044571 PMCID: PMC9432829 DOI: 10.1126/sciadv.abq2157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Genome-scale functional screening accelerates comprehensive assessment of gene function in cells. Here, we have established a genome-scale loss-of-function screening strategy that combined a cytosine base editor with approximately 12,000 parallel sgRNAs targeting 98.1% of total genes in Corynebacterium glutamicum ATCC 13032. Unlike previous data processing methods developed in yeast or mammalian cells, we developed a new data processing procedure to locate candidate genes by statistical sgRNA enrichment analysis. Known and novel functional genes related to 5-fluorouracil resistance, 5-fluoroorotate resistance, oxidative stress tolerance, or furfural tolerance have been identified. In particular, purU and serA were proven to be related to the furfural tolerance in C. glutamicum. A cloud platform named FSsgRNA-Analyzer was provided to accelerate sequencing data processing for CRISPR-based functional screening. Our method would be broadly useful to functional genomics study and strain engineering in other microorganisms.
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Affiliation(s)
- Ye Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ruoyu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jiahui Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hui Lu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Haoran Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Junwei Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoping Liao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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20
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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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21
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Mulakala BK, Smith KM, Snider MA, Ayers A, Honan MC, Greenwood SL. Influence of dietary carbohydrate profile on the dairy cow rumen meta-proteome. J Dairy Sci 2022; 105:8485-8496. [PMID: 36028341 DOI: 10.3168/jds.2022-21812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022]
Abstract
Diet starch and fiber contents influence the rumen microbial profile and its fermentation products, yet no information exists about the effects of these dietary carbohydrate fractions on the metabolic activity of these microbes. The objective of this experiment was to evaluate the effects of dietary carbohydrate profile changes on the rumen meta-proteome profile. Eight cannulated Holstein cows were assigned to the study as part of a 4 × 4 Latin square design with a 2 × 2 factorial treatment arrangement including four 28-d periods. Cows received 1 of 4 dietary treatments on a dry matter (DM) basis. Diets included different concentrations of rumen fermentable starch (RFS) and physically effective undigested NDF (peuNDF240) content in the diet: (1) low peuNDF240, low RFS (LNLS); (2) high peuNDF240, low RFS (HNLS); (3) low peuNDF240, high RFS (LNHS); and (4) high peuNDF240, high RFS (HNHS). Rumen fluid samples were collected from each cow on the last 2 d of each period at 3 time points (0600, 1000, and 1400 h). The microbial protein fraction was isolated, isobarically labeled, and analyzed using liquid chromatography combined with tandem mass spectrometry techniques. Product ion spectra were searched using the SEQUEST search on Proteome Discoverer 2.4 (Thermo Scientific) against 71 curated microbe-specific databases. Data were analyzed using PROC MIXED procedure in SAS 9.4 (SAS Institute Inc.). A total of 138 proteins were characterized across 26 of the searched microbial species. In total, 46 proteins were affected by treatments across 17 of the searched microbial species. Of these 46 proteins, 28 were affected by RFS content across 13 microbial species, with 20 proteins having higher abundance with higher dietary RFS and 8 proteins having higher abundance with lower dietary RFS. The majority of these proteins have roles in energetics, carbon metabolism, and protein synthesis. Examples include pyruvate, phosphate dikinase (Ruminococcus albus SY3), 30S ribosomal protein S11 (Clostridium aminophilum), and methyl-coenzyme M reductase subunit α (Methanobrevibacter ruminantium strain 35063), which had higher abundances with higher dietary RFS. Conversely, glutamate dehydrogenase (Butyrivibrio fibrisolvens) and 50S ribosomal protein L5 (Pseudobutyrivibrio ruminis) and L15 (Ruminococcus bromii) had lower abundances with higher dietary RFS content. Among the remaining 18 proteins unaffected by RFS content alone, 5 proteins were affected by peuNDF240 content, and 13 were affected by peuNDF240 × RFS interactions. Our results suggest that the RFS content of the diet may have a greater influence on rumen microbial protein abundances than dietary peuNDF240 content or peuNDF240 × RFS interactions. This research highlights that dietary carbohydrate profile changes can influence rumen microbial protein abundances. Further research is needed to fully characterize the effects of diet on the rumen meta-proteome and manipulate the various roles of rumen microbes. This will aid in designing the strategies to maximize the efficiency of nutrient use in the rumen.
