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Esteban-Amo MJ, Jiménez-Cuadrado P, Serrano-Lorenzo P, de la Fuente MÁ, Simarro M. Succinate Dehydrogenase and Human Disease: Novel Insights into a Well-Known Enzyme. Biomedicines 2024; 12:2050. [PMID: 39335562 PMCID: PMC11429145 DOI: 10.3390/biomedicines12092050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/26/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
Succinate dehydrogenase (also known as complex II) plays a dual role in respiration by catalyzing the oxidation of succinate to fumarate in the tricarboxylic acid (TCA) cycle and transferring electrons from succinate to ubiquinone in the mitochondrial electron transport chain (ETC). Owing to the privileged position of SDH/CII, its dysfunction leads to TCA cycle arrest and altered respiration. This review aims to elucidate the widely documented profound metabolic effects of SDH/CII deficiency, along with the newly unveiled survival mechanisms in SDH/CII-deficient cells. Such an understanding reveals exploitable vulnerabilities for strategic targeting, which is crucial for the development of novel and more precise therapies for primary mitochondrial diseases, as well as for familial and sporadic cancers associated with SDH/CII mutations.
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Affiliation(s)
- María J. Esteban-Amo
- Department of Cell Biology, Genetics, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (M.J.E.-A.); (P.J.-C.); (M.Á.d.l.F.)
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| | - Patricia Jiménez-Cuadrado
- Department of Cell Biology, Genetics, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (M.J.E.-A.); (P.J.-C.); (M.Á.d.l.F.)
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| | - Pablo Serrano-Lorenzo
- Mitochondrial Disorders Laboratory, Clinical Biochemistry Department, Hospital 12 de Octubre Research Institute (imas12), 28041 Madrid, Spain;
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel Á. de la Fuente
- Department of Cell Biology, Genetics, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (M.J.E.-A.); (P.J.-C.); (M.Á.d.l.F.)
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| | - María Simarro
- Department of Cell Biology, Genetics, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (M.J.E.-A.); (P.J.-C.); (M.Á.d.l.F.)
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
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2
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Gou Y, Li T, Wang Y. Active-Site Oxygen Accessibility and Catalytic Loop Dynamics of Plant Aromatic Amino Acid Decarboxylases from Molecular Simulations. Biochemistry 2024; 63:1980-1990. [PMID: 39008055 PMCID: PMC11308512 DOI: 10.1021/acs.biochem.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
Aromatic amino acid decarboxylases (AAADs) are pyridoxal-5'-phosphate (PLP)-dependent enzymes that catalyze the decarboxylation of aromatic amino acid l-amino acids. In plants, apart from canonical AAADs that catalyze the straightforward decarboxylation reaction, other members of the AAAD family function as aromatic acetaldehyde synthases (AASs) and catalyze more complex decarboxylation-dependent oxidative deamination. The interconversion between a canonical AAAD and an AAS can be achieved by a single tyrosine-phenylalanine mutation in the large catalytic loop of the enzymes. In this work, we report implicit ligand sampling (ILS) calculations of the canonical l-tyrosine decarboxylase from Papaver somniferum (PsTyDC) that catalyzes l-tyrosine decarboxylation and its Y350F mutant that instead catalyzes the decarboxylation-dependent oxidative deamination of the same substrate. Through comparative analysis of the resulting three-dimensional (3D) O2 free energy profiles, we evaluate the impact of the key tyrosine/phenylalanine mutation on oxygen accessibility to both the wild type and Y350F mutant of PsTyDC. Additionally, using molecular dynamics (MD) simulations of the l-tryptophan decarboxylase from Catharanthus roseus (CrTDC), we further investigate the dynamics of a large catalytic loop known to be indispensable to all AAADs. Results of our ILS and MD calculations shed new light on how key structural elements and loop conformational dynamics underlie the enzymatic functions of different members of the plant AAAD family.
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Affiliation(s)
- Yitao Gou
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tianjie Li
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yi Wang
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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3
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Cui JJ, Zhang Y, Ju KS. Phosphonoalamides Reveal the Biosynthetic Origin of Phosphonoalanine Natural Products and a Convergent Pathway for Their Diversification. Angew Chem Int Ed Engl 2024; 63:e202405052. [PMID: 38780891 DOI: 10.1002/anie.202405052] [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: 03/13/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Phosphonate natural products, with their potent inhibitory activity, have found widespread use across multiple industries. Their success has inspired development of genome mining approaches that continue to reveal previously unknown bioactive scaffolds and biosynthetic insights. However, a greater understanding of phosphonate metabolism is required to enable prediction of compounds and their bioactivities from sequence information alone. Here, we expand our knowledge of this natural product class by reporting the complete biosynthesis of the phosphonoalamides, antimicrobial tripeptides with a conserved N-terminal l-phosphonoalanine (PnAla) residue produced by Streptomyces. The phosphonoalamides result from the convergence of PnAla biosynthesis and peptide ligation pathways. We elucidate the biochemistry underlying the transamination of phosphonopyruvate to PnAla, a new early branchpoint in phosphonate biosynthesis catalyzed by an aminotransferase with evolved specificity for phosphonate metabolism. Peptide formation is catalyzed by two ATP-grasp ligases, the first of which produces dipeptides, and a second which ligates dipeptides to PnAla to produce phosphonoalamides. Substrate specificity profiling revealed a dramatic expansion of dipeptide and tripeptide products, while finding PnaC to be the most promiscuous dipeptide ligase reported thus far. Our findings highlight previously unknown transformations in natural product biosynthesis, promising enzyme biocatalysts, and unveil insights into the diversity of phosphonopeptide natural products.
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Affiliation(s)
- Jerry J Cui
- Department of Microbiology, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
| | - Yeying Zhang
- Department of Microbiology, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
- Division of Medicinal Chemistry and Pharmacognosy, Center for Applied Plant Sciences, Infectious Disease Institute, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
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4
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Gul A, Rao AQ, Ahmed M, Latif A, Bakhsh A, Iftikhar S. The Increased aspartate levels in transgenic cotton (Gossypium hirsutum L.) lead to improved tolerance against whitefly (Bemisia tabaci, Gennadius). PHYSIOLOGIA PLANTARUM 2024; 176:e14491. [PMID: 39171614 DOI: 10.1111/ppl.14491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/07/2024] [Indexed: 08/23/2024]
Abstract
The whitefly, a polyphagous insect pest feeding on nearly 1328 plant species, is a major threat to global cotton production and incurs up to 50% yield losses in cotton production in Pakistan. We investigated whether increased aspartate in phloem sap imparts whitefly toxicity and protects cotton plants from intense damage. The enzymatic step for aspartate production is carried through aspartate aminotransferase (AAT). In this study, we constitutively overexpressed the Oryza sativa cytoplasmic AAT (OsAAT2) under the CaMV35S promoter in Gossypium hirsutum cv. CIM-482. Real-time PCR analysis of the AAT transcripts revealed a 2.85- to 31.7-fold increase in mRNA levels between the different cotton lines. A substantial increase in the free-amino acid content of the major N-assimilation and transport amino acids (aspartate, glutamate, asparagine, and glutamine) was seen in the phloem sap of the transgenic cotton lines. The bioassay revealed that the two transgenic cotton lines with the highest free aspartate content in the phloem sap exhibited 97 and 94% mortality in the adult whitefly population and a 98 and 96% decline in subsequent nymph populations, respectively. There was also a significant change in the physiological behaviour of the transgenic cotton lines, with an increased net assimilation (A), gaseous exchange (Gs) and rate of transpiration (E). Improved morphological characteristics like plant height, total number of bolls and fiber yield were recorded in transgenic cotton lines. The AAT gene shows promise in mitigating whitefly infestations and enhancing the overall health and yield of cotton plants.
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Affiliation(s)
- Ambreen Gul
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mukhtar Ahmed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ayesha Latif
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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5
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Koper K, Han SW, Kothadia R, Salamon H, Yoshikuni Y, Maeda HA. Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proc Natl Acad Sci U S A 2024; 121:e2405524121. [PMID: 38885378 PMCID: PMC11214133 DOI: 10.1073/pnas.2405524121] [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: 04/02/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism, essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here, we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread nonorthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterization of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multisubstrate specificity by employing different nonconserved active site residues. These findings illustrate that AT family enzymes had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multifunctional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Sang-Woo Han
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Biotechnology, Konkuk University, Chungju27478, South Korea
| | - Ramani Kothadia
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Hugh Salamon
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan 060-8589
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo183-8538, Japan
| | - Hiroshi A. Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
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6
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Zhang DK, Song KY, Yan YQ, Zheng JT, Xu J, Da LT, Xu MJ. Structural and mechanistic investigations on CC bond forming α-oxoamine synthase allowing L-glutamate as substrate. Int J Biol Macromol 2024; 268:131696. [PMID: 38642679 DOI: 10.1016/j.ijbiomac.2024.131696] [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: 01/07/2024] [Revised: 03/23/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Carbon‑carbon (C-C) bonds serve as the fundamental structural backbone of organic molecules. As a critical CC bond forming enzyme, α-oxoamine synthase is responsible for the synthesis of α-amino ketones by performing the condensation reaction between amino acids and acyl-CoAs. We previously identified an α-oxoamine synthase (AOS), named as Alb29, involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072. This enzyme belongs to the α-oxoamine synthase family, a subfamily under the pyridoxal 5'-phosphate (PLP) dependent enzyme superfamily. In this study, we report the crystal structures of Alb29 bound to PLP and L-Glu, which provide the atomic-level structural insights into the substrate recognition by Alb29. We discover that Alb29 can catalyze the amino transformation from L-Gln to L-Glu, besides the condensation of L-Glu with β-methylcrotonyl coenzyme A. Subsequent structural analysis has revealed that one flexible loop in Alb29 plays an important role in both amino transformation and condensation. Based on the crystal structure of the S87G mutant in the loop region, we capture two distinct conformations of the flexible loop in the active site, compared with the wild-type Alb29. Our study offers valuable insights into the catalytic mechanism underlying substrate recognition of Alb29.
