1
|
Campero-Basaldua C, González J, García JA, Ramírez E, Hernández H, Aguirre B, Torres-Ramírez N, Márquez D, Sánchez NS, Gómez-Hernández N, Torres-Machorro AL, Riego-Ruiz L, Scazzocchio C, González A. Neo-functionalization in Saccharomyces cerevisiae: a novel Nrg1-Rtg3 chimeric transcriptional modulator is essential to maintain mitochondrial DNA integrity. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231209. [PMID: 37920568 PMCID: PMC10618058 DOI: 10.1098/rsos.231209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023]
Abstract
In Saccharomyces cerevisiae, the transcriptional repressor Nrg1 (Negative Regulator of Glucose-repressed genes) and the β-Zip transcription factor Rtg3 (ReTroGrade regulation) mediate glucose repression and signalling from the mitochondria to the nucleus, respectively. Here, we show a novel function of these two proteins, in which alanine promotes the formation of a chimeric Nrg1/Rtg3 regulator that represses the ALT2 gene (encoding an alanine transaminase paralog of unknown function). An NRG1/NRG2 paralogous pair, resulting from a post-wide genome small-scale duplication event, is present in the Saccharomyces genus. Neo-functionalization of only one paralog resulted in the ability of Nrg1 to interact with Rtg3. Both nrg1Δ and rtg3Δ single mutant strains were unable to use ethanol and showed a typical petite (small) phenotype on glucose. Neither of the wild-type genes complemented the petite phenotype, suggesting irreversible mitochondrial DNA damage in these mutants. Neither nrg1Δ nor rtg3Δ mutant strains expressed genes encoded by any of the five polycistronic units transcribed from mitochondrial DNA in S. cerevisiae. This, and the direct measurement of the mitochondrial DNA gene complement, confirmed that irreversible damage of the mitochondrial DNA occurred in both mutant strains, which is consistent with the essential role of the chimeric Nrg1/Rtg3 regulator in mitochondrial DNA maintenance.
Collapse
Affiliation(s)
- Carlos Campero-Basaldua
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - James González
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Janeth Alejandra García
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Edgar Ramírez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Hugo Hernández
- Departamento de Biología, Facultad de Química, UNAM, México City, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Beatriz Aguirre
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Nayeli Torres-Ramírez
- Laboratorio de Microscopía Electrónica Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Dariel Márquez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Norma Silvia Sánchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Nicolás Gómez-Hernández
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, SLP, México
| | - Ana Lilia Torres-Machorro
- Laboratorio de Biología Celular, Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias ‘Ismael Cosío Villegas', Tlalpan, Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, SLP, México
| | - Claudio Scazzocchio
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| |
Collapse
|
2
|
Tapia SM, Macías LG, Pérez-Torrado R, Daroqui N, Manzanares P, Querol A, Barrio E. A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event. BMC Biol 2023; 21:102. [PMID: 37158891 PMCID: PMC10169451 DOI: 10.1186/s12915-023-01566-6] [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: 10/17/2022] [Accepted: 03/16/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes. RESULTS Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces. CONCLUSIONS The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.
Collapse
Affiliation(s)
- Sebastián M Tapia
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Laura G Macías
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | | | - Noemi Daroqui
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Paloma Manzanares
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain.
- Departament de Genètica, Universitat de València, Valencia, Spain.
| |
Collapse
|
3
|
Muratovska N, Carlquist M. Recombinant yeast for production of the pain receptor modulator nonivamide from vanillin. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2022.1097215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We report on the development of a method based on recombinant yeast Saccharomyces cerevisiae to produce nonivamide, a capsaicinoid and potent agonist of the pain receptor TRPV1. Nonivamide was produced in a two-step batch process where yeast was i) grown aerobically on glucose and ii) used to produce nonivamide from vanillin and non-anoic acid by bioconversion. The yeast was engineered to express multiple copies of an amine transaminase from Chromobacterium violaceum (CvTA), along with an NADH-dependent alanine dehydrogenase from Bacillus subtilis (BsAlaDH) to enable efficient reductive amination of vanillin. Oxygen-limited conditions and the use of ethanol as a co-substrate to regenerate NADH were identified to favour amination over the formation of the by-products vanillic alcohol and vanillic acid. The native alcohol dehydrogenase ADH6 was deleted to further reduce the formation of vanillic alcohol. A two-enzyme system consisting of an N-acyltransferase from Capsicum annuum (CaAT), and a CoA ligase from Sphingomonas sp. Ibu-2 (IpfF) was co-expressed to produce the amide. This study provides proof of concept for yeast-based production of non-ivamide by combined transamination and amidation of vanillin.