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Affiliation(s)
- B K Mulakala
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington 05405
| | - K M Smith
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - M A Snider
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington 05405
| | - A Ayers
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington 05405
| | - M C Honan
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington 05405; Department of Animal Science, University of California, Davis 95616
| | - S L Greenwood
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington 05405.
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22
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Shen X, Cai Y, Lu L, Huang H, Yan H, Paty PB, Muca E, Ahuja N, Zhang Y, Johnson CH, Khan SA. Asparagine Metabolism in Tumors Is Linked to Poor Survival in Females with Colorectal Cancer: A Cohort Study. Metabolites 2022; 12:metabo12020164. [PMID: 35208238 PMCID: PMC8875032 DOI: 10.3390/metabo12020164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 01/02/2023] Open
Abstract
The interplay between the sex-specific differences in tumor metabolome and colorectal cancer (CRC) prognosis has never been studied and represents an opportunity to improve patient outcomes. This study examines the link between tumor metabolome and prognosis by sex for CRC patients. Using untargeted metabolomics analysis, abundances of 91 metabolites were obtained from primary tumor tissues from 197 patients (N = 95 females, N = 102 males) after surgical colectomy for stage I-III CRC. Cox Proportional hazard (PH) regression models estimated the associations between tumor metabolome and 5-year overall survival (OS) and recurrence-free survival (RFS), and their interactions with sex. Eleven metabolites had significant sex differences in their associations with 5-year OS, and five metabolites for 5-year RFS. The metabolites asparagine and serine had sex interactions for both OS and RFS. Furthermore, in the asparagine synthetase (ASNS)-catalyzed asparagine synthesis pathway, asparagine was associated with substantially poorer OS (HR (95% CI): 6.39 (1.78–22.91)) and RFS (HR (95% CI): 4.36 (1.39–13.68)) for female patients only. Similar prognostic disadvantages in females were seen in lysophospholipid and polyamine synthesis. Unique metabolite profiles indicated that increased asparagine synthesis was associated with poorer prognosis for females only, providing insight into precision medicine for CRC treatment stratified by sex.
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Affiliation(s)
- Xinyi Shen
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (X.S.); (L.L.)
| | - Yuping Cai
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (Y.C.); (H.H.); (H.Y.); (Y.Z.)
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (X.S.); (L.L.)
| | - Huang Huang
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (Y.C.); (H.H.); (H.Y.); (Y.Z.)
| | - Hong Yan
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (Y.C.); (H.H.); (H.Y.); (Y.Z.)
| | - Philip B. Paty
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.B.P.); (E.M.)
| | - Engjel Muca
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.B.P.); (E.M.)
| | - Nita Ahuja
- Division of Surgical Oncology, Department of Surgery, Yale University School of Medicine, New Haven, CT 06510, USA;
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (Y.C.); (H.H.); (H.Y.); (Y.Z.)
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06510, USA
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Caroline H. Johnson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT 06510, USA; (Y.C.); (H.H.); (H.Y.); (Y.Z.)
- Correspondence: (C.H.J.); (S.A.K.)
| | - Sajid A. Khan
- Division of Surgical Oncology, Department of Surgery, Yale University School of Medicine, New Haven, CT 06510, USA;
- Correspondence: (C.H.J.); (S.A.K.)
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23
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Chen C, Zhu T, Liu X, Zhu D, Zhang Y, Wu S, Han C, Zhang H, Luo J, Kong L. Identification of a novel PHGDH covalent inhibitor by chemical proteomics and phenotypic profiling. Acta Pharm Sin B 2022; 12:246-261. [PMID: 35127383 PMCID: PMC8799887 DOI: 10.1016/j.apsb.2021.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
The first rate-limiting enzyme of the serine synthesis pathway (SSP), phosphoglycerate dehydrogenase (PHGDH), is hyperactive in multiple tumors, which leads to the activation of SSP and promotes tumorigenesis. However, only a few inhibitors of PHGDH have been discovered to date, especially the covalent inhibitors of PHGDH. Here, we identified withangulatin A (WA), a natural small molecule, as a novel covalent inhibitor of PHGDH. Affinity-based protein profiling identified that WA could directly bind to PHGDH and inactivate the enzyme activity of PHGDH. Biolayer interferometry and LC-MS/MS analysis further demonstrated the selective covalent binding of WA to the cysteine 295 residue (Cys295) of PHGDH. With the covalent modification of Cys295, WA blocked the substrate-binding domain (SBD) of PHGDH and exerted an allosteric effect to induce PHGDH inactivation. Further studies revealed that with the inhibition of PHGDH mediated by WA, the glutathione synthesis was decreased and intracellular levels of reactive oxygen species (ROS) were elevated, leading to the inhibition of tumor proliferation. This study indicates WA as a novel PHGDH covalent inhibitor, which identifies Cys295 as a novel allosteric regulatory site of PHGDH and holds great potential in developing anti-tumor agents for targeting PHGDH.