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Affiliation(s)
- Dai-Ke Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Kai-Yuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ya-Qian Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jian-Ting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
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7
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Chen Z, Zhang S, Sun X, Meng D, Lai C, Zhang M, Wang P, Huang X, Gao X. Analysis of the Protective Effects of Rosa roxburghii-Fermented Juice on Lipopolysaccharide-Induced Acute Lung Injury in Mice through Network Pharmacology and Metabolomics. Nutrients 2024; 16:1376. [PMID: 38732622 PMCID: PMC11085916 DOI: 10.3390/nu16091376] [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: 03/27/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Acute lung injury, a fatal condition characterized by a high mortality rate, necessitates urgent exploration of treatment modalities. Utilizing UHPLS-Q-Exactive Orbitrap/MS, our study scrutinized the active constituents present in Rosa roxburghii-fermented juice (RRFJ) while also assessing its protective efficacy against LPS-induced ALI in mice through lung histopathological analysis, cytokine profiling, and oxidative stress assessment. The protective mechanism of RRFJ against ALI in mice was elucidated utilizing metabolomics, network pharmacology, and molecular docking methodologies. Our experimental findings demonstrate that RRFJ markedly ameliorates pathological injuries in ALI-afflicted mice, mitigates systemic inflammation and oxidative stress, enhances energy metabolism, and restores dysregulated amino acid and arachidonic acid metabolic pathways. This study indicates that RRFJ can serve as a functional food for adjuvant treatment of ALI.
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Affiliation(s)
- Zhiyu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Shuo Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Experimental Animal Center of Guizhou Medical University, Guiyang 550025, China
| | - Xiaodong Sun
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Duo Meng
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Chencen Lai
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Min Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Pengjiao Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Xuncai Huang
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Xiuli Gao
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China; (Z.C.); (S.Z.); (X.S.); (D.M.); (C.L.); (M.Z.); (P.W.); (X.H.)
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
- Guizhou Provincial Engineering Research Center of Food Nutrition and Health, Guizhou Medical University, Guiyang 550025, China
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8
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Drago VN, Devos JM, Blakeley MP, Forsyth VT, Parks JM, Kovalevsky A, Mueser TC. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101827. [PMID: 38645802 PMCID: PMC11027755 DOI: 10.1016/j.xcrp.2024.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
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Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Lead contact
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9
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Han SW, Jang Y, Kook J, Jang J, Shin JS. Reprogramming biocatalytic futile cycles through computational engineering of stereochemical promiscuity to create an amine racemase. Nat Commun 2024; 15:49. [PMID: 38169460 PMCID: PMC10761954 DOI: 10.1038/s41467-023-44218-7] [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: 05/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Repurposing the intrinsic properties of natural enzymes can offer a viable solution to current synthetic challenges through the development of novel biocatalytic processes. Although amino acid racemases are ubiquitous in living organisms, an amine racemase (AR) has not yet been discovered despite its synthetic potential for producing chiral amines. Here, we report the creation of an AR based on the serendipitous discovery that amine transaminases (ATAs) can perform stereoinversion of 2-aminobutane. Kinetic modeling revealed that the unexpected off-pathway activity results from stereochemically promiscuous futile cycles due to incomplete stereoselectivity for 2-aminobutane. This finding motivated us to engineer an S-selective ATA through in silico alanine scanning and empirical combinatorial mutations, creating an AR with broad substrate specificity. The resulting AR, carrying double point mutations, enables the racemization of both enantiomers of diverse chiral amines in the presence of a cognate ketone. This strategy may be generally applicable to a wide range of transaminases, paving the way for the development of new-to-nature racemases.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Department of Biotechnology, Konkuk University, Chungju, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jihyun Kook
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jeesu Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
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10
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Lian L, Qiao J, Guo X, Xing Z, Ren A, Zhao M, Zhu J. The transcription factor GCN4 contributes to maintaining intracellular amino acid contents under nitrogen-limiting conditions in the mushroom Ganoderma lucidum. Microb Cell Fact 2023; 22:205. [PMID: 37817159 PMCID: PMC10563202 DOI: 10.1186/s12934-023-02213-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Edible mushrooms are delicious in flavour and rich in high-quality protein and amino acids required by humans. A transcription factor, general control nonderepressible 4 (GCN4), can regulate the expression of genes involved in amino acid metabolism in yeast and mammals. A previous study revealed that GCN4 plays a pivotal role in nitrogen utilization and growth in Ganoderma lucidum. However, its regulation is nearly unknown in mushrooms. RESULTS In this study, we found that the amino acid contents reached 120.51 mg per gram of mycelia in the WT strain under 60 mM asparagine (Asn) conditions, but decreased by 62.96% under 3 mM Asn conditions. Second, silencing of gcn4 resulted in a 54.2% decrease in amino acid contents under 60 mM Asn, especially for the essential and monosodium glutamate-like flavour amino acids. However, these effects were more pronounced under 3 mM Asn. Third, silencing of gcn4 markedly inhibited the expression of amino acid biosynthesis and transport genes. In addition, GCN4 enhanced the tricarboxylic acid cycle (TCA) and glycolytic pathway and inhibited the activity of target of rapamycin complex 1 (TORC1), thus being beneficial for maintaining amino acid homeostasis. CONCLUSION This study confirmed that GCN4 contributes to maintaining the amino acid contents in mushrooms under low concentrations of nitrogen. In conclusion, our study provides a research basis for GCN4 to regulate amino acid synthesis and improve the nutrient contents of edible mushrooms.
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Affiliation(s)
- Lingdan Lian
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jinjin Qiao
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Xiaoyu Guo
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Zhenzhen Xing
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Ang Ren
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Microbiology Department, College of Life Sciences, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China.
- College of Life Sciences, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, PR China.
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11
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Melkonian TR, Vuksanovic N, Silvaggi NR. Probing mechanistic questions in the PLP- and O 2-dependent l-Arg oxidases. Methods Enzymol 2023; 685:493-529. [PMID: 37245913 DOI: 10.1016/bs.mie.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The pyridoxal-5'-phosphate-dependent l-Arg oxidases are unusual in that they are able to catalyze 4-electron oxidations of arginine using only the PLP cofactor. No metals or other accessory cosubstrates are involved; only arginine, dioxygen, and PLP. The catalytic cycles of these enzymes are replete with colored intermediates whose accumulation and decay can be monitored spectrophotometrically. This makes the l-Arg oxidases excellent subjects for detailed mechanistic investigations. They are worth studying, because they can teach us much about how PLP-dependent enzymes modulate the cofactor (structure-function-dynamics) and how new activities can arise from existing enzyme scaffolds. Herein we describe a series of experiments that can be used to probe the mechanisms of l-Arg oxidases. These methods by no means originated in our lab but were learned from talented researchers in other enzyme fields (flavoenzymes and Fe(II)-dependent oxygenases) and have been adapted to fit the requirements of our system. We present practical information for expressing and purifying the l-Arg oxidases, protocols for running stopped-flow experiments to examine the reactions with l-Arg and with dioxygen, and a tandem mass spectrometry-based quench-flow assay to follow the accumulation of the products of the hydroxylating l-Arg oxidases.
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Affiliation(s)
- Trevor R Melkonian
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | | | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, United States.
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12
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Li S, Shao Z, Lu C, Duan D. Isolation and functional verification of an aspartate aminotransferase gene from Neoporphyra haitanensis. BMC PLANT BIOLOGY 2023; 23:150. [PMID: 36941626 PMCID: PMC10029208 DOI: 10.1186/s12870-023-04158-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Neoporphyra haitanensis is a commercial laver species in China. Aspartic acid is an important flavor amino acid, and aspartate aminotransferase (AAT) is a crucial enzyme in its biosynthesis. In this study, we cloned one AAT gene (NhAAT) from the red alga N. haitanensis and investigated its sequence structure, transcriptional expression and enzymatic characteristics. The purpose of our research is to obtain a functional AAT responsible for the biosynthesis of aspartic acid from red seaweeds, which has the potential to influence the flavor of N. haitanensis. RESULTS Sequence analysis showed that NhAAT contains a conserved domain of Aminotran_1_2, which belongs to the transaminase superfamily. The secondary structure of NhAAT is dominated by α-helix. The results of enzymatic characterization illustrated that the NhAAT has highest catalytic activity at 45 °C and pH 7.5 in both forward and reverse reactions. The calculated Km values of NhAAT was 5.67 and 6.16 mM for L-glutamic acid and L-aspartic acid, respectively. Quantitative analysis showed that the NhAAT expression of N. haitanensis collected in late harvest (Dec) was 4.5 times that of N. haitanensis collected in early harvest (Oct), while the aspartic acid content of N. haitanensis collected in late harvest (Dec) was 1.2 times that of N. haitanensis collected in early harvest (Oct). CONCLUSION The results of enzyme kinetics indicated that NhAAT prefers to catalyze the reaction in the direction of aspartic acid production. Moreover, the trend of NhAAT expression level was consistent with that of aspartic acid content in N. haitanensis in different harvest periods. Our research is helpful to understand the accumulation and regulation of amino acids in N. haitanensis in different habitats and the taste difference of N. haitanensis in different harvest periods.