Collapse
|
4
|
Bruner J, Marcus A, Fox G. Changes in Diacetyl and Amino Acid Concentration during the Fermentation of Dry-Hopped Beer: A Look at Twelve Saccharomyces Species and Strains. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2078946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- James Bruner
- Food Science and Technology Department, University of California, Davis, CA, U.S.A
- Creature Comforts Brewing Company, Los Angeles, CA, U.S.A
| | - Andrew Marcus
- Food Science and Technology Department, University of California, Davis, CA, U.S.A
| | - Glen Fox
- Food Science and Technology Department, University of California, Davis, CA, U.S.A
| |
Collapse
|
5
|
Martino MR, Gutiérrez-Aguilar M, Yiew NKH, Lutkewitte AJ, Singer JM, McCommis KS, Ferguson D, Liss KHH, Yoshino J, Renkemeyer MK, Smith GI, Cho K, Fletcher JA, Klein S, Patti GJ, Burgess SC, Finck BN. Silencing alanine transaminase 2 in diabetic liver attenuates hyperglycemia by reducing gluconeogenesis from amino acids. Cell Rep 2022; 39:110733. [PMID: 35476997 PMCID: PMC9121396 DOI: 10.1016/j.celrep.2022.110733] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/21/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022] Open
Abstract
Hepatic gluconeogenesis from amino acids contributes significantly to diabetic hyperglycemia, but the molecular mechanisms involved are incompletely understood. Alanine transaminases (ALT1 and ALT2) catalyze the interconversion of alanine and pyruvate, which is required for gluconeogenesis from alanine. We find that ALT2 is overexpressed in the liver of diet-induced obese and db/db mice and that the expression of the gene encoding ALT2 (GPT2) is downregulated following bariatric surgery in people with obesity. The increased hepatic expression of Gpt2 in db/db liver is mediated by activating transcription factor 4, an endoplasmic reticulum stress-activated transcription factor. Hepatocyte-specific knockout of Gpt2 attenuates incorporation of 13C-alanine into newly synthesized glucose by hepatocytes. In vivo Gpt2 knockdown or knockout in liver has no effect on glucose concentrations in lean mice, but Gpt2 suppression alleviates hyperglycemia in db/db mice. These data suggest that ALT2 plays a significant role in hepatic gluconeogenesis from amino acids in diabetes. Martino et al. find that alanine transaminase 2 (ALT2), which is encoded by Gpt2, is increased in liver of mice and people with obesity by activating transcription factor 4. Suppression of Gpt2 expression in obese, but not lean mice, lowers blood glucose by suppressing alanine-mediated gluconeogenesis.
Collapse
Affiliation(s)
- Michael R Martino
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Manuel Gutiérrez-Aguilar
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Nicole K H Yiew
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Andrew J Lutkewitte
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jason M Singer
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kyle S McCommis
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Daniel Ferguson
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kim H H Liss
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jun Yoshino
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - M Katie Renkemeyer
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Gordon I Smith
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Justin A Fletcher
- Center for Human Nutrition, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Samuel Klein
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Gary J Patti
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Shawn C Burgess
- Center for Human Nutrition, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Brian N Finck
- Department of Medicine, Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO 63110, USA.