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Key Words
- 3-PG, 3-phosphoglycerate
- 3-PHP, 3-phosphohydroxypyruvate
- ABPP, affinity-based protein profiling
- BLI, biolayer interferometry assay
- CETSA, cellular thermal shift assay
- Chemical proteomics
- Colon cancer
- Covalent inhibitor
- CuAAC, copper-catalyzed alkyne–azide cycloaddition
- DARTS, drug affinity responsive target stability
- GSH, glutathione
- MD, molecular dynamics
- NADPH, nicotinamide adenine dinucleotide phosphate
- Oxidative stress
- PHGDH, phosphoglycerate dehydrogenase
- PSAT, phosphoserine aminotransferase
- Phosphoglycerate dehydrogenase
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- ROS, reactive oxygen species
- SBD, substrate-binding domain
- SSP, serine synthesis pathway
- Serine synthesis pathway
- TBTA, tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine
- TCEP, tris(2-carboxyethyl) phosphine
- Withangulatin A
- Withanolides
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jianguang Luo
- Corresponding authors. Tel./fax: +86 25 83271405, +86 25 83271402.
| | - Lingyi Kong
- Corresponding authors. Tel./fax: +86 25 83271405, +86 25 83271402.
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24
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Truman JP, Ruiz CF, Montal E, Garcia-Barros M, Mileva I, Snider AJ, Hannun YA, Obeid LM, Mao C. 1-Deoxysphinganine initiates adaptive responses to serine and glycine starvation in cancer cells via proteolysis of sphingosine kinase. J Lipid Res 2022; 63:100154. [PMID: 34838542 PMCID: PMC8953655 DOI: 10.1016/j.jlr.2021.100154] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer cells may depend on exogenous serine, depletion of which results in slower growth and activation of adaptive metabolic changes. We previously demonstrated that serine and glycine (SG) deprivation causes loss of sphingosine kinase 1 (SK1) in cancer cells, thereby increasing the levels of its lipid substrate, sphingosine (Sph), which mediates several adaptive biological responses. However, the signaling molecules regulating SK1 and Sph levels in response to SG deprivation have yet to be defined. Here, we identify 1-deoxysphinganine (dSA), a noncanonical sphingoid base generated in the absence of serine from the alternative condensation of alanine and palmitoyl CoA by serine palmitoyl transferase, as a proximal mediator of SG deprivation in SK1 loss and Sph level elevation upon SG deprivation in cancer cells. SG starvation increased dSA levels in vitro and in vivo and in turn induced SK1 degradation through a serine palmitoyl transferase-dependent mechanism, thereby increasing Sph levels. Addition of exogenous dSA caused a moderate increase in intracellular reactive oxygen species, which in turn decreased pyruvate kinase PKM2 activity while increasing phosphoglycerate dehydrogenase levels, and thereby promoted serine synthesis. We further showed that increased dSA induces the adaptive cellular and metabolic functions in the response of cells to decreased availability of serine likely by increasing Sph levels. Thus, we conclude that dSA functions as an initial sensor of serine loss, SK1 functions as its direct target, and Sph functions as a downstream effector of cellular and metabolic adaptations. These studies define a previously unrecognized "physiological" nontoxic function for dSA.