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Affiliation(s)
- Shuang Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Chang Lu
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai, 264005, P. R. China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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13
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Li ZM, Bai F, Wang X, Xie C, Wan Y, Li Y, Liu J, Li Z. Kinetic Characterization and Catalytic Mechanism of N-Acetylornithine Aminotransferase Encoded by slr1022 Gene from Synechocystis sp. PCC6803. Int J Mol Sci 2023; 24:ijms24065853. [PMID: 36982927 PMCID: PMC10057298 DOI: 10.3390/ijms24065853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The enzyme encoded by slr1022 gene from Synechocystis sp. PCC6803 was reported to function as N-acetylornithine aminotransferase, γ-aminobutyric acid aminotransferase, and ornithine aminotransferase, which played important roles in multiple metabolic pathways. Among these functions, N-acetylornithine aminotransferase catalyzes the reversible conversion of N-acetylornithine to N-acetylglutamate-5-semialdehyde with PLP as cofactor, which is a key step in the arginine biosynthesis pathway. However, the investigation of the detailed kinetic characteristics and catalytic mechanism of Slr1022 has not been carried out yet. In this study, the exploration of kinetics of recombinant Slr1022 illustrated that Slr1022 mainly functioned as N-acetylornithine aminotransferase with low substrate specificity to γ-aminobutyric acid and ornithine. Kinetic assay of Slr1022 variants and the model structure of Slr1022 with N-acetylornithine-PLP complex revealed that Lys280 and Asp251 residues were the key amino acids of Slr1022. The respective mutation of the above two residues to Ala resulted in the activity depletion of Slr1022. Meanwhile, Glu223 residue was involved in substrate binding and it served as a switch between the two half reactions. Other residues such as Thr308, Gln254, Tyr39, Arg163, and Arg402 implicated a substrate recognition and catalytic process of the reaction. The results of this study further enriched the understanding of the catalytic kinetics and mechanism of N-acetylornithine aminotransferase, especially from cyanobacteria.
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Affiliation(s)
- Zhi-Min Li
- College of Chemistry and Materials, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fumei Bai
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoqin Wang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Congcong Xie
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuting Wan
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yating Li
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianping Liu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
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14
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Effects of glutamate oxaloacetate transaminase on reactive oxygen species in Ganoderma lucidum. Appl Microbiol Biotechnol 2023; 107:1845-1861. [PMID: 36754884 DOI: 10.1007/s00253-023-12417-3] [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: 08/05/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/10/2023]
Abstract
Nitrogen metabolism can regulate mycelial growth and secondary metabolism in Ganoderma lucidum. As an important enzyme in intracellular amino acid metabolism, glutamate oxaloacetate transaminase (GOT) has many physiological functions in animals and plants, but its function in fungi has been less studied. In the present study, two GOT isoenzymes were found in G. lucidum; one is located in the mitochondria (GOT1), and the other is located in the cytoplasm (GOT2). The reactive oxygen species (ROS) level was increased in got1 silenced strains and was approximately 1.5-fold higher than that in the wild-type (WT) strain, while silencing got2 did not affect the ROS level. To explore how GOT affects ROS in G. lucidum, experiments related to the generation and elimination of intracellular ROS were conducted. First, compared with that in the WT strain, the glutamate content, one of the substrates of GOT, decreased when got1 or got2 was knocked down, and the glutathione (l-γ-glutamyl-l-cysteinylglycine) (GSH) content decreased by approximately 38.6%, 19.3%, and 40.1% in got1 silenced strains, got2 silenced strains, and got1/2 co-silenced strains respectively. Second, GOT also affects glucose metabolism. The pyruvate (PA), acetyl-CoA and α-ketoglutarate (α-KG) contents decreased in got1 and got2 silenced strains, and the transcription levels of most genes involved in the glycolytic pathway and the tricarboxylic acid cycle increased. The NADH content was increased in got1 silenced strains and got2 silenced strains, and the NAD+/NADH ratio was decreased, which might result in mitochondrial ROS production. Compared with the WT strain, the mitochondrial ROS level was approximately 1.5-fold higher in the got1 silenced strains. In addition, silencing of got1 or got2 resulted in a decrease in antioxidant enzymes, including superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase. Finally, ganoderic acid (GA) was increased by approximately 40% in got1 silenced strains compared with the WT strain, while silencing of got2 resulted in a 10% increase in GA biosynthesis. These findings provide new insights into the effect of GOT on ROS and secondary metabolism in fungi. KEY POINTS: • GOT plays important roles in ROS level in Ganoderma lucidum. • Silencing of got1 resulted in decrease in GSH content and antioxidant enzymes activities, but an increase in mitochondrial ROS level in G. lucidum. • Silencing of got1 and got2 resulted in an increase in ganoderic acid biosynthesis in G. lucidum.
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15
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Koper K, Hataya S, Hall AG, Takasuka TE, Maeda HA. Biochemical characterization of plant aromatic aminotransferases. Methods Enzymol 2023; 680:35-83. [PMID: 36710018 DOI: 10.1016/bs.mie.2022.07.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aromatic aminotransferases (Aro ATs) are pyridoxal-5-phosphate (PLP)-dependent enzymes that catalyze the transamination reactions of an aromatic amino acid (AAA) or a keto acid. Aro ATs are involved in biosynthesis or degradation of AAAs and play important functions in controlling the production of plant hormones and secondary metabolites, such as auxin, tocopherols, flavonoids, and lignin. Most Aro ATs show substrate promiscuity and can accept multiple aromatic and non-aromatic amino and keto acid substrates, which complicates and limits our understanding of their in planta functions. Considering the critical roles Aro ATs play in plant primary and secondary metabolism, it is important to accurately determine substrate specificity and kinetic properties of Aro ATs. This chapter describes various methodologies of protein expression, purification and enzymatic assays, which can be used for biochemical characterization of Aro ATs.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States.
| | - Shogo Hataya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Andrew G Hall
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States.
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16
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Xu T, Qin Z, Wang X, Dong C, Driggers EM, Ding S. Reply to: GOT1 constrains T H17 cell differentiation, while promoting iT reg cell differentiation. Nature 2023; 614:E12-E14. [PMID: 36725991 DOI: 10.1038/s41586-022-05603-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Tao Xu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Zhen Qin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Chen Dong
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China.
| | | | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
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17
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de Raad M, Koper K, Deng K, Bowen BP, Maeda HA, Northen TR. Mass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme. J Biol Chem 2023; 299:102939. [PMID: 36702250 PMCID: PMC9957770 DOI: 10.1016/j.jbc.2023.102939] [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: 09/27/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Aminotransferases (ATs) catalyze pyridoxal 5'-phosphate-dependent transamination reactions between amino donor and keto acceptor substrates and play central roles in nitrogen metabolism of all organisms. ATs are involved in the biosynthesis and degradation of both proteinogenic and nonproteinogenic amino acids and also carry out a wide variety of functions in photorespiration, detoxification, and secondary metabolism. Despite the importance of ATs, their functionality is poorly understood as only a small fraction of putative ATs, predicted from DNA sequences, are associated with experimental data. Even for characterized ATs, the full spectrum of substrate specificity, among many potential substrates, has not been explored in most cases. This is largely due to the lack of suitable high-throughput assays that can screen for AT activity and specificity at scale. Here we present a new high-throughput platform for screening AT activity using bioconjugate chemistry and mass spectrometry imaging-based analysis. Detection of AT reaction products is achieved by forming an oxime linkage between the ketone groups of transaminated amino donors and a probe molecule that facilitates mass spectrometry-based analysis using nanostructure-initiator mass spectrometry or MALDI-mass spectrometry. As a proof-of-principle, we applied the newly established method and found that a previously uncharacterized Arabidopsis thaliana tryptophan AT-related protein 1 is a highly promiscuous enzyme that can utilize 13 amino acid donors and three keto acid acceptors. These results demonstrate that this oxime-mass spectrometry imaging AT assay enables high-throughput discovery and comprehensive characterization of AT enzymes, leading to an accurate understanding of the nitrogen metabolic network.
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Affiliation(s)
- Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | - Kaan Koper
- Department of Botany, University of Wisconsin-Madison; Madison, Wisconsin, USA
| | - Kai Deng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison; Madison, Wisconsin, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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18
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Hofmeister DL, Seltzner CA, Bockhaus NJ, Thoden JB, Holden HM. Investigation of the enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-glucuronic acid in Psychrobacter cryohalolentis K5 T. Protein Sci 2023; 32:e4502. [PMID: 36346293 PMCID: PMC9794024 DOI: 10.1002/pro.4502] [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: 09/28/2022] [Revised: 10/29/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022]
Abstract
Psychrobacter cryohalolentis K5T is a Gram-negative bacterium first isolated from Siberian permafrost in 2006. It has a complex O-antigen containing l-rhamnose, d-galactose, two diacetamido-sugars, and one triacetamido-sugar. The biosynthetic pathway for one of the diacetamido-sugars, namely 2,3-diacetamido-2,3-dideoxy-d-glucuronic acid, is presently unknown. Utilizing the published genome sequence of P. cryohalolentis K5T , we hypothesized that the genes designated Pcryo_0613, Pcryo_0614, Pcryo_0616, and Pcryo_0615 encode for a uridine dinucleotide (UDP)-N-acetyl-d-glucosamine 6-dehydrogenase, an nicotinamide adenine dinucleotide (oxidized) (NAD+ )-dependent dehydrogenase, a pyridoxal 5'-phosphate (PLP)-dependent aminotransferase, and an N-acetyltransferase, respectively, activities of which would be required for the biosynthesis of this unusual carbohydrate. Here we present the cloning, overexpression, and purification of these hypothetical proteins. Kinetic data on the enzymes encoded by Pcryo_0613, Pcryo_0614, and Pcryo_0615 confirmed their postulated biochemical activities. In addition, the high-resolution X-ray structures of both the internal and external aldimine forms of the aminotransferase were determined to 1.25 and 1.0 Å, respectively. Finally, the three-dimensional architecture of the N-acetyltransferase in complex with its substrate and coenzyme A was solved to 1.8 Å resolution. Strikingly, the N-acetyltransferase was shown to adopt a new motif for UDP-sugar binding. The data presented herein provide additional insight into sugar biosynthesis in Gram-negative bacteria.