| |
Collapse
|
6
|
Márquez D, Escalera-Fanjul X, El Hafidi M, Aguirre-López B, Riego-Ruiz L, González A. Alanine Represses γ-Aminobutyric Acid Utilization and Induces Alanine Transaminase Required for Mitochondrial Function in Saccharomyces cerevisiae. Front Microbiol 2021; 12:695382. [PMID: 34421848 PMCID: PMC8371705 DOI: 10.3389/fmicb.2021.695382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/05/2021] [Indexed: 11/24/2022] Open
Abstract
The γ-aminobutyric acid (GABA) shunt constitutes a conserved metabolic route generating nicotinamide adenine dinucleotide phosphate (NADPH) and regulating stress response in most organisms. Here we show that in the presence of GABA, Saccharomyces cerevisiae produces glutamate and alanine through the irreversible action of Uga1 transaminase. Alanine induces expression of alanine transaminase (ALT1) gene. In an alt1Δ mutant grown on GABA, alanine accumulation leads to repression of the GAD1, UGA1, and UGA2 genes, involved in the GABA shunt, which could result in growth impairment. Induced ALT1 expression and negative modulation of the GABA shunt by alanine constitute a novel regulatory circuit controlling both alanine biosynthesis and catabolism. Consistent with this, the GABA shunt and the production of NADPH are repressed in a wild-type strain grown in alanine, as compared to those detected in the wild-type strain grown on GABA. We also show that heat shock induces alanine biosynthesis and ALT1, UGA1, UGA2, and GAD1 gene expression, whereas an uga1Δ mutant shows heat sensitivity and reduced NADPH pools, as compared with those observed in the wild-type strain. Additionally, an alt1Δ mutant shows an unexpected alanine-independent phenotype, displaying null expression of mitochondrial COX2, COX3, and ATP6 genes and a notable decrease in mitochondrial/nuclear DNA ratio, as compared to a wild-type strain, which results in a petite phenotype. Our results uncover a new negative role of alanine in stress defense, repressing the transcription of the GABA shunt genes, and support a novel Alt1 moonlighting function related to the maintenance of mitochondrial DNA integrity and mitochondrial gene expression.
Collapse
Affiliation(s)
- Dariel Márquez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | | | - Mohammed El Hafidi
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico, Mexico
| | - Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, México
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| |
Collapse
|
7
|
Batista JM, Neves MJ, Pereira AG, Gonçalves LS, Menezes HC, Cardeal ZL. Metabolomic studies of amino acid analysis in Saccharomyces cells exposed to selenium and gamma irradiation. Anal Biochem 2020; 597:113666. [PMID: 32142760 DOI: 10.1016/j.ab.2020.113666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 01/22/2023]
Abstract
Metabolomic studies are essential to identify and quantify key metabolites in biological systems. Analysis of amino acids (AA) is very important in target metabolomics studies. Chromatographic methods are used to support metabolite determinations. Therefore, this work presents analysis of 17 AA in Saccharomyces cerevisiae cells (a useful model in the study of cancer metabolism) exposed to sodium selenite and gamma radiation. An improved GC/MS method using propyl chloroformate/propanol as derivatizing reagent was applied to AA determinations. The method exhibited good linearity in the range of 0.08-600.00 mg L-1; limits of determination from 0.04 to 1.60 mg L-1; limits of quantification from 0.08 to 2.76 mg L-1; repeatability ranging from 1.9 to 11.4 %; and precision ranging from 2.8 to 13.8 %. The correlations between selenite/gamma radiation with AA profile was investigated to establish candidates for cancer biomarkers. The analyses of yeast cultures found high concentrations of amino acids, such as Alanine, Serine, Glutamate, and Lysine, which might be associated with the development of metabolic adaptations of cancer based on its high demand for biomass and energy, found both in this model and neoplastic cells.
Collapse
Affiliation(s)
- Josimar M Batista
- Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627-31270901, Belo Horizonte, MG, Brazil
| | - Maria J Neves
- Nuclear Technology Development Center/National Nuclear Energy Commission (CDTN/CNEN), Belo Horizonte, MG, Brazil
| | - Alline G Pereira
- Nuclear Technology Development Center/National Nuclear Energy Commission (CDTN/CNEN), Belo Horizonte, MG, Brazil
| | - Letícia S Gonçalves
- Nuclear Technology Development Center/National Nuclear Energy Commission (CDTN/CNEN), Belo Horizonte, MG, Brazil
| | - Helvécio C Menezes
- Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627-31270901, Belo Horizonte, MG, Brazil
| | - Zenilda L Cardeal
- Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627-31270901, Belo Horizonte, MG, Brazil.