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Affiliation(s)
- Jean-Philip Truman
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Christian F Ruiz
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Emily Montal
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY, USA
| | - Monica Garcia-Barros
- Biorepository and Pathology Laboratory, Mount Sinai Icahn School of Medicine, New York, NY, USA
| | - Izolda Mileva
- Lipidomics Core, Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Ashley J Snider
- Department of Nutritional Sciences, College of Agriculture and Life Sciences, BIO5 Institute, Tucson, AZ, USA
| | - Yusuf A Hannun
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Departments of Biochemistry and Pathology, Stony Brook University, Stony Brook, NY, USA; Northport Veterans Affairs Medical Center, Northport, NY, USA.
| | - Lina M Obeid
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Northport Veterans Affairs Medical Center, Northport, NY, USA
| | - Cungui Mao
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
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25
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Frare R, Stritzler M, Pascuan C, Liebrenz K, Galindo-Sotomonte L, Soto G, Nikel PI, Ayub N. Elimination of GlnKAmtB affects serine biosynthesis and improves growth and stress tolerance of Escherichia coli under nutrient-rich conditions. FEMS Microbiol Lett 2021; 367:6006877. [PMID: 33242092 DOI: 10.1093/femsle/fnaa197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Nitrogen is a most important nutrient resource for Escherichia coli and other bacteria that harbor the glnKamtB operon, a high-affinity ammonium uptake system highly interconnected with cellular metabolism. Although this system confers an advantage to bacteria when growing under nitrogen-limiting conditions, little is known about the impact of these genes on microbial fitness under nutrient-rich conditions. Here, the genetically tractable E. coli BW25113 strain and its glnKamtB-null mutant (JW0441) were used to analyze the impact of GlnK-AmtB on growth rates and oxidative stress tolerance. Strain JW0441 showed a shorter initial lag phase, higher growth rate, higher citrate synthase activity, higher oxidative stress tolerance and lower expression of serA than strain BW25113 under nutrient-rich conditions, suggesting a fitness cost to increase metabolic plasticity associated with serine metabolism. The overexpression of serA in strain JW0441 resulted in a decreased growth rate and stress tolerance in nutrient-rich conditions similar to that of strain BW25113, suggesting that the negative influence on bacterial fitness imposed by GlnK-AmtB can be traced to the control of serine biosynthesis. Finally, we discuss the potential applications of glnKamtB mutants in bioproduction processes.
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Affiliation(s)
- Romina Frare
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Karen Liebrenz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Luisa Galindo-Sotomonte
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
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26
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Tang C, Li W, Klosterman SJ, Wang Y. Transcriptome Variations in Verticillium dahliae in Response to Two Different Inorganic Nitrogen Sources. Front Microbiol 2021; 12:712701. [PMID: 34394062 PMCID: PMC8355529 DOI: 10.3389/fmicb.2021.712701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The fungus Verticillium dahliae causes vascular wilt disease on hundreds of plant species. The main focus of the research to control this fungus has been aimed at infection processes such as penetration peg formation and effector secretion, but the ability of the fungus to acquire and utilize nutrients are often overlooked and may hold additional potential to formulate new disease control approaches. Little is known about the molecular mechanisms of nitrogen acquisition and assimilation processes in V. dahliae. In this present study, RNA sequencing and gene expression analysis were used to examine differentially expressed genes in response to the different nitrogen sources, nitrate and ammonium, in V. dahliae. A total of 3244 and 2528 differentially expressed genes were identified in response to nitrate and ammonium treatments, respectively. The data indicated nitrate metabolism requires additional energy input while ammonium metabolism is accompanied by reductions in particular cellular processes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of DEGs during nitrate metabolism revealed that many of the genes encoded those involved in protein biosynthetic and metabolic processes, especially ribosome and RNA polymerase biosynthesis, but also other processes including transport and organonitrogen compound metabolism. Analysis of DEGs in the ammonium treatment indicated that cell cycle, oxidoreductase, and certain metabolic activities were reduced. In addition, DEGs participating in the utilization of both nitrate and ammonium were related to L-serine biosynthesis, energy-dependent multidrug efflux pump activity, and glycerol transport. We further showed that the mutants of three differentially expressed transcription factors (VdMcm1, VdHapX, and VDAG_08640) exhibited abnormal phenotypes under nitrate and ammonium treatment compared with the wild type strain. Deletion of VdMcm1 displayed slower growth when utilizing both nitrogen sources, while deletion of VdHapX and VDAG_08640 only affected nitrate metabolism, inferring that nitrogen assimilation required regulation of bZIP transcription factor family and participation of cell cycle. Taken together, our findings illustrate the convergent and distinctive regulatory mechanisms between preferred (ammonium) and alternative nitrogen (nitrate) metabolism at the transcriptome level, leading to better understanding of inorganic nitrogen metabolism in V. dahliae.
