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Garrigós V, Picazo C, Matallana E, Aranda A. Activation of the yeast Retrograde Response pathway by adaptive laboratory evolution with S-(2-aminoethyl)-L-cysteine reduces ethanol and increases glycerol during winemaking. Microb Cell Fact 2024; 23:231. [PMID: 39164751 PMCID: PMC11337681 DOI: 10.1186/s12934-024-02504-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Global warming causes an increase in the levels of sugars in grapes and hence in ethanol after wine fermentation. Therefore, alcohol reduction is a major target in modern oenology. Deletion of the MKS1 gene, a negative regulator of the Retrograde Response pathway, in Saccharomyces cerevisiae was reported to increase glycerol and reduce ethanol and acetic acid in wine. This study aimed to obtain mutants with a phenotype similar to that of the MKS1 deletion strain by subjecting commercial S. cerevisiae wine strains to an adaptive laboratory evolution (ALE) experiment with the lysine toxic analogue S-(2-aminoethyl)-L-cysteine (AEC). RESULTS In laboratory-scale wine fermentation, isolated AEC-resistant mutants overproduced glycerol and reduced acetic acid. In some cases, ethanol was also reduced. Whole-genome sequencing revealed point mutations in the Retrograde Response activator Rtg2 and in the homocitrate synthases Lys20 and Lys21. However, only mutations in Rtg2 were responsible for the overactivation of the Retrograde Response pathway and ethanol reduction during vinification. Finally, wine fermentation was scaled up in an experimental cellar for one evolved mutant to confirm laboratory-scale results, and any potential negative sensory impact was ruled out. CONCLUSIONS Overall, we have shown that hyperactivation of the Retrograde Response pathway by ALE with AEC is a valid approach for generating ready-to-use mutants with a desirable phenotype in winemaking.
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Affiliation(s)
- Víctor Garrigós
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, 46980, Paterna, Valencia, Spain.
| | - Cecilia Picazo
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, 46980, Paterna, Valencia, Spain
| | - Emilia Matallana
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, 46980, Paterna, Valencia, Spain
| | - Agustín Aranda
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, 46980, Paterna, Valencia, Spain.
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Vigueras-Meneses LG, Escalera-Fanjul X, El-Hafidi M, Montalvo-Arredondo J, Gomez-Hernandez N, Colón M, Granados E, Campero-Basaldua C, Riego-Ruiz L, Scazzocchio C, González A, Quezada H. Two alpha isopropylmalate synthase isozymes with similar kinetic properties are extant in the yeast Lachancea kluyveri. FEMS Yeast Res 2022; 22:6546212. [PMID: 35266531 DOI: 10.1093/femsyr/foac016] [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: 12/12/2021] [Revised: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
The first committed step in the leucine biosynthetic pathway is catalyzed by α-isopropylmalate synthase (α-IPMS, EC 2.3.3.13), which in the Saccaromycotina subphylum of Ascomycete yeasts is frequently encoded by duplicated genes. Following a gene duplication event, the two copies may be preserved presumably because the encoded proteins diverge in either functional properties and/or cellular localization. The genome of the petite-negative budding yeast Lachancea kluyveri includes two SAKL0E10472 (LkLEU4) and SAKL0F05170g (LKLEU4BIS) paralogous genes, which are homologous to other yeast α-IPMS sequences. Here, we investigate whether these paralogous genes encode functional α-IPMS isozymes and whether their functions have diverged. Molecular phylogeny suggested that the LkLeu4 isozyme is located in the mitochondria and LkLeu4BIS in the cytosol. Comparison of growth rates, leucine intracellular pools and mRNA levels, indicate that the LkLeu4 isozyme is the predominant α-IPMS enzyme during growth on glucose as carbon source. Determination of the kinetic parameters indicates that the isozymes have similar affinities for the substrates and for the feedback inhibitor leucine. Thus, the diversification of the physiological roles of the genes LkLEU4 and LKLEU4BIS involves preferential transcription of the LkLEU4 gene during growth on glucose and different subcellular localization, although ligand interactions have not diverged.