| |
Collapse
|
8
|
Cao W, Wang G, Lu H, Ouyang L, Chu J, Sui Y, Zhuang Y. Improving cytosolic aspartate biosynthesis increases glucoamylase production in Aspergillus niger under oxygen limitation. Microb Cell Fact 2020; 19:81. [PMID: 32245432 PMCID: PMC7118866 DOI: 10.1186/s12934-020-01340-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/24/2020] [Indexed: 01/27/2023] Open
Abstract
Background Glucoamylase is one of the most industrially applied enzymes, produced by Aspergillus species, like Aspergillus niger. Compared to the traditional ways of process optimization, the metabolic engineering strategies to improve glucoamylase production are relatively scarce. Results In the previous study combined multi-omics integrative analysis and amino acid supplementation experiment, we predicted four amino acids (alanine, glutamate, glycine and aspartate) as the limited precursors for glucoamylase production in A. niger. To further verify this, five mutants namely OE-ala, OE-glu, OE-gly, OE-asp1 and OE-asp2, derived from the parental strain A. niger CBS 513.88, were constructed respectively for the overexpression of five genes responsible for the biosynthesis of the four kinds of amino acids (An11g02620, An04g00990, An05g00410, An04g06380 and An16g05570). Real-time quantitative PCR revealed that all these genes were successfully overexpressed at the mRNA level while the five mutants exhibited different performance in glucoamylase production in shake flask cultivation. Notably, the results demonstrated that mutant OE-asp2 which was constructed for reinforcing cytosolic aspartate synthetic pathway, exhibited significantly increased glucoamylase activity by 23.5% and 60.3% compared to CBS 513.88 in the cultivation of shake flask and the 5 L fermentor, respectively. Compared to A. niger CBS 513.88, mutant OE-asp2 has a higher intracellular amino acid pool, in particular, alanine, leucine, glycine and glutamine, while the pool of glutamate was decreased. Conclusion Our study combines the target prediction from multi-omics analysis with the experimental validation and proves the possibility of increasing glucoamylase production by enhancing limited amino acid biosynthesis. In short, this systematically conducted study will surely deepen the understanding of resources allocation in cell factory and provide new strategies for the rational design of enzyme production strains.
Collapse
Affiliation(s)
- Weiqiang Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yufei Sui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.
| |
Collapse
|
9
|
Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
Collapse
Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| |
Collapse
|
10
|
Deed RC, Hou R, Kinzurik MI, Gardner RC, Fedrizzi B. The role of yeast ARO8, ARO9 and ARO10 genes in the biosynthesis of 3-(methylthio)-1-propanol from L-methionine during fermentation in synthetic grape medium. FEMS Yeast Res 2019; 19:5113456. [PMID: 30277518 DOI: 10.1093/femsyr/foy109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/30/2018] [Indexed: 11/14/2022] Open
Abstract
3-(methylthio)-1-propanol (methionol), produced by yeast as an end-product of L-methionine (L-Met) catabolism, imparts off-odours reminiscent of cauliflower and potato to wine. Saccharomyces cerevisiae ARO genes, including transaminases Aro8p and Aro9p, and decarboxylase Aro10p, catalyse two key steps forming methionol via the Ehrlich pathway. We compared methionol concentrations in wines fermented by single Δaro8, Δaro9 and Δaro10 deletants in lab strain BY4743 versus wine strain Zymaflore F15, and F15 double- and triple-aro deletants versus single-aro deletants, using headspace-solid phase microextraction coupled with gas chromatography-mass spectrometry.Deletion of two or more aro genes increased growth lag phase, with the greatest delay exhibited by F15 Δaro8 Δaro9. The single Δaro8 deletion decreased methionol by 44% in BY4743 and 92% in F15, while the Δaro9 deletion increased methionol by 46% in F15 but not BY4743. Single deletion of Δaro10 had no effect on methionol.Unexpectedly, F15 Δaro8 Δaro9 and F15 Δaro8 Δaro9 Δaro10 produced more methionol than F15 Δaro8. In the absence of Aro8p and Aro9p, other transaminases may compensate or an alternative pathway may convert methanethiol to methionol. Our results confirm that Ehrlich pathway genes differ greatly between lab and wine yeast strains, impacting downstream products such as methionol.