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Affiliation(s)
| | - Chase A. Seltzner
- Department of BiochemistryUniversity of WisconsinMadisonWisconsinUSA
| | | | - James B. Thoden
- Department of BiochemistryUniversity of WisconsinMadisonWisconsinUSA
| | - Hazel M. Holden
- Department of BiochemistryUniversity of WisconsinMadisonWisconsinUSA
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19
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van Dyk H, Jacobs FJF, Kroon RE, Makhafola TJ, Brink A. Characterisation, structural investigations and biological activity of substituted salicylidene-based compounds. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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20
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Sinha N, Eirich J, Finkemeier I, Grimm B. Glutamate 1-semialdehyde aminotransferase is connected to GluTR by GluTR-binding protein and contributes to the rate-limiting step of 5-aminolevulinic acid synthesis. THE PLANT CELL 2022; 34:4623-4640. [PMID: 35972388 PMCID: PMC9614494 DOI: 10.1093/plcell/koac237] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/28/2022] [Indexed: 06/01/2023]
Abstract
Tetrapyrroles play fundamental roles in crucial processes including photosynthesis, respiration, and catalysis. In plants, 5-aminolevulinic acid (ALA) is the common precursor of tetrapyrroles. ALA is synthesized from activated glutamate by the enzymes glutamyl-tRNA reductase (GluTR) and glutamate-1-semialdehyde aminotransferase (GSAAT). ALA synthesis is recognized as the rate-limiting step in this pathway. We aimed to explore the contribution of GSAAT to the control of ALA synthesis and the formation of a protein complex with GluTR. In Arabidopsis thaliana, two genes encode GSAAT isoforms: GSA1 and GSA2. A comparison of two GSA knockout mutants with the wild-type revealed the correlation of reduced GSAAT activity and ALA-synthesizing capacity in leaves with lower chlorophyll content. Growth and green pigmentation were more severely impaired in gsa2 than in gsa1, indicating the predominant role of GSAAT2 in ALA synthesis. Interestingly, GluTR accumulated to higher levels in gsa2 than in the wild-type and was mainly associated with the plastid membrane. We propose that the GSAAT content modulates the amount of soluble GluTR available for ALA synthesis. Several different biochemical approaches revealed the GSAAT-GluTR interaction through the assistance of GluTR-binding protein (GBP). A modeled structure of the tripartite protein complex indicated that GBP mediates the stable association of GluTR and GSAAT for adequate ALA synthesis.
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Affiliation(s)
- Neha Sinha
- Institute of Biology/Plant Physiology, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, Plant Physiology, Westfälische Wilhelms-Universität, 48149 Muenster, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, Plant Physiology, Westfälische Wilhelms-Universität, 48149 Muenster, Germany
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21
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Proteomic Analysis of the Effect of Salmonella Challenge on Broiler Chicken. Molecules 2022; 27:molecules27217277. [PMID: 36364100 PMCID: PMC9658033 DOI: 10.3390/molecules27217277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Abstract
Salmonella enteritidis is a foodborne pathogen that causes high morbidity in poultry. Proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to study the effects of Salmonella infection on spleen proteome in broiler chickens. Day-old broilers were assigned to control (CON; n = 60) or Salmonella challenge (CON−SE; n = 60), and gavaged with Tryptic soy agar broth or SE. A subset of chicks was euthanized on D3 and D7 (n = 4/group/day) and the spleen was removed, and rapidly frozen, subsequently proteome was measured using label-free LC-MS/MS. Protein spectra were mapped to Gallus gallus Uniprot database. Differentially abundant proteins (DAP; FDR < 0.05) between days and treatments were identified using ANOVA. Cecal content of Salmonella in CON−SE was 3.37 log10 CFU/g and CON were negative. Across the 16 samples, 2625 proteins were identified. Proteins that decreased in abundance between days mediated cell cycle progression, while those that increased in abundance function in cytoskeleton and mRNA processing. SE infection caused an increase in proteins that mediated redox homeostasis, lysosomal activities, and energy production, while proteins decreased in abundance-mediated developmental progression. Proteomic signatures of spleen suggest SE infection was metabolically costly, and energy was diverted from normal developmental processes to potentiate disease resistance mechanisms.
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22
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Kunk C, Kruger J, Mendoza G, Markitan J, Bias T, Mann A, Nath A, Geldenhuys WJ, Menze MA, Konkle ME. MitoNEET's Reactivity of Lys55 toward Pyridoxal Phosphate Demonstrates its Activity as a Transaminase Enzyme. ACS Chem Biol 2022; 17:2716-2722. [PMID: 36194135 DOI: 10.1021/acschembio.2c00572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
MitoNEET is a [2Fe-2S] redox active mitochondrial protein belonging to the CDGSH iron-sulfur domain (CISD) family of proteins. MitoNEET has been implicated as a potential target for drug development to treat various disorders, including type-2 diabetes, cancer, and Parkinson's disease. However, the specific cellular function(s) for mitoNEET still remains to be fully elucidated, and this presents a significant roadblock in rational drug development. Here, we show that mitoNEET binds the enzymatic cofactor pyridoxal phosphate (PLP) specifically at only one of its 11 lysine residues, Lys55. Lys55 is part of the soluble portion of the protein and is in a hydrogen-bonding network with the histidine residue that ligates the [2Fe-2S] cluster. In the presence of mitoNEET, PLP catalyzes the transamination reaction of the amino acid cysteine and the alpha-keto acid 2-oxoglutarate to form 3-mercaptopyruvate and glutamate. This work identifies, for the first time, mitoNEET as an enzyme with cysteine transaminase activity.
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Affiliation(s)
- Courtney Kunk
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Josh Kruger
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - George Mendoza
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Joey Markitan
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Taylor Bias
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Alexis Mann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Werner J Geldenhuys
- School of Pharmacology, University of West Virginia, Morgantown, West Virginia 26506, United States
| | - Michael A Menze
- Department of Biology, University of Louisville, Louisville, Kentucky 40292, United States
| | - Mary E Konkle
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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Drago VN, Dajnowicz S, Parks JM, Blakeley MP, Keen DA, Coquelle N, Weiss KL, Gerlits O, Kovalevsky A, Mueser TC. An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Chem Sci 2022; 13:10057-10065. [PMID: 36128223 PMCID: PMC9430417 DOI: 10.1039/d2sc02285k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP NSB and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction.
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Affiliation(s)
- Victoria N Drago
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin 71 Avenue des Martyrs 38000 Grenoble France
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus Didcot OX11 0QX UK
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue-Langevin 71 Avenue des Martyrs 38000 Grenoble France
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University Athens TN 37303 USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
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Petrosino M, Zuhra K, Kopec J, Hutchin A, Szabo C, Majtan T. H 2S biogenesis by cystathionine beta-synthase: mechanism of inhibition by aminooxyacetic acid and unexpected role of serine. Cell Mol Life Sci 2022; 79:438. [PMID: 35864237 PMCID: PMC9304066 DOI: 10.1007/s00018-022-04479-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 12/19/2022]
Abstract
Cystathionine beta-synthase (CBS) is a pivotal enzyme of the transsulfuration pathway responsible for diverting homocysteine to the biosynthesis of cysteine and production of hydrogen sulfide (H2S). Aberrant upregulation of CBS and overproduction of H2S contribute to pathophysiology of several diseases including cancer and Down syndrome. Therefore, pharmacological CBS inhibition has emerged as a prospective therapeutic approach. Here, we characterized binding and inhibitory mechanism of aminooxyacetic acid (AOAA), the most commonly used CBS inhibitor. We found that AOAA binds CBS tighter than its respective substrates and forms a dead-end PLP-bound intermediate featuring an oxime bond. Surprisingly, serine, but not cysteine, replaced AOAA from CBS and formed an aminoacrylate reaction intermediate, which allowed for the continuation of the catalytic cycle. Indeed, serine rescued and essentially normalized the enzymatic activity of AOAA-inhibited CBS. Cellular studies confirmed that AOAA decreased H2S production and bioenergetics, while additional serine rescued CBS activity, H2S production and mitochondrial function. The crystal structure of AOAA-bound human CBS showed a lack of hydrogen bonding with residues G305 and Y308, found in the serine-bound model. Thus, AOAA-inhibited CBS could be reactivated by serine. This difference may be important in a cellular environment in multiple pathophysiological conditions and may modulate the CBS-inhibitory activity of AOAA. In addition, our results demonstrate additional complexities of using AOAA as a CBS-specific inhibitor of H2S biogenesis and point to the urgent need to develop a potent, selective and specific pharmacological CBS inhibitor.