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Affiliation(s)
- Chen Tang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Wenwen Li
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Steven J Klosterman
- Agricultural Research Service, United States Department of Agriculture, Salinas, CA, United States
| | - Yonglin Wang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
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27
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Characterization of ETFDH and PHGDH Mutations in a Patient with Mild Glutaric Aciduria Type II and Serine Deficiency. Genes (Basel) 2021; 12:genes12050703. [PMID: 34066864 PMCID: PMC8150808 DOI: 10.3390/genes12050703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Glutaric aciduria type II (GA-II) is a rare autosomal recessive disease caused by defects in electron transfer flavoprotein (ETF), ultimately causing insufficiencies in multiple acyl-CoA dehydrogenase (MAD). 3-phosphoglycerate dehydrogenase (3-PHGDH) deficiency, is another rare autosomal disorder that appears due to a defect in the synthesis of L-serine amino acid. Several mutations of ETFDH and PHGDH genes have been associated with different forms of GA-II and serine deficiency, respectively. In this study, we report a unique case of GA-II with serine deficiency using biochemical, genetic, and in silico approaches. The proband of Syrian descent had positive newborn screening (NBS) for GA-II. At two years of age, the patient presented with developmental regression, ataxia, and intractable seizures. Results of amino acid profiling demonstrated extremely low levels of serine. Confirmatory tests for GA-II and whole exome sequencing (WES) were performed to determine the etiology of intractable seizure. Sequencing results indicated a previously reported homozygous missense mutation, c.679 C>A (p.Pro227Thr) in the ETFDH gene and a novel missense homozygous mutation c.1219 T>C (p.Ser407Pro) in the PHGDH gene. In silico tools predicted these mutations as deleterious. Here, the clinical and biochemical investigations indicate that ETFDH:p.Pro227Thr and PHGDH:p.Ser407Pro variants likely underlie the pathogenesis of GA-II and serine deficiency, respectively. This study indicates that two rare autosomal recessive disorders should be considered in consanguineous families, more specifically in those with atypical presentation.
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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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Xu H, Qing X, Wang Q, Li C, Lai L. Dimerization of PHGDH via the catalytic unit is essential for its enzymatic function. J Biol Chem 2021; 296:100572. [PMID: 33753166 PMCID: PMC8081924 DOI: 10.1016/j.jbc.2021.100572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022] Open
Abstract
Human D-3-phosphoglycerate dehydrogenase (PHGDH), a key enzyme in de novo serine biosynthesis, is amplified in various cancers and serves as a potential target for anticancer drug development. To facilitate this process, more information is needed on the basic biochemistry of this enzyme. For example, PHGDH was found to form tetramers in solution and the structure of its catalytic unit (sPHGDH) was solved as a dimer. However, how the oligomeric states affect PHGDH enzyme activity remains elusive. We studied the dependence of PHGDH enzymatic activity on its oligomeric states. We found that sPHGDH forms a mixture of monomers and dimers in solution with a dimer dissociation constant of ∼0.58 μM, with the enzyme activity depending on the dimer content. We computationally identified hotspot residues at the sPHGDH dimer interface. Single-point mutants at these sites disrupt dimer formation and abolish enzyme activity. Molecular dynamics simulations showed that dimer formation facilitates substrate binding and maintains the correct conformation required for enzyme catalysis. We further showed that the full-length PHGDH exists as a dynamic mixture of monomers, dimers, and tetramers in solution with enzyme concentration-dependent activity. Mutations that can completely disrupt the sPHGDH dimer show different abilities to interrupt the full-length PHGDH tetramer. Among them, E108A and I121A can also disrupt the oligomeric structures of the full-length PHGDH and abolish its enzyme activity. Our study indicates that disrupting the oligomeric structure of PHGDH serves as a novel strategy for PHGDH drug design and the hotspot residues identified can guide the design process.