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Affiliation(s)
- Liliana Guadalupe Vigueras-Meneses
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ximena Escalera-Fanjul
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mohammed El-Hafidi
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Javier Montalvo-Arredondo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, Mexico
| | - Nicolás Gomez-Hernandez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, Mexico
| | - Maritrini Colón
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Estefany Granados
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Campero-Basaldua
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, Mexico
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College London, London, United Kingdom.,Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Héctor Quezada
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Isogai S, Matsushita T, Imanishi H, Koonthongkaew J, Toyokawa Y, Nishimura A, Yi X, Kazlauskas R, Takagi H. High-Level Production of Lysine in the Yeast Saccharomyces cerevisiae by Rational Design of Homocitrate Synthase. Appl Environ Microbiol 2021; 87:e0060021. [PMID: 33990312 PMCID: PMC8276798 DOI: 10.1128/aem.00600-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes the aldol condensation of 2-oxoglutarate (2-OG) and acetyl coenzyme A (AcCoA) to form homocitrate, which is the first enzyme of the lysine biosynthetic pathway in the yeast Saccharomyces cerevisiae. The HCS activity is tightly regulated via feedback inhibition by the end product lysine. Here, we designed a feedback inhibition-insensitive HCS of S. cerevisiae (ScLys20) for high-level production of lysine in yeast cells. In silico docking of the substrate 2-OG and the inhibitor lysine to ScLys20 predicted that the substitution of serine with glutamate at position 385 would be more suitable for desensitization of the lysine feedback inhibition than the substitution from serine to phenylalanine in the already known Ser385Phe variant. Enzymatic analysis revealed that the Ser385Glu variant is far more insensitive to feedback inhibition than the Ser385Phe variant. We also found that the lysine contents in yeast cells expressing the Ser385Glu variant were 4.62- and 1.47-fold higher than those of cells expressing the wild-type HCS and Ser385Phe variant, respectively, due to the extreme desensitization to feedback inhibition. In this study, we obtained highly feedback inhibition-insensitive HCS using in silico docking and enzymatic analysis. Our results indicate that the rational engineering of HCS for feedback inhibition desensitization by lysine could be useful for constructing new yeast strains with higher lysine productivity. IMPORTANCE A traditional method for screening toxic analogue-resistant mutants has been established for the breeding of microbes that produce high levels of amino acids, including lysine. However, another efficient strategy is required to further improve their productivity. Homocitrate synthase (HCS) catalyzes the first step of lysine biosynthesis in the yeast Saccharomyces cerevisiae, and its activity is subject to feedback inhibition by lysine. Here, in silico design of a key enzyme that regulates the biosynthesis of lysine was utilized to increase the productivity of lysine. We designed HCS for the high-level production of lysine in yeast cells by in silico docking simulation. The engineered HCS exhibited much less sensitivity to lysine and conferred higher production of lysine than the already known variant obtained by traditional breeding. The combination of in silico design and experimental analysis of a key enzyme will contribute to advances in metabolic engineering for the construction of industrial microorganisms.
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Affiliation(s)
- Shota Isogai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tomonori Matsushita
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroyuki Imanishi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Jirasin Koonthongkaew
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yoichi Toyokawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Xiao Yi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- The BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- The BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Wang SY, Zhou ZH. Molybdenum imidazole citrate and bipyridine homocitrate in different oxidation states – balance between coordinated α-hydroxy and α-alkoxy groups. RSC Adv 2019; 9:519-528. [PMID: 35521591 PMCID: PMC9059298 DOI: 10.1039/c8ra09134j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/11/2018] [Indexed: 01/28/2023] Open
Abstract