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Affiliation(s)
- Maria Petrosino
- Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, PER17, 1700, Fribourg, Switzerland
| | - Karim Zuhra
- Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, PER17, 1700, Fribourg, Switzerland
| | - Jola Kopec
- Structural Biology Unit, Evotec Ltd, 114 Innovation Drive, Abingdon, OX14 4RZ, UK
| | - Andrew Hutchin
- Structural Biology Unit, Evotec Ltd, 114 Innovation Drive, Abingdon, OX14 4RZ, UK
| | - Csaba Szabo
- Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, PER17, 1700, Fribourg, Switzerland
| | - Tomas Majtan
- Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, PER17, 1700, Fribourg, Switzerland.
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25
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Hunter GA, Ferreira GC. An Extended C-Terminus, the Possible Culprit for Differential Regulation of 5-Aminolevulinate Synthase Isoforms. Front Mol Biosci 2022; 9:920668. [PMID: 35911972 PMCID: PMC9329541 DOI: 10.3389/fmolb.2022.920668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
5-Aminolevulinate synthase (ALAS; E.C. 2.3.1.37) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the key regulatory step of porphyrin biosynthesis in metazoa, fungi, and α-proteobacteria. ALAS is evolutionarily related to transaminases and is therefore classified as a fold type I PLP-dependent enzyme. As an enzyme controlling the key committed and rate-determining step of a crucial biochemical pathway ALAS is ideally positioned to be subject to allosteric feedback inhibition. Extensive kinetic and mutational studies demonstrated that the overall enzyme reaction is limited by subtle conformational changes of a hairpin loop gating the active site. These findings, coupled with structural information, facilitated early prediction of allosteric regulation of activity via an extended C-terminal tail unique to eukaryotic forms of the enzyme. This prediction was subsequently supported by the discoveries that mutations in the extended C-terminus of the erythroid ALAS isoform (ALAS2) cause a metabolic disorder known as X-linked protoporphyria not by diminishing activity, but by enhancing it. Furthermore, kinetic, structural, and molecular modeling studies demonstrated that the extended C-terminal tail controls the catalytic rate by modulating conformational flexibility of the active site loop. However, the precise identity of any such molecule remains to be defined. Here we discuss the most plausible allosteric regulators of ALAS activity based on divergences in AlphaFold-predicted ALAS structures and suggest how the mystery of the mechanism whereby the extended C-terminus of mammalian ALASs allosterically controls the rate of porphyrin biosynthesis might be unraveled.
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Affiliation(s)
- Gregory A. Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
| | - Gloria C. Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL, United States
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
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The discovery of a non-competitive GOT1 inhibitor, hydralazine hydrochloride, via a coupling reaction-based high-throughput screening assay. Bioorg Med Chem Lett 2022; 73:128883. [PMID: 35820623 DOI: 10.1016/j.bmcl.2022.128883] [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: 04/13/2022] [Revised: 06/08/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022]
Abstract
Glutamate oxaloacetate transaminase 1 (GOT1) plays a key role in aberrant glutamine metabolism. GOT1 suppression can arrest tumor growth and prevent the development of cancer, indicating GOT1 as a potential anticancer target. Reported GOT1 inhibitors, on the other hand, are quite restricted. Here, we developed and optimized a coupling reaction-based high-throughput screening assay for the discovery of GOT1 inhibitors. By using this screening assay, we found that the cardiovascular drug hydralazine hydrochloride inhibited GOT1 catalytic activity, with an IC50 of 26.62 ± 7.45 μM, in a non-competitive and partial-reversible manner. In addition, we determined the binding affinity of hydralazine hydrochloride to GOT1, with a Kd of 16.54 ± 8.59 μM, using a microscale thermophoresis assay. According to structure-activity relationship analysis, the inhibitory activity of hydralazine hydrochloride is mainly derived from its hydrazine group. Furthermore, it inhibits the proliferation of cancer cells MCF-7 and MDA-MB-468 with a slight inhibitory effect compared to other tested cancer cells, highlighting GOT1 as a promising therapeutic target for the treatment of breast cancer.
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27
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Han SW, Shin JS. Aromatic L-amino acid decarboxylases: mechanistic features and microbial applications. Appl Microbiol Biotechnol 2022; 106:4445-4458. [DOI: 10.1007/s00253-022-12028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 11/02/2022]
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28
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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29
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Koper K, Han SW, Pastor DC, Yoshikuni Y, Maeda HA. Evolutionary Origin and Functional Diversification of Aminotransferases. J Biol Chem 2022; 298:102122. [PMID: 35697072 PMCID: PMC9309667 DOI: 10.1016/j.jbc.2022.102122] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sang-Woo Han
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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30
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Kumar S, Li X, McDew-White M, Reyes A, Delgado E, Sayeed A, Haile MT, Abatiyow BA, Kennedy SY, Camargo N, Checkley LA, Brenneman KV, Button-Simons KA, Duraisingh MT, Cheeseman IH, Kappe SHI, Nosten F, Ferdig MT, Vaughan AM, Anderson TJC. A Malaria Parasite Cross Reveals Genetic Determinants of Plasmodium falciparum Growth in Different Culture Media. Front Cell Infect Microbiol 2022; 12:878496. [PMID: 35711667 PMCID: PMC9197316 DOI: 10.3389/fcimb.2022.878496] [Citation(s) in RCA: 2] [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: 02/18/2022] [Accepted: 04/28/2022] [Indexed: 12/21/2022] Open
Abstract
What genes determine in vitro growth and nutrient utilization in asexual blood-stage malaria parasites? Competition experiments between NF54, clone 3D7, a lab-adapted African parasite, and a recently isolated Asian parasite (NHP4026) reveal contrasting outcomes in different media: 3D7 outcompetes NHP4026 in media containing human serum, while NHP4026 outcompetes 3D7 in media containing AlbuMAX, a commercial lipid-rich bovine serum formulation. To determine the basis for this polymorphism, we conducted parasite genetic crosses using humanized mice and compared genome-wide allele frequency changes in three independent progeny populations cultured in media containing human serum or AlbuMAX. This bulk segregant analysis detected three quantitative trait loci (QTL) regions [on chromosome (chr) 2 containing aspartate transaminase AST; chr 13 containing EBA-140; and chr 14 containing cysteine protease ATG4] linked with differential growth in serum or AlbuMAX in each of the three independent progeny pools. Selection driving differential growth was strong (s = 0.10 – 0.23 per 48-hour lifecycle). We conducted validation experiments for the strongest QTL on chr 13: competition experiments between ΔEBA-140 and 3D7 wildtype parasites showed fitness reversals in the two medium types as seen in the parental parasites, validating this locus as the causative gene. These results (i) demonstrate the effectiveness of bulk segregant analysis for dissecting fitness traits in P. falciparum genetic crosses, and (ii) reveal intimate links between red blood cell invasion and nutrient composition of growth media. Use of parasite crosses combined with bulk segregant analysis will allow systematic dissection of key nutrient acquisition/metabolism and red blood cell invasion pathways in P. falciparum.
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Affiliation(s)
- Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Marina McDew-White
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ann Reyes
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Elizabeth Delgado
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Abeer Sayeed
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Spencer Y. Kennedy
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Nelly Camargo
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Lisa A. Checkley
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Katelyn V. Brenneman
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Katrina A. Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Manoj T. Duraisingh
- Immunology and Infectious Diseases Department, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Ian H. Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Oxford, United Kingdom
| | - Michael T. Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- *Correspondence: Ashley M. Vaughan, ; Tim J. C. Anderson,
| | - Tim J. C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Ashley M. Vaughan, ; Tim J. C. Anderson,
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31
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Brinca AT, Ramalhinho AC, Sousa Â, Oliani AH, Breitenfeld L, Passarinha LA, Gallardo E. Follicular Fluid: A Powerful Tool for the Understanding and Diagnosis of Polycystic Ovary Syndrome. Biomedicines 2022; 10:1254. [PMID: 35740276 PMCID: PMC9219683 DOI: 10.3390/biomedicines10061254] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) represents one of the leading causes of anovulatory infertility and affects 5% to 20% of women worldwide. Until today, both the subsequent etiology and pathophysiology of PCOS remain unclear, and patients with PCOS that undergo assisted reproductive techniques (ART) might present a poor to exaggerated response, low oocyte quality, ovarian hyperstimulation syndrome, as well as changes in the follicular fluid metabolites pattern. These abnormalities originate a decrease of Metaphase II (MII) oocytes and decreased rates for fertilization, cleavage, implantation, blastocyst conversion, poor egg to follicle ratio, and increased miscarriages. Focus on obtaining high-quality embryos has been taken into more consideration over the years. Nowadays, the use of metabolomic analysis in the quantification of proteins and peptides in biological matrices might predict, with more accuracy, the success in assisted reproductive technology. In this article, we review the use of human follicular fluid as the matrix in metabolomic analysis for diagnostic and ART predictor of success for PCOS patients.