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Affiliation(s)
- Hanyu Xu
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaoyu Qing
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Li M, Wu C, Yang Y, Zheng M, Yu S, Wang J, Chen L, Li H. 3-Phosphoglycerate dehydrogenase: a potential target for cancer treatment. Cell Oncol (Dordr) 2021; 44:541-556. [PMID: 33735398 DOI: 10.1007/s13402-021-00599-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Metabolic changes have been recognized as an important hallmark of cancer cells. Cancer cells can promote their own growth and proliferation through metabolic reprogramming. Particularly, serine metabolism has frequently been reported to be dysregulated in tumor cells. 3-Phosphoglycerate dehydrogenase (PHGDH) catalyzes the first step in the serine biosynthesis pathway and acts as a rate-limiting enzyme involved in metabolic reprogramming. PHGDH upregulation has been observed in many tumor types, and inhibition of PHGDH expression has been reported to inhibit the proliferation of PHGDH-overexpressing tumor cells, indicating that it may be utilized as a target for cancer treatment. Recently identified inhibitors targeting PHGDH have already shown effectiveness. A further in-depth analysis and concomitant development of PHGDH inhibitors will be of great value for the treatment of cancer. CONCLUSIONS In this review we describe in detail the role of PHGDH in various cancers and inhibitors that have recently been identified to highlight progression in cancer treatment. We also discuss the development of new drugs and treatment modalities based on PHGDH targets. Overexpression of PHGDH has been observed in melanoma, breast cancer, nasopharyngeal carcinoma, parathyroid adenoma, glioma, cervical cancer and others. PHGDH may serve as a molecular biomarker for the diagnosis, prognosis and treatment of these cancers. The design and development of novel PHGDH inhibitors may have broad implications for cancer treatment. Therapeutic strategies of PHGDH inhibitors in combination with traditional chemotherapeutic drugs may provide new perspectives for precision medicine and effective personalized treatment for cancer patients.
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Affiliation(s)
- Mingxue Li
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Canrong Wu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yueying Yang
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Silin Yu
- Department of Medicinal Chemistry and Natural Medicine Chemistry (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, 150081, China
| | - Jinhui Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, 150081, China.
| | - Lixia Chen
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Hua Li
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China.
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31
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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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Kim TK, Tirloni L, Bencosme-Cuevas E, Kim TH, Diedrich JK, Yates JR, Mulenga A. Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs. BMC Genomics 2021; 22:152. [PMID: 33663385 PMCID: PMC7930271 DOI: 10.1186/s12864-021-07429-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lyme disease (LD) caused by Borrelia burgdorferi is the most prevalent tick-borne disease. There is evidence that vaccines based on tick proteins that promote tick transmission of B. burgdorferi could prevent LD. As Ixodes scapularis nymph tick bites are responsible for most LD cases, this study sought to identify nymph tick saliva proteins associated with B. burgdorferi transmission using LC-MS/MS. Tick saliva was collected using a non-invasive method of stimulating ticks (uninfected and infected: unfed, and every 12 h during feeding through 72 h, and fully-fed) to salivate into 2% pilocarpine-PBS for protein identification using LC-MS/MS. RESULTS We identified a combined 747 tick saliva proteins of uninfected and B. burgdorferi infected ticks that were classified into 25 functional categories: housekeeping-like (48%), unknown function (18%), protease inhibitors (9%), immune-related (6%), proteases (8%), extracellular matrix (7%), and small categories that account for <5% each. Notably, B. burgdorferi infected ticks secreted high number of saliva proteins (n=645) than uninfected ticks (n=376). Counter-intuitively, antimicrobial peptides, which function to block bacterial infection at tick feeding site were suppressed 23-85 folds in B. burgdorferi infected ticks. Similar to glycolysis enzymes being enhanced in mammalian cells exposed to B. burgdorferi : eight of the 10-glycolysis pathway enzymes were secreted at high abundance by B. burgdorferi infected ticks. Of significance, rabbits exposed to B. burgdorferi infected ticks acquired potent immunity that caused 40-60% mortality of B. burgdorferi infected ticks during the second infestation compared to 15-28% for the uninfected. This might be explained by ELISA data that show that high expression levels of immunogenic proteins in B. burgdorferi infected ticks. CONCLUSION Data here suggest that B. burgdorferi infection modified protein content in tick saliva to promote its survival at the tick feeding site. For instance, enzymes; copper/zinc superoxide dismutase that led to production of H2O2 that is toxic to B. burgdorferi were suppressed, while, catalase and thioredoxin that neutralize H2O2, and pyruvate kinase which yields pyruvate that protects Bb from H2O2 killing were enhanced. We conclude data here is an important resource for discovery of effective antigens for a vaccine to prevent LD.