Oxo and thiomolybdenum(iv/vi) imidazole hydrocitrates K2{MoIV3O4(im)3[MoVIO3(Hcit)]2}·3im·4H2O (1), (Him)2{MoIV3SO3(im)3[MoVIO3(Hcit)]2}·im·6H2O (2), molybdenum(v) bipyridine homocitrate trans-[(MoVO)2O(H2homocit)2(bpy)2]·4H2O (3) and molybdenum(vi) citrate (Et4N)[MoVIO2Cl(H2cit)]·H2O (4) (H4cit = citric acid, H4homocit = homocitric acid, im = imidazole and bpy = 2,2′-bipyridine) with different oxidation states were prepared. 1 and 2 are the coupling products of [MoVIO3(Hcit)]3− anions and incomplete cubane units [MoIV3O4]4+ ([MoIV3SO3]4+) with monodentate imidazoles, respectively, where tridentate citrates coordinate with α-hydroxy, α-carboxy and β-carboxy groups, forming pentanuclear skeleton structures. The molybdenum atoms in 1 and 2 show unusual +4 and +6 valences based on charge balances, theoretical bond valence calculations and Mo XPS spectrum. The coordinated citrates in 1 and 2 are protonated with α-hydroxy groups, while 3 and 4 with higher oxidation states of +5 and +6 are deprotonated with α-alkoxy group even under strong acidic condition, respectively. This shows the relationship between the oxidation state and protonation of the α-alkoxy group in citrate or homocitrate, which is related to the protonation state of homocitrate in FeMo-cofactor of nitrogenase. The homocitrate in 3 chelates to molybdenum(v) with bidentate α-alkoxy and monodentate α-carboxy groups. Molybdenum(vi) citrate 4 is only protonated with coordinated and uncoordinated β-carboxy groups. The solution behaviours of 1 and 2 are discussed based on 1H and 13C NMR spectroscopies and cyclic voltammograms, showing no decomposition of the species. Oxo and thiomolybdenum(iv/vi) citrates, molybdenum(v) homocitrate and molybdenum(vi) citrate were obtained, showing the influence of coordinated α-hydroxy and α-alkoxy groups with different oxidation states.![]()
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Affiliation(s)
- Si-Yuan Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
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Escalera-Fanjul X, Quezada H, Riego-Ruiz L, González A. Whole-Genome Duplication and Yeast’s Fruitful Way of Life. Trends Genet 2019; 35:42-54. [DOI: 10.1016/j.tig.2018.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Accepted: 09/27/2018] [Indexed: 01/30/2023]
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Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of Saccharomyces cerevisiae. INTERNATIONAL JOURNAL OF PROTEOMICS 2016; 2016:8302423. [PMID: 26881076 PMCID: PMC4737026 DOI: 10.1155/2016/8302423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/08/2015] [Accepted: 12/16/2015] [Indexed: 11/30/2022]
Abstract
Yeast flavohemoglobin, YHb, encoded by the nuclear gene YHB1, has been implicated in the nitrosative stress responses in Saccharomyces cerevisiae. It is still unclear how S. cerevisiae can withstand this NO level in the absence of flavohemoglobin. To better understand the physiological function of flavohemoglobin in yeast, in the present study a label-free differential proteomics study has been carried out in wild-type and YHB1 deleted strains of S. cerevisiae grown under fermentative conditions. From the analysis, 417 proteins in Y190 and 392 proteins in ΔYHB1 were identified with high confidence. Interestingly, among the differentially expressed identified proteins, 40 proteins were found to be downregulated whereas 41 were found to be upregulated in ΔYHB1 strain of S. cerevisiae (p value < 0.05). The differentially expressed proteins were also classified according to gene ontology (GO) terms. The most enriched and significant GO terms included nitrogen compound biosynthesis, amino acid biosynthesis, translational regulation, and protein folding. Interactions of differentially expressed proteins were generated using Search Tool for the Retrieval of Interacting Genes (STRING) database. This is the first report which offers a more complete view of the proteome changes in S. cerevisiae in the absence of flavohemoglobin.
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Diversification of Paralogous α-Isopropylmalate Synthases by Modulation of Feedback Control and Hetero-Oligomerization in Saccharomyces cerevisiae. EUKARYOTIC CELL 2015; 14:564-77. [PMID: 25841022 DOI: 10.1128/ec.00033-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/01/2015] [Indexed: 11/20/2022]
Abstract
Production of α-isopropylmalate (α-IPM) is critical for leucine biosynthesis and for the global control of metabolism. The budding yeast Saccharomyces cerevisiae has two paralogous genes, LEU4 and LEU9, that encode α-IPM synthase (α-IPMS) isozymes. Little is known about the biochemical differences between these two α-IPMS isoenzymes. Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. The leu4Δ mutant, which expresses only the feedback-resistant Leu9 homodimer, grows slowly with either glucose or ethanol and accumulates elevated pools of leucine; this phenotype is alleviated by the addition of leucine. Transformation of the leu4Δ mutant with a centromeric plasmid carrying LEU4 restored the wild-type phenotype. Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed in vivo. Purification and kinetic analysis showed that the hetero-oligomeric isozyme has a distinct leucine sensitivity behavior. Determination of α-IPMS activity in ethanol-grown cultures showed that α-IPM biosynthesis and growth under these respiratory conditions depend on the feedback-sensitive Leu4 homodimer. We conclude that retention and further diversification of two yeast α-IPMSs have resulted in a specific regulatory system that controls the leucine-α-IPM biosynthetic pathway by selective feedback sensitivity of homomeric and heterodimeric isoforms.