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Affiliation(s)
- Ana Teresa Brinca
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
| | - Ana Cristina Ramalhinho
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira, 6200-251 Covilhã, Portugal;
- C4-Cloud Computing Competence Centre, University of Beira Interior, 6201-001 Covilhã, Portugal
| | - Ângela Sousa
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
| | - António Hélio Oliani
- Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira, 6200-251 Covilhã, Portugal;
- São José do Rio Preto School of Medicine, Gynaecology and Obstetrics, São José do Rio Preto 15090-000, Brazil
| | - Luiza Breitenfeld
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- C4-Cloud Computing Competence Centre, University of Beira Interior, 6201-001 Covilhã, Portugal
| | - Luís A. Passarinha
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- UCIBIO–Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Laboratório de Fármaco-Toxicologia, UBIMedical, University of Beira Interior, 6200-284 Covilhã, Portugal
| | - Eugenia Gallardo
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, University of Beira Interior, 6200-284 Covilhã, Portugal
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32
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Maity AN, Chen JR, Li QY, Ke SC. The Nitrogen Atom of Vitamin B 6 Is Essential for the Catalysis of Radical Aminomutases. Int J Mol Sci 2022; 23:ijms23095210. [PMID: 35563602 PMCID: PMC9105233 DOI: 10.3390/ijms23095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.
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33
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Choi M, Rhee S. Structural and biochemical basis for the substrate specificity of Pad-1, an indole-3-pyruvic acid aminotransferase in auxin homeostasis. J Struct Biol 2022; 214:107857. [PMID: 35395410 DOI: 10.1016/j.jsb.2022.107857] [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: 12/17/2021] [Revised: 02/15/2022] [Accepted: 04/01/2022] [Indexed: 11/18/2022]
Abstract
Phytohormone indole-3-acetic acid (IAA) plays a vital role in regulating plant growth and development. Tryptophan-dependent IAA biosynthesis participates in IAA homeostasis by producing IAA via two sequential reactions, which involve a conversion of tryptophan to indole-3-pyruvic acid (IPyA) by tryptophan aminotransferase (TAA1) followed by the irreversible formation of IAA in the second reaction. Pad-1 from Solanaceae plants regulates IAA levels by catalyzing a reverse reaction of the first step of IAA biosynthesis. Pad-1 is a pyridoxal phosphate (PLP)-dependent aminotransferase, with IPyA as the amino acceptor and l-glutamine as the amino donor. Currently, the structural and functional basis for the substrate specificity of Pad-1 remains poorly understood. In this study, we carried out structural and kinetic analyses of Pad-1 from Solanum melongena. Pad-1 is a homodimeric enzyme, with coenzyme PLP present between a central large α/β domain and a protruding small domain. The active site of Pad-1 includes a vacancy near the phosphate group (P-side) and the 3'-O (O-side) of PLP. These features are distinct from those of TAA1, which is homologous in an overall structure with Pad-1 but includes only the P-side region in the active site. Kinetic analysis suggests that P-side residues constitute a binding pocket for l-glutamine, and O-side residues of Phe124 and Ile350 are involved in the binding of IPyA. These studies illuminate distinct differences in the active site between Pad-1 and TAA1, and provide structural and functional insights into the substrate specificity of Pad-1.
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Affiliation(s)
- Minyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
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34
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Noguchi T, Isogai S, Terada T, Nishiyama M, Kuzuyama T. Cryptic Oxidative Transamination of Hydroxynaphthoquinone in Natural Product Biosynthesis. J Am Chem Soc 2022; 144:5435-5440. [PMID: 35293722 DOI: 10.1021/jacs.1c13074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a group of versatile enzymes that catalyze various reactions, but only a small number of them react with O2. Here, we report an unprecedented PLP-dependent enzyme, NphE, that catalyzes both transamination and two-electron oxidation using O2 as an oxidant. Our intensive analysis reveals that NphE transfers the l-glutamate-derived amine to 1,3,6,8-tetrahydroxynaphthalene-derived mompain to form 8-amino-flaviolin (8-AF) via a highly conjugated quinonoid intermediate that is reactive with O2. During the NphE reaction, O2 is reduced to yield H2O2. An integrated technique involving NphE structure prediction by AlphaFold v2.0 and molecular dynamics simulation suggested the O2-accessible cavity. Our in vivo results demonstrated that 8-AF is a genuine biosynthetic intermediate for the 1,3,6,8-tetrahydroxynaphthalene-derived meroterpenoid naphterpin without an amino group, which was supported by site-directed mutagenesis. This study clearly establishes the NphE reaction product 8-AF as a common intermediate with a cryptic amino group for the biosynthesis of terpenoid-polyketide hybrid natural products.
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Affiliation(s)
- Tomohiro Noguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN
| | - Shota Isogai
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JAPAN
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An amino acid-defined diet impairs tumour growth in mice by promoting endoplasmic reticulum stress and mTOR inhibition. Mol Metab 2022; 60:101478. [PMID: 35367410 PMCID: PMC9014392 DOI: 10.1016/j.molmet.2022.101478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 12/17/2022] Open
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Ye Z, Zhang C, Wang S, Zhang Y, Li R, Zhao Y, Qiao J. Amino acid signatures in relation to polycystic ovary syndrome and increased risk of different metabolic disturbances. Reprod Biomed Online 2021; 44:737-746. [DOI: 10.1016/j.rbmo.2021.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]
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Tribe AK, McConnell MJ, Teesdale-Spittle PH. The Big Picture of Glioblastoma Malignancy: A Meta-Analysis of Glioblastoma Proteomics to Identify Altered Biological Pathways. ACS OMEGA 2021; 6:24535-24544. [PMID: 34604635 PMCID: PMC8482494 DOI: 10.1021/acsomega.1c02991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 05/08/2023]
Abstract
Glioblastoma is a highly malignant cancer with no effective treatment. It is vital to elucidate the mechanisms which drive glioblastoma in order to identify therapeutic targets. The differences in protein expression between glioblastoma, grade I-III glioma, and normal brain tissue reflect the functional alterations driving malignancy. However, proteomic analysis of glioblastoma has been hampered by the heterogeneity of glioblastoma and the variety of methodology used in its study. To reduce these inconsistencies, we performed a meta-analysis of the literature published since 2015, including 14 datasets from eight papers comparing the whole proteome of glioblastoma to normal brain or grade I-III glioma. We found that 154 proteins were commonly upregulated and 116 proteins were commonly downregulated in glioblastoma compared to normal brain. Meanwhile, 240 proteins were commonly upregulated and 125 proteins were commonly downregulated in glioblastoma compared to grade I-III glioma. Functional enrichment analysis revealed upregulation of proteins involved in mRNA splicing and the immune system and downregulation of proteins involved in synaptic signaling and glucose and glutamine metabolism. The identification of these altered biological pathways provides a basis for deeper investigation in the pursuit of an effective treatment for glioblastoma.
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Liu L, Wang B, Li S, Xu F, He Q, Pan C, Gao X, Yao W, Song X. Convenient Genetic Encoding of Phenylalanine Derivatives through Their α-Keto Acid Precursors. Biomolecules 2021; 11:1358. [PMID: 34572570 PMCID: PMC8470325 DOI: 10.3390/biom11091358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
The activity and function of proteins can be improved by incorporation of non-canonical amino acids (ncAAs). To avoid the tedious synthesis of a large number of chiral phenylalanine derivatives, we synthesized the corresponding phenylpyruvic acid precursors. Escherichia coli strain DH10B and strain C321.ΔA.expΔPBAD were selected as hosts for phenylpyruvic acid bioconversion and genetic code expansion using the MmPylRS/pyltRNACUA system. The concentrations of keto acids, PLP and amino donors were optimized in the process. Eight keto acids that can be biotransformed and their coupled genetic code expansions were identified. Finally, the genetic encoded ncAAs were tested for incorporation into fluorescent proteins with keto acids.
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Affiliation(s)
- Li Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Bohao Wang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Sheng Li
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Fengyuan Xu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Qi He
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Chun Pan
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Southeast University, Nanjing 210009, China;
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Xiaoda Song
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
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Heisdorf CJ, Griffiths WA, Thoden JB, Holden HM. Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis. Protein Sci 2021; 30:2144-2160. [PMID: 34379357 DOI: 10.1002/pro.4169] [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: 07/09/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 01/10/2023]
Abstract
It is now well established that the Gram-negative bacterium, Helicobacter pylori, causes gastritis in humans. In recent years, it has become apparent that the so-called non-pylori Helicobacters, normally infecting pigs, cats, and dogs, may also be involved in human pathology via zoonotic transmission. Indeed, more than 30 species of non-pylori Helicobacters have been identified thus far. One such organism is Helicobacter canadensis, an emerging pathogen whose genome sequence was published in 2009. Given our long-standing interest in the biosynthesis of N-formylated sugars found in the O-antigens of some Gram-negative bacteria, we were curious as to whether H. canadensis produces such unusual carbohydrates. Here, we demonstrate using both biochemical and structural techniques that the proteins encoded by the HCAN_0198, HCAN_0204, and HCAN_0200 genes in H. canadensis, correspond to a 3,4-ketoisomerase, a pyridoxal 5'-phosphate aminotransferase, and an N-formyltransferase, respectively. For this investigation, five high-resolution X-ray structures were determined and the kinetic parameters for the isomerase and the N-formyltransferase were measured. Based on these data, we suggest that the unusual sugar, 3-formamido-3,6-dideoxy-d-glucose, will most likely be found in the O-antigen of H. canadensis. Whether N-formylated sugars found in the O-antigen contribute to virulence is presently unclear, but it is intriguing that they have been observed in such pathogens as Francisella tularensis, Mycobacterium tuberculosis, and Brucella melitensis.