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Affiliation(s)
- Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Department of Diagnostic Medicine and Veterinary Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, United States of America
| | - Emily Bencosme-Cuevas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Tae Heung Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
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Wang D, Mu Y, Hu X, Ma B, Wang Z, Zhu L, Xu J, Huang C, Pan Y. Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively. BMC PLANT BIOLOGY 2021; 21:34. [PMID: 33422018 PMCID: PMC7796551 DOI: 10.1186/s12870-020-02806-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/20/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids. RESULTS Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. CONCLUSIONS Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.
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Affiliation(s)
- Daoping Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yongying Mu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xiaojiao Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, People's Republic of China
| | - Bo Ma
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Zhibo Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Jiang Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Changling Huang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, People's Republic of China.
| | - Yinghong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, People's Republic of China.
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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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35
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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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Yoshida K, Ohtaka K, Hirai MY, Hisabori T. Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana. J Biol Chem 2020; 295:14906-14915. [PMID: 32848019 PMCID: PMC7606689 DOI: 10.1074/jbc.ra120.014263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/22/2020] [Indexed: 12/22/2022] Open
Abstract
Thiol-based redox regulation is a post-translational protein modification for controlling enzyme activity by switching oxidation/reduction states of Cys residues. In plant cells, numerous proteins involved in a wide range of biological systems have been suggested as the target of redox regulation; however, our knowledge on this issue is still incomplete. Here we report that 3-phosphoglycerate dehydrogenase (PGDH) is a novel redox-regulated protein. PGDH catalyzes the first committed step of Ser biosynthetic pathway in plastids. Using an affinity chromatography-based method, we found that PGDH physically interacts with thioredoxin (Trx), a key factor of redox regulation. The in vitro studies using recombinant proteins from Arabidopsis thaliana showed that a specific PGDH isoform, PGDH1, forms the intramolecular disulfide bond under nonreducing conditions, which lowers PGDH enzyme activity. MS and site-directed mutagenesis analyses allowed us to identify the redox-active Cys pair that is mainly involved in disulfide bond formation in PGDH1; this Cys pair is uniquely found in land plant PGDH. Furthermore, we revealed that some plastidial Trx subtypes support the reductive activation of PGDH1. The present data show previously uncharacterized regulatory mechanisms of PGDH and expand our understanding of the Trx-mediated redox-regulatory network in plants.
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Affiliation(s)
- Keisuke Yoshida
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Kinuka Ohtaka
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan; Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, Japan
| | | | - Toru Hisabori
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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37
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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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Maldonado JA, Firneno TJ, Roelke CE, Rains ND, Mwgiri J, Fujita MK. Transcriptome sequencing reveals signatures of positive selection in the Spot-Tailed Earless Lizard. PLoS One 2020; 15:e0234504. [PMID: 32542006 PMCID: PMC7295237 DOI: 10.1371/journal.pone.0234504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/26/2020] [Indexed: 11/21/2022] Open
Abstract
The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless Lizard (Holbrookia subcaudalis), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (Holbrookia maculata). Our efforts produced high quality and robust transcriptome assemblies validated by 1) quantifying the number of processed reads represented in the transcriptome assembly and 2) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three Holbrookia species, Anolis carolinensis, and Sceloporus undulatus. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the Holbrookia lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern H. lacerata and Southern H. subcaudalis that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species.