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Erives AJ, Fassler JS. Metabolic and chaperone gene loss marks the origin of animals: evidence for Hsp104 and Hsp78 chaperones sharing mitochondrial enzymes as clients. PLoS One 2015; 10:e0117192. [PMID: 25710177 PMCID: PMC4339202 DOI: 10.1371/journal.pone.0117192] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/17/2014] [Indexed: 12/31/2022] Open
Abstract
The evolution of animals involved acquisition of an emergent gene repertoire for gastrulation. Whether loss of genes also co-evolved with this developmental reprogramming has not yet been addressed. Here, we identify twenty-four genetic functions that are retained in fungi and choanoflagellates but undetectable in animals. These lost genes encode: (i) sixteen distinct biosynthetic functions; (ii) the two ancestral eukaryotic ClpB disaggregases, Hsp78 and Hsp104, which function in the mitochondria and cytosol, respectively; and (iii) six other assorted functions. We present computational and experimental data that are consistent with a joint function for the differentially localized ClpB disaggregases, and with the possibility of a shared client/chaperone relationship between the mitochondrial Fe/S homoaconitase encoded by the lost LYS4 gene and the two ClpBs. Our analyses lead to the hypothesis that the evolution of gastrulation-based multicellularity in animals led to efficient extraction of nutrients from dietary sources, loss of natural selection for maintenance of energetically expensive biosynthetic pathways, and subsequent loss of their attendant ClpB chaperones.
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Affiliation(s)
- Albert J. Erives
- Department of Biology, University of Iowa, Iowa City, IA, 52242–1324, United States of America
- * E-mail: (AJE); (JSF)
| | - Jan S. Fassler
- Department of Biology, University of Iowa, Iowa City, IA, 52242–1324, United States of America
- * E-mail: (AJE); (JSF)
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Quezada H, Marín-Hernández A, Arreguín-Espinosa R, Rumjanek FD, Moreno-Sánchez R, Saavedra E. The 2-oxoglutarate supply exerts significant control on the lysine synthesis flux in Saccharomyces cerevisiae. FEBS J 2013; 280:5737-49. [PMID: 24034837 DOI: 10.1111/febs.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 08/05/2013] [Accepted: 08/19/2013] [Indexed: 11/28/2022]
Abstract
To determine the extent to which the supply of the precursor 2-oxoglutarate (2-OG) controls the synthesis of lysine in Saccharomyces cerevisiae growing exponentially in high glucose, top-down elasticity analysis was used. Three groups of reactions linked by 2-OG were defined. The 2-OG supply group comprised all metabolic steps leading to its formation, and the two 2-OG consumer groups comprised the enzymes and transporters involved in 2-OG transformation into lysine and glutamate and their further utilization for protein synthesis and storage. Various 2-OG steady-state concentrations that produced different fluxes to lysine and glutamate were attained using yeast mutants with increasing activities of Krebs cycle enzymes and decreased activities of Lys synthesis enzymes. The elasticity coefficients of the three enzyme groups were determined from the dependence of the amino acid fluxes on the 2-OG concentration. The respective degrees of control on the flux towards lysine (flux control coefficients) were determined from their elasticities, and were 1.1, 0.41 and -0.52 for the 2-OG producer group and the Lys and Glu branches, respectively. Thus, the predominant control exerted by the 2-OG supply on the rate of lysine synthesis suggests that over-expression of 2-OG producer enzymes may be a highly effective strategy to enhance Lys production.
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Affiliation(s)
- Héctor Quezada
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Tlalpan, Mexico
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Olin-Sandoval V, González-Chávez Z, Berzunza-Cruz M, Martínez I, Jasso-Chávez R, Becker I, Espinoza B, Moreno-Sánchez R, Saavedra E. Drug target validation of the trypanothione pathway enzymes through metabolic modelling. FEBS J 2012; 279:1811-33. [DOI: 10.1111/j.1742-4658.2012.08557.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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