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Affiliation(s)
- Colton J Heisdorf
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - William A Griffiths
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
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Abstract
Reports of biogenic methane (CH4) synthesis associated with a range of organisms have steadily accumulated in the literature. This has not happened without controversy and in most cases the process is poorly understood at the gene and enzyme levels. In marine and freshwater environments, CH4 supersaturation of oxic surface waters has been termed the "methane paradox" because biological CH4 synthesis is viewed to be a strictly anaerobic process carried out by O2-sensitive methanogens. Interest in this phenomenon has surged within the past decade because of the importance of understanding sources and sinks of this potent greenhouse gas. In our work on Yellowstone Lake in Yellowstone National Park, we demonstrate microbiological conversion of methylamine to CH4 and isolate and characterize an Acidovorax sp. capable of this activity. Furthermore, we identify and clone a gene critical to this process (encodes pyridoxylamine phosphate-dependent aspartate aminotransferase) and demonstrate that this property can be transferred to Escherichia coli with this gene and will occur as a purified enzyme. This previously unrecognized process sheds light on environmental cycling of CH4, suggesting that O2-insensitive, ecologically relevant aerobic CH4 synthesis is likely of widespread distribution in the environment and should be considered in CH4 modeling efforts.
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Seltzner CA, Ferek JD, Thoden JB, Holden HM. Characterization of an aminotransferase from Acanthamoeba polyphaga Mimivirus. Protein Sci 2021; 30:1882-1894. [PMID: 34076307 DOI: 10.1002/pro.4139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/03/2023]
Abstract
Acanthamoeba polyphaga Mimivirus, a complex virus that infects amoeba, was first reported in 2003. It is now known that its DNA genome encodes for nearly 1,000 proteins including enzymes that are required for the biosynthesis of the unusual sugar 4-amino-4,6-dideoxy-d-glucose, also known as d-viosamine. As observed in some bacteria, the pathway for the production of this sugar initiates with a nucleotide-linked sugar, which in the Mimivirus is thought to be UDP-d-glucose. The enzyme required for the installment of the amino group at the C-4' position of the pyranosyl moiety is encoded in the Mimivirus by the L136 gene. Here, we describe a structural and functional analysis of this pyridoxal 5'-phosphate-dependent enzyme, referred to as L136. For this analysis, three high-resolution X-ray structures were determined: the wildtype enzyme/pyridoxamine 5'-phosphate/dTDP complex and the site-directed mutant variant K185A in the presence of either UDP-4-amino-4,6-dideoxy-d-glucose or dTDP-4-amino-4,6-dideoxy-d-glucose. Additionally, the kinetic parameters of the enzyme utilizing either UDP-d-glucose or dTDP-d-glucose were measured and demonstrated that L136 is efficient with both substrates. This is in sharp contrast to the structurally related DesI from Streptomyces venezuelae, whose three-dimensional architecture was previously reported by this laboratory. As determined in this investigation, DesI shows a profound preference in its catalytic efficiency for the dTDP-linked sugar substrate. This difference can be explained in part by a hydrophobic patch in DesI that is missing in L136. Notably, the structure of L136 reported here represents the first three-dimensional model for a virally encoded PLP-dependent enzyme and thus provides new information on sugar aminotransferases in general.
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Affiliation(s)
- Chase A Seltzner
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Justin D Ferek
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
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Gerlach T, Nugroho DL, Rother D. The Effect of Visible Light on the Catalytic Activity of PLP-Dependent Enzymes. ChemCatChem 2021; 13:2398-2406. [PMID: 34249169 PMCID: PMC8251830 DOI: 10.1002/cctc.202100163] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/26/2021] [Indexed: 11/08/2022]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a versatile class of biocatalysts and feature a variety of industrial applications. However, PLP is light sensitive and can cause inactivation of enzymes in certain light conditions. As most of the PLP-dependent enzymes are usually not handled in dark conditions, we evaluated the effect of visible light on the activity of PLP-dependent enzymes during production as well as transformation. We tested four amine transaminases, from Chromobacterium violaceum, Bacillus megaterium, Vibrio fluvialis and a variant from Arthrobacter species as well as two lysine decarboxylases, from Selenomonas ruminantium and the LDCc from Escherichia coli. It appeared that five of these six enzymes suffered from a significant decrease in activity by up to 90 % when handled in laboratory light conditions. Surprisingly, only the amine transaminase variant from Arthrobacter species appeared to be unaffected by light exposure and even showed an activation to 150 % relative activity over the course of 6 h regardless of the light conditions.
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Affiliation(s)
- Tim Gerlach
- Institute of Bio- and Geosciences: Biotechnology Forschungszentrum Jülich GmbHWilhelm-Johnen-Straße52428JülichGermany
- Department Aachen Biology and BiotechnologyRWTH Aachen UniversityWorringer Weg 152062AachenGermany
| | - David Limanhadi Nugroho
- Institute of Bio- and Geosciences: Biotechnology Forschungszentrum Jülich GmbHWilhelm-Johnen-Straße52428JülichGermany
| | - Dörte Rother
- Institute of Bio- and Geosciences: Biotechnology Forschungszentrum Jülich GmbHWilhelm-Johnen-Straße52428JülichGermany
- Department Aachen Biology and BiotechnologyRWTH Aachen UniversityWorringer Weg 152062AachenGermany
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Weerawarna PM, Moschitto MJ, Silverman RB. Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115. ACS Chem Biol 2021; 16:615-630. [PMID: 33735567 DOI: 10.1021/acschembio.0c00784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
((S)-3-Amino-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329) is a recently discovered inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), which has 10 times better inactivation efficiency than its predecessor, CPP-115, despite the only structural difference being an endocyclic double bond in OV329. Both compounds are mechanism-based enzyme inactivators (MBEIs), which inactivate GABA-AT by a similar mechanism. Here, a combination of a variety of computational chemistry tools and experimental methods, including quantum mechanical (QM) calculations, molecular dynamic simulations, progress curve analysis, and deuterium kinetic isotope effect (KIE) experiments, are utilized to comprehensively study the mechanism of inactivation of GABA-AT by CPP-115 and OV329 and account for their experimentally obtained global kinetic parameters kinact and KI. Our first key finding is that the rate-limiting step of the inactivation mechanism is the deprotonation step, and according to QM calculations and the KIE experiments, kinact accurately represents the enhancement of the rate-limiting step for the given mechanism. Second, the present study shows that the widely used simple QM models do not accurately represent the geometric criteria that are present in the enzyme for the deprotonation step. In contrast, QM cluster models successfully represent both the ground state destabilization and the transition state stabilization, as revealed by natural bond orbital analysis. Furthermore, the globally derived KI values for both of the inactivators represent the inhibitor constants for the initial binding complexes (Kd) and indicate the inactivator competition with the substrate according to progress curve analysis and the observed binding isotope effect. The configurational entropy loss accounts for the difference in KI values between the inactivators. The approach we describe in this work can be employed to determine the validity of globally derived parameters in the process of MBEI optimization for given inactivation mechanisms.
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Affiliation(s)
- Pathum M. Weerawarna
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew J. Moschitto
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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Han M, Zhang C, Suglo P, Sun S, Wang M, Su T. l-Aspartate: An Essential Metabolite for Plant Growth and Stress Acclimation. Molecules 2021; 26:molecules26071887. [PMID: 33810495 PMCID: PMC8037285 DOI: 10.3390/molecules26071887] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023] Open
Abstract
L-aspartate (Asp) serves as a central building block, in addition to being a constituent of proteins, for many metabolic processes in most organisms, such as biosynthesis of other amino acids, nucleotides, nicotinamide adenine dinucleotide (NAD), the tricarboxylic acid (TCA) cycle and glycolysis pathway intermediates, and hormones, which are vital for growth and defense. In animals and humans, lines of data have proved that Asp is indispensable for cell proliferation. However, in plants, despite the extensive study of the Asp family amino acid pathway, little attention has been paid to the function of Asp through the other numerous pathways. This review aims to elucidate the most important aspects of Asp in plants, from biosynthesis to catabolism and the role of Asp and its metabolic derivatives in response to changing environmental conditions. It considers the distribution of Asp in various cell compartments and the change of Asp level, and its significance in the whole plant under various stresses. Moreover, it provides evidence of the interconnection between Asp and phytohormones, which have prominent functions in plant growth, development, and defense. The updated information will help improve our understanding of the physiological role of Asp and Asp-borne metabolic fluxes, supporting the modular operation of these networks.