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Affiliation(s)
- Jose A. Maldonado
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America
| | - Thomas J. Firneno
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America
| | - Corey E. Roelke
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America
| | - Nathan D. Rains
- Texas Parks and Wildlife Department, Austin, Texas, TX, United States of America
| | - Juliet Mwgiri
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America
| | - Matthew K. Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America
- * E-mail:
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Petchampai N, Isoe J, Horvath TD, Dagan S, Tan L, Lorenzi PL, Hawke DH, Scaraffia PY. Mass spectrometry-based stable-isotope tracing uncovers metabolic alterations in pyruvate kinase-deficient Aedes aegypti mosquitoes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 121:103366. [PMID: 32276114 PMCID: PMC7249512 DOI: 10.1016/j.ibmb.2020.103366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 05/11/2023]
Abstract
A recent in vitro characterization of a recombinant pyruvate kinase (PK) from Aedes aegypti mosquitoes demonstrated that the enzyme is uniquely regulated by multiple allosteric effectors. Here, we further explored PK gene and protein expression, and enzymatic activity in key metabolic tissues of mosquitoes maintained under different nutritional conditions. We also studied the metabolic effects of PK depletion using several techniques including RNA interference and mass spectrometry-based stable-isotope tracing. Transcriptional analysis showed a dynamic post-feeding PK mRNA expression pattern within and across mosquito tissues, whereas corresponding protein levels remained stable throughout the time course analyzed. Nevertheless, PK activity significantly differed in the fat body of sucrose-, blood-fed, and starved mosquitoes. Genetic silencing of PK did not alter survival in blood-fed females maintained on sucrose. However, an enhanced survivorship was observed in PK-deficient females maintained under different nutritional regimens. Our results indicate that mosquitoes overcame PK deficiency by up-regulating the expression of genes encoding NADP-malic enzyme-1, phosphoenolpyruvate carboxykinase-1, phosphoglycerate dehydrogenase and glutamate dehydrogenase, and by decreasing glucose oxidation and metabolic pathways associated with ammonia detoxification. Taken together, our data demonstrate that PK confers to A. aegypti a metabolic plasticity to tightly regulate both carbon and nitrogen metabolism.
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Affiliation(s)
- Natthida Petchampai
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Jun Isoe
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Thomas D Horvath
- Department of Bioinformatics and Computational Biology, Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shai Dagan
- Israel Institute for Biological Research (IIBR), Ness Ziona, 74100, Israel
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David H Hawke
- Department of Systems Biology, Proteomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Patricia Y Scaraffia
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
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Abstract
Warburg and coworkers' observation of altered glucose metabolism in tumours has been neglected for several decades, which, in part, was because of an initial misinterpretation of the basis of their finding. Following the realisation that genetic alterations are often linked to metabolism, and that the tumour micro-environment imposes different demands on cancer cells, has led to a reinvestigation of cancer metabolism in recent years. Increasing our understanding of the drivers and consequences of the Warburg effect in cancer and beyond will help to identify new therapeutic strategies as well as to identify new prognostic and therapeutic biomarkers. Here we discuss the initial findings of Warburg and coworkers regarding cancer cell glucose metabolism, how these studies came into focus again in recent years following the discovery of metabolic oncogenes, and the therapeutic potential that lies within targeting the altered metabolic phenotype in cancer. In addition, another essential nutrient in cancer metabolism, glutamine, will be discussed.
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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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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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Haque MR, Hirowatari A, Koyanagi A, Ichinose T, Abiru M, Mohri S, Furuya S, Yamamoto K. Molecular characterization and expression analysis of a phosphoserine aminotransferase involving l-serine synthesis from silkworm, Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 101:e21553. [PMID: 31004387 DOI: 10.1002/arch.21553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
In this study, we identified and characterized a phosphoserine aminotransferase (bmPSAT) from Bombyx mori (B. mori) that is responsible for l-serine biosynthesis. A complementary DNA that encodes bmPSAT was cloned by reverse transcriptase polymerase reaction and sequenced. The presumed amino acid sequence revealed 47-87% identity with known PSATs from insects, humans, plants, and bacteria. Through phylogenetic analysis, we found that bmPSAT is evolutionary related to insect PSATs. Recombinant bmPSAT was produced in Escherichia coli by using a cold-shock promotor and purified to homogeneity. This enzyme utilizes phosphohydroxypyruvate and glutamate for transamination. bmPSAT messenger RNA (mRNA) was expressed at higher levels in several tissues of standard strain silkworm including the silk gland, whereas a sericin-deficient silkworm strain exhibited a diminished expression of bmPSAT mRNA in the silk gland. These findings indicate that bmPSAT may play an important role in synthesizing and supplying l-serine in the larva of B. mori.
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Affiliation(s)
- Mohammad R Haque
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Aiko Hirowatari
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Ayumi Koyanagi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takashi Ichinose
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Maiko Abiru
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Shinya Mohri
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Shigeki Furuya
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kohji Yamamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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