Collapse
Affiliation(s)
- Rebecca C Deed
- School of Chemical Sciences, University of Auckland, 32 Symonds St, Auckland 1142, New Zealand.,School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand
| | - Ruoyu Hou
- School of Chemical Sciences, University of Auckland, 32 Symonds St, Auckland 1142, New Zealand
| | - Matias I Kinzurik
- School of Chemical Sciences, University of Auckland, 32 Symonds St, Auckland 1142, New Zealand.,New Zealand Winegrowers, 52 Symonds St, Auckland 1010, New Zealand
| | - Richard C Gardner
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand
| | - Bruno Fedrizzi
- School of Chemical Sciences, University of Auckland, 32 Symonds St, Auckland 1142, New Zealand
| |
Collapse
|
11
|
Malina C, Larsson C, Nielsen J. Yeast mitochondria: an overview of mitochondrial biology and the potential of mitochondrial systems biology. FEMS Yeast Res 2019; 18:4969682. [PMID: 29788060 DOI: 10.1093/femsyr/foy040] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 12/29/2022] Open
Abstract
Mitochondria are dynamic organelles of endosymbiotic origin that are essential components of eukaryal cells. They contain their own genetic machinery, have multicopy genomes and like their bacterial ancestors they consist of two membranes. However, the majority of the ancestral genome has been lost or transferred to the nuclear genome of the host, preserving only a core set of genes involved in oxidative phosphorylation. Mitochondria perform numerous biological tasks ranging from bioenergetics to production of protein co-factors, including heme and iron-sulfur clusters. Due to the importance of mitochondria in many cellular processes, mitochondrial dysfunction is implicated in a wide variety of human disorders. Much of our current knowledge on mitochondrial function and dysfunction comes from studies using Saccharomyces cerevisiae. This yeast has good fermenting capacity, rendering tolerance to mutations that inactivate oxidative phosphorylation and complete loss of mitochondrial DNA. Here, we review yeast mitochondrial metabolism and function with focus on S. cerevisiae and its contribution in understanding mitochondrial biology. We further review how systems biology studies, including mathematical modeling, has allowed gaining new insight into mitochondrial function, and argue that this approach may enable us to gain a holistic view on how mitochondrial function interacts with different cellular processes.
Collapse
Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Christer Larsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| |
Collapse
|
12
|
Rojas-Ortega E, Aguirre-López B, Reyes-Vivas H, González-Andrade M, Campero-Basaldúa JC, Pardo JP, González A. Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions. Front Microbiol 2018; 9:944. [PMID: 29867852 PMCID: PMC5960717 DOI: 10.3389/fmicb.2018.00944] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/23/2018] [Indexed: 12/16/2022] Open
Abstract
Saccharomyces cerevisiae arose from an interspecies hybridization (allopolyploidiza-tion), followed by Whole Genome Duplication. Diversification analysis of ScAlt1/ScAlt2 indicated that while ScAlt1 is an alanine transaminase, ScAlt2 lost this activity, constituting an example in which one of the members of the gene pair lacks the apparent ancestral physiological role. This paper analyzes structural organization and pyridoxal phosphate (PLP) binding properties of ScAlt1 and ScAlt2 indicating functional diversification could have determined loss of ScAlt2 alanine transaminase activity and thus its role in alanine metabolism. It was found that ScAlt1 and ScAlt2 are dimeric enzymes harboring 67% identity and intact conservation of the catalytic residues, with very similar structures. However, tertiary structure analysis indicated that ScAlt2 has a more open conformation than that of ScAlt1 so that under physiological conditions, while PLP interaction with ScAlt1 allows the formation of two tautomeric PLP isomers (enolimine and ketoenamine) ScAlt2 preferentially forms the ketoenamine PLP tautomer, indicating a modified polarity of the active sites which affect the interaction of PLP with these proteins, that could result in lack of alanine transaminase activity in ScAlt2. The fact that ScAlt2 forms a catalytically active Schiff base with PLP and its position in an independent clade in "sensu strictu" yeasts suggests this protein has a yet undiscovered physiological function.
Collapse
Affiliation(s)
- Erendira Rojas-Ortega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City, Mexico
| | - Martín González-Andrade
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jose C Campero-Basaldúa
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan P Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
13
|
Nishida I, Watanabe D, Takagi H. Putative mitochondrial α-ketoglutarate-dependent dioxygenase Fmp12 controls utilization of proline as an energy source in Saccharomyces cerevisiae. MICROBIAL CELL 2016; 3:522-528. [PMID: 28357320 PMCID: PMC5348986 DOI: 10.15698/mic2016.10.535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The amino acid proline functions as a nitrogen source and as a stress protectant in the yeast Saccharomyces cerevisiae. However, utilization of proline as a carbon source in S. cerevisiae cells has not been studied yet. In the process of study on the physiological roles of the found-in-mitochondrial-proteome (FMP) genes in proline metabolism, we found that Δfmp12 cells could grow better than wild-type cells on agar plate medium containing proline as the sole nitrogen and carbon sources. In contrast, overexpression of FMP12 negatively affected cell growth under the same condition. The Fmp12 protein was localized in the mitochondria and was constitutively expressed. Deletion of the genes that encode mitochondrial enzymes, such as proline dehydrogenase (PUT1), Δ1-pyrroline-5-carboxylate dehydrogenase (PUT2), alanine transaminase (ALT1), and α-ketoglutarate dehydrogenase subunit (KGD1), abolished the enhanced cell growth in Δfmp12. These results provided the first evidence that proline can be utilized as a carbon source via the mitochondrial proline metabolic pathway and the subsequent tricarboxylic acid (TCA) cycle in S. cerevisiae. The function of Fmp12, which has a similarity with α-ketoglutarate-dependent dioxygenases of the yeast Candida species and human, might inhibit cell growth by skipping the ATP production step of the TCA cycle.