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Affiliation(s)
- Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Can Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Peter Suglo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Shuyue Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Mingyao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
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Raza A, Su W, Hussain MA, Mehmood SS, Zhang X, Cheng Y, Zou X, Lv Y. Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2021; 12:721681. [PMID: 34691103 PMCID: PMC8532563 DOI: 10.3389/fpls.2021.721681] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop in the world. Its productivity is significantly influenced by numerous abiotic stresses, including cold stress (CS). Consequently, enhancement in CS tolerance is becoming an important area for agricultural investigation and crop improvement. Therefore, the current study aimed to identify the stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the CS responses and tolerance mechanisms in the cold-tolerant (C18) and cold-sensitive (C6) rapeseed varieties. Based on the metabolome analysis, 31 differentially accumulated metabolites (DAMs) were identified between different comparisons of both varieties at the same time points. From the transcriptome analysis, 2,845, 3,358, and 2,819 differentially expressed genes (DEGs) were detected from the comparison of C6-0 vs. C18-0, C6-1 vs. C18-1, and C6-7 vs. C18-7. By combining the transcriptome and metabolome data sets, we found that numerous DAMs were strongly correlated with several differentially expressed genes (DEGs). A functional enrichment analysis of the DAMs and the correlated DEGs specified that most DEGs and DAMs were mainly enriched in diverse carbohydrates and amino acid metabolisms. Among them, starch and sucrose metabolism and phenylalanine metabolism were significantly enriched and played a vital role in the CS adaption of rapeseed. Six candidate genes were selected from the two pathways for controlling the adaption to low temperature. In a further validation, the T-DNA insertion mutants of their Arabidopsis homologous, including 4cl3, cel5, fruct4, ugp1, axs1, and bam2/9, were characterized and six lines differed significantly in levels of freezing tolerance. The outcome of the current study provided new prospects for the understanding of the molecular basis of CS responses and tolerance mechanisms in rapeseed and present a set of candidate genes for use in improving CS adaptability in the same plant.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Wei Su
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Muhammad Azhar Hussain
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Sundas Saher Mehmood
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xuekun Zhang
- College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University, Jingzhou, China
| | - Yong Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
- *Correspondence: Yan Lv
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Gayathri SC, Manoj N. Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases. J Mol Biol 2020; 432:166692. [PMID: 33122004 DOI: 10.1016/j.jmb.2020.10.026] [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: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023]
Abstract
PLP-dependent enzymes catalyze a plethora of chemical reactions affecting diverse physiological functions. Here we report the structural determinants of the reaction mechanism in a Group II PLP-dependent decarboxylase by assigning two early intermediates. The in-crystallo complexes of the PLP bound form, and the Dunathan and quinonoid intermediates, allowed direct observation of the active site interactions. The structures reveal that a subtle rearrangement of a conserved Arg residue in concert with a water-mediated interaction with the carboxylate of the Dunathan intermediate, appears to directly stabilize the alignment and facilitate the release of CO2 to yield the quinonoid. Modeling indicates that the conformational change of a dynamic catalytic loop to a closed form controls a conserved network of hydrogen bond interactions between catalytic residues to protonate the quinonoid. Our results provide a structural framework to elucidate mechanistic roles of residues that govern reaction specificity and catalysis in PLP-dependent decarboxylation.
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Affiliation(s)
- Subash Chellam Gayathri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Zaghmi A, Dopico-López A, Pérez-Mato M, Iglesias-Rey R, Hervella P, Greschner AA, Bugallo-Casal A, da Silva A, Gutiérrez-Fernández M, Castillo J, Pérez FC, Gauthier MA. Sustained blood glutamate scavenging enhances protection in ischemic stroke. Commun Biol 2020; 3:729. [PMID: 33273696 PMCID: PMC7713697 DOI: 10.1038/s42003-020-01406-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Stroke is a major cause of morbidity, mortality, and disability. During ischemic stroke, a marked and prolonged rise of glutamate concentration in the brain causes neuronal cell death. This study explores the protective effect of a bioconjugate form of glutamate oxaloacetate transaminase (hrGOT), which catalyzes the depletion of blood glutamate in the bloodstream for ~6 days following a single administration. When treated with this bioconjugate, a significant reduction of the infarct volume and a better retention of sensorimotor function was observed for ischemic rats compared to those treated with saline. Moreover, the equivalent dose of native hrGOT yielded similar results to the saline treated group for some tests. Targeting the bioconjugate to the blood-brain-barrier did not improve its performance. The data suggest that the bioconjugates draw glutamate out of the brain by displacing homeostasis between the different glutamate pools of the body.
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Affiliation(s)
- Ahlem Zaghmi
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Qc, J3X 1S2, Canada
| | - Antonio Dopico-López
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - María Pérez-Mato
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Neuroscience and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, La Paz University Hospital, Neuroscience Area of IdiPAZ Health Research Institute, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ramón Iglesias-Rey
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Pablo Hervella
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Andrea A Greschner
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Qc, J3X 1S2, Canada
| | - Ana Bugallo-Casal
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Andrés da Silva
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - María Gutiérrez-Fernández
- Neuroscience and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, La Paz University Hospital, Neuroscience Area of IdiPAZ Health Research Institute, Universidad Autónoma de Madrid, Madrid, Spain
| | - José Castillo
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Francisco Campos Pérez
- Clinical Neuroscience Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Qc, J3X 1S2, Canada.
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48
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Wang Y, Wu Y, Chen J, Guo X, Yan L, Guo Y, Wang B, Yuan J. The duration of food withdrawal affects the intestinal structure, nutrients absorption, and utilization in broiler chicken. FASEB J 2020; 35:e21178. [PMID: 33190300 DOI: 10.1096/fj.202001773r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/09/2020] [Accepted: 10/26/2020] [Indexed: 01/03/2023]
Abstract
Food withdrawal is usually used for accurate feed metabolizable energy (ME) assessment in poultry, but its effects on intestinal structure and the absorption of nutrients are unclear. In this study, broilers were fed ad libitum (CT) or withdrew food for 12 (FH12), 24 (FH24), 36 (FH36), or 48 hours (FH48). We showed that food withdrawal increased the energy assimilation when compared with the CT. Food withdrawal improved the digestibility of ether extract and the level of lipid substances and fatty acid-derived β-hydroxybutyrate in serum. Compared to the CT, food withdrawal did not influence the digestibility of starch. Due to 12 hours or longer food withdrawal duration increased glutamate oxidation and uric acid excretion, the analyzed digestibility of crude protein was underestimated, although the upregulated amino acid transporter genes. In addition, histological analysis showed that short-term food withdrawal (12 hours) increased intestinal villus height, crypt depth, and proliferative cell, whereas prolonged food withdrawal (more than 24 hours) impaired villus structure due to the decreased cell proliferation. Moreover, proteomics analysis revealed upregulated pathways in birds withdrawn food for 36 hours involved in nutrient absorption and amino acid oxidation. In conclusion, food withdrawal changes nutrient absorption and utilization, especially for amino acid and ether extract, and results in increased ME. Both glutamate oxidation and fatty acid incomplete oxidation are involved in energy supply after refeeding. In contrast to short-term food withdrawal, prolonged food withdrawal impairs the intestinal structure and villus renewal. Our findings deserve attention from nutritionists who are analyzing food digestibility.
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Affiliation(s)
- Youli Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuqin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jing Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaorui Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Yan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bo Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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49
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Lin X, Yang M, Liu X, Cheng Z, Ge F. Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:289-304. [PMID: 33130100 PMCID: PMC7801250 DOI: 10.1016/j.gpb.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 03/03/2019] [Accepted: 04/19/2019] [Indexed: 12/25/2022]
Abstract
Protein lysine methylation is a prevalent post-translational modification (PTM) and plays critical roles in all domains of life. However, its extent and function in photosynthetic organisms are still largely unknown. Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation. Here we integrated propionylation of monomethylated proteins, enrichment of the modified peptides, and mass spectrometry (MS) analysis to identify monomethylated proteins in Synechocystis sp. PCC 6803 (Synechocystis). Overall, we identified 376 monomethylation sites in 270 proteins, with numerous monomethylated proteins participating in photosynthesis and carbon metabolism. We subsequently demonstrated that CpcM, a previously identified asparagine methyltransferase in Synechocystis, could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480. The loss of CpcM led to decreases in the maximum quantum yield in primary photosystem II (PSII) and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis. We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria. The large number of monomethylated proteins and the identification of CpcM as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.
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Affiliation(s)
- Xiaohuang Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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50
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Hipólito A, Nunes SC, Vicente JB, Serpa J. Cysteine Aminotransferase (CAT): A Pivotal Sponsor in Metabolic Remodeling and an Ally of 3-Mercaptopyruvate Sulfurtransferase (MST) in Cancer. Molecules 2020; 25:molecules25173984. [PMID: 32882966 PMCID: PMC7504796 DOI: 10.3390/molecules25173984] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolic remodeling is a critical skill of malignant cells, allowing their survival and spread. The metabolic dynamics and adaptation capacity of cancer cells allow them to escape from damaging stimuli, including breakage or cross-links in DNA strands and increased reactive oxygen species (ROS) levels, promoting resistance to currently available therapies, such as alkylating or oxidative agents. Therefore, it is essential to understand how metabolic pathways and the corresponding enzymatic systems can impact on tumor behavior. Cysteine aminotransferase (CAT) per se, as well as a component of the CAT: 3-mercaptopyruvate sulfurtransferase (MST) axis, is pivotal for this metabolic rewiring, constituting a central mechanism in amino acid metabolism and fulfilling the metabolic needs of cancer cells, thereby supplying other different pathways. In this review, we explore the current state-of-art on CAT function and its role on cancer cell metabolic rewiring as MST partner, and its relevance in cancer cells' fitness.
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Affiliation(s)
- Ana Hipólito
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculty of Medical Sciences, University NOVA of Lisbon, Campus dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal; (A.H.); (S.C.N.)
- Institute of Oncology Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisbon, Portugal
| | - Sofia C. Nunes
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculty of Medical Sciences, University NOVA of Lisbon, Campus dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal; (A.H.); (S.C.N.)
- Institute of Oncology Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisbon, Portugal
| | - João B. Vicente
- Institute of Technology, Chemistry and Biology António Xavier (ITQB NOVA), Avenida da República (EAN), 2780-157 Oeiras, Portugal
- Correspondence: (J.B.V.); (J.S.)
| | - Jacinta Serpa
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculty of Medical Sciences, University NOVA of Lisbon, Campus dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal; (A.H.); (S.C.N.)
- Institute of Oncology Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisbon, Portugal
- Correspondence: (J.B.V.); (J.S.)
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