Collapse
Affiliation(s)
- Ikuhisa Nishida
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| |
Collapse
|
14
|
Sun Z, Meng H, Li J, Wang J, Li Q, Wang Y, Zhang Y. Identification of novel knockout targets for improving terpenoids biosynthesis in Saccharomyces cerevisiae. PLoS One 2014; 9:e112615. [PMID: 25386654 PMCID: PMC4227703 DOI: 10.1371/journal.pone.0112615] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/09/2014] [Indexed: 11/24/2022] Open
Abstract
Many terpenoids have important pharmacological activity and commercial value; however, application of these terpenoids is often limited by problems associated with the production of sufficient amounts of these molecules. The use of Saccharomyces cerevisiae (S. cerevisiae) for the production of heterologous terpenoids has achieved some success. The objective of this study was to identify S. cerevisiae knockout targets for improving the synthesis of heterologous terpeniods. On the basis of computational analysis of the S. cerevisiae metabolic network, we identified the knockout sites with the potential to promote terpenoid production and the corresponding single mutant was constructed by molecular manipulations. The growth rates of these strains were measured and the results indicated that the gene deletion had no adverse effects. Using the expression of amorphadiene biosynthesis as a testing model, the gene deletion was assessed for its effect on the production of exogenous terpenoids. The results showed that the dysfunction of most genes led to increased production of amorphadiene. The yield of amorphadiene produced by most single mutants was 8–10-fold greater compared to the wild type, indicating that the knockout sites can be engineered to promote the synthesis of exogenous terpenoids.
Collapse
Affiliation(s)
- Zhiqiang Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hailin Meng
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- GIAT-HKU joint Center for Synthetic Biology Engineering Research, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jianfeng Wang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yong Wang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (YW); (YZ)
| | - Yansheng Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (YW); (YZ)
| |
Collapse
|
15
|
Yang S, Chen X, Xu N, Liu L, Chen J. Urea enhances cell growth and pyruvate production in Torulopsis glabrata. Biotechnol Prog 2014; 30:19-27. [PMID: 24124177 DOI: 10.1002/btpr.1817] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 12/13/2022]
Abstract
Torulopsis glabrata is a strain of yeast that is used for the industrial production of pyruvate. Determination of the optimal nutrient environment is vital for obtaining the most efficient production system. In this study, the fermentation parameters, gene transcription levels, activities of key enzymes and metabolites levels were analyzed when either urea or ammonium chloride was used as the sole source of nitrogen. Urea caused an increase in the dry cell weight (18%) and pyruvate productivity was significantly increased (14%). The transcription levels of CAGL0M05533g (DUR1,2), CAGL0J07612g (ZWF1), and CAGL0I02200g (SOL3) were upregulated, but CAGL0G05698g (GDH2) and CAGL0L01089g (GLT1) were down-regulated. The activities of urea amidolyase, NADPH dependent glutamate dehydrogenase and glucose-6-phosphate dehydrogenase were increased by 380, 430, and 140%, respectively. The activities of arginase and glutamate synthase were decreased by 40 and 35%, respectively. The NADPH content was increased by 33%, whilst ATP content was decreased by 37%. This changed the intracellular levels of organic acids and amino acids. The results expand the understanding of the physiological characteristics of yeast species grown with different sources of nitrogen.
Collapse
|
16
|
Sieg AG, Trotter PJ. Differential contribution of the proline and glutamine pathways to glutamate biosynthesis and nitrogen assimilation in yeast lacking glutamate dehydrogenase. Microbiol Res 2014; 169:709-16. [PMID: 24629525 DOI: 10.1016/j.micres.2014.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 02/03/2014] [Accepted: 02/10/2014] [Indexed: 11/16/2022]
Abstract
In Saccharomyces cerevisiae, the glutamate dehydrogenase (GDH) enzymes play a pivotal role in glutamate biosynthesis and nitrogen assimilation. It has been proposed that, in GDH-deficient yeast, either the proline utilization (PUT) or the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway serves as the alternative pathway for glutamate production and nitrogen assimilation to the exclusion of the other. Using a gdh-null mutant (gdh1Δ2Δ3Δ), this ambiguity was addressed using a combination of growth studies and pathway-specific enzyme assays on a variety of nitrogen sources (ammonia, glutamine, proline and urea). The GDH-null mutant was viable on all nitrogen sources tested, confirming that alternate pathways for nitrogen assimilation exist in the gdh-null strain. Enzyme assays point to GS/GOGAT as the primary alternative pathway on the preferred nitrogen sources ammonia and glutamine, whereas growth on proline required both the PUT and GS/GOGAT pathways. In contrast, growth on glucose-urea media elicited a decrease in GOGAT activity along with an increase in activity of the PUT pathway specific enzyme Δ(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH). Together, these results suggest the alternative pathway for nitrogen assimilation in strains lacking the preferred GDH-dependent route is nitrogen source dependent and that neither GS/GOGAT nor PUT serves as the sole compensatory pathway.
Collapse
Affiliation(s)
- Alex G Sieg
- Guehler Biochemistry Laboratory, Department of Chemistry, Augustana College, 639-38th Street, Rock Island, IL 61201, United States
| | - Pamela J Trotter
- Guehler Biochemistry Laboratory, Department of Chemistry, Augustana College, 639-38th Street, Rock Island, IL 61201, United States.
| |
Collapse
|
17
|
Yu SL, An YJ, Yang HJ, Kang MS, Kim HY, Wen H, Jin X, Kwon HN, Min KJ, Lee SK, Park S. Alanine-Metabolizing Enzyme Alt1 Is Critical in Determining Yeast Life Span, As Revealed by Combined Metabolomic and Genetic Studies. J Proteome Res 2013; 12:1619-27. [DOI: 10.1021/pr300979r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sung-Lim Yu
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Yong Jin An
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Hey-ji Yang
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Mi-Sun Kang
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Ho-Yeol Kim
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - He Wen
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Xing Jin
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Hyuk Nam Kwon
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Kyung-Jin Min
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Sung-Keun Lee
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Sunghyouk Park
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| |
Collapse
|
18
|
Peñalosa-Ruiz G, Aranda C, Ongay-Larios L, Colon M, Quezada H, Gonzalez A. Paralogous ALT1 and ALT2 retention and diversification have generated catalytically active and inactive aminotransferases in Saccharomyces cerevisiae. PLoS One 2012; 7:e45702. [PMID: 23049841 PMCID: PMC3458083 DOI: 10.1371/journal.pone.0045702] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 08/22/2012] [Indexed: 11/21/2022] Open
Abstract
Background Gene duplication and the subsequent divergence of paralogous pairs play a central role in the evolution of novel gene functions. S. cerevisiae possesses two paralogous genes (ALT1/ALT2) which presumably encode alanine aminotransferases. It has been previously shown that Alt1 encodes an alanine aminotransferase, involved in alanine metabolism; however the physiological role of Alt2 is not known. Here we investigate whether ALT2 encodes an active alanine aminotransferase. Principal Findings Our results show that although ALT1 and ALT2 encode 65% identical proteins, only Alt1 displays alanine aminotransferase activity; in contrast ALT2 encodes a catalytically inert protein. ALT1 and ALT2 expression is modulated by Nrg1 and by the intracellular alanine pool. ALT1 is alanine-induced showing a regulatory profile of a gene encoding an enzyme involved in amino acid catabolism, in agreement with the fact that Alt1 is the sole pathway for alanine catabolism present in S. cerevisiae. Conversely, ALT2 expression is alanine-repressed, indicating a role in alanine biosynthesis, although the encoded-protein has no alanine aminotransferase enzymatic activity. In the ancestral-like yeast L. kluyveri, the alanine aminotransferase activity was higher in the presence of alanine than in the presence of ammonium, suggesting that as for ALT1, LkALT1 expression could be alanine-induced. ALT2 retention poses the questions of whether the encoded protein plays a particular function, and if this function was present in the ancestral gene. It could be hypotesized that ALT2 diverged after duplication, through neo-functionalization or that ALT2 function was present in the ancestral gene, with a yet undiscovered function. Conclusions ALT1 and ALT2 divergence has resulted in delegation of alanine aminotransferase activity to Alt1. These genes display opposed regulatory profiles: ALT1 is alanine-induced, while ALT2 is alanine repressed. Both genes are negatively regulated by the Nrg1 repressor. Presented results indicate that alanine could act as ALT2 Nrg1-co-repressor.
Collapse
Affiliation(s)
- Georgina Peñalosa-Ruiz
- Departamento de Bioquímica y Biología Estructural, División de Ciencia Básica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Cristina Aranda
- Departamento de Bioquímica y Biología Estructural, División de Ciencia Básica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Maritrini Colon
- Departamento de Bioquímica y Biología Estructural, División de Ciencia Básica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Hector Quezada
- Departamento de Bioquímica, Instituto Nacional de Cardiología, México City, México
| | - Alicia Gonzalez
- Departamento de Bioquímica y Biología Estructural, División de Ciencia Básica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
- * E-mail:
| |
Collapse
|
19
|
Blank LM, Desphande RR, Schmid A, Hayen H. Analysis of carbon and nitrogen co-metabolism in yeast by ultrahigh-resolution mass spectrometry applying 13C- and 15N-labeled substrates simultaneously. Anal Bioanal Chem 2012; 403:2291-305. [PMID: 22543713 DOI: 10.1007/s00216-012-6009-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 03/29/2012] [Accepted: 03/30/2012] [Indexed: 01/10/2023]
Abstract
Alternative metabolic pathways inside a cell can be deduced using stable isotopically labeled substrates. One prerequisite is accurate measurement of the labeling pattern of targeted metabolites. Experiments are generally limited to the use of single-element isotopes, mainly (13)C. Here, we demonstrate the application of direct infusion nanospray, ultrahigh-resolution Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) for metabolic studies using differently labeled elemental isotopes simultaneously--i.e., (13)C and (15)N--in amino acids of a total protein hydrolysate. The optimized strategy for the analysis of metabolism by a hybrid linear ion trap-FTICR-MS comprises the collection of multiple adjacent selected ion monitoring scans. By limiting both the width of the mass range and the number of ions entering the ICR cell with automated gain control, sensitive measurements of isotopologue distribution were possible without compromising mass accuracy and isotope intensity mapping. The required mass-resolving power of more than 60,000 is only achievable on a routine basis by FTICR and Orbitrap mass spectrometers. Evaluation of the method was carried out by comparison of the experimental data to the natural isotope abundances of selected amino acids and by comparison to GC/MS results obtained from a labeling experiment with (13)C-labeled glucose. The developed method was used to shed light on the complexity of the yeast Saccharomyces cerevisiae carbon-nitrogen co-metabolism by administering both (13)C-labeled glucose and (15)N-labeled alanine. The results indicate that not only glutamate but also alanine acts as an amino donor during alanine and valine synthesis. Metabolic studies using FTICR-MS can exploit new possibilities by the use of multiple-labeled elemental isotopes.
Collapse
Affiliation(s)
- Lars M Blank
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | | | | | | |
Collapse
|
20
|
Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
21
|
Tumor cell energy metabolism and its common features with yeast metabolism. Biochim Biophys Acta Rev Cancer 2009; 1796:252-65. [PMID: 19682552 DOI: 10.1016/j.bbcan.2009.07.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/28/2009] [Accepted: 07/31/2009] [Indexed: 12/21/2022]
Abstract
During the last decades a considerable amount of research has been focused on cancer. A number of genetic and signaling defects have been identified. This has allowed the design and screening of a number of anti-tumor drugs for therapeutic use. One of the main challenges of anti-cancer therapy is to specifically target these drugs to malignant cells. Recently, tumor cell metabolism has been considered as a possible target for cancer therapy. It is widely accepted that tumors display an enhanced glycolytic activity and oxidative phosphorylation down-regulation (Warburg effect). Therefore, it seems reasonable that disruption of glycolysis might be a promising candidate for specific anti-cancer therapy. Nonetheless, the concept of aerobic glycolysis as the paradigm of tumor cell metabolism has been challenged, as some tumor cells use oxidative phosphorylation. Mitochondria are of special interest in cancer cell energy metabolism, as their physiology is linked to the Warburg effect. Besides, their central role in apoptosis makes these organelles a promising "dual hit target" for selectively eliminate tumor cells. Thus, it is desirable to have an easy-to-use and reliable model in order to do the screening for energy metabolism-inhibiting drugs to be used in cancer therapy. From a metabolic point of view, the fermenting yeast Saccharomyces cerevisiae and tumor cells share several features. In this paper we will review these common metabolic properties and we will discuss the possibility of using S. cerevisiae as an early screening test in the research for novel anti-tumor compounds used for the inhibition of tumor cell metabolism.
Collapse
|