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Rußmayer H, Buchetics M, Mattanovich M, Neubauer S, Steiger M, Graf AB, Koellensperger G, Hann S, Sauer M, Gasser B, Mattanovich D. Customizing amino acid metabolism of Pichia pastoris for recombinant protein production. Biotechnol J 2023; 18:e2300033. [PMID: 37668396 DOI: 10.1002/biot.202300033] [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: 01/19/2023] [Revised: 07/31/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Amino acids are the building blocks of proteins. In this respect, a reciprocal effect of recombinant protein production on amino acid biosynthesis as well as the impact of the availability of free amino acids on protein production can be anticipated. In this study, the impact of engineering the amino acid metabolism on the production of recombinant proteins was investigated in the yeast Pichia pastoris (syn Komagataella phaffii). Based on comprehensive systems-level analyses of the metabolomes and transcriptomes of different P. pastoris strains secreting antibody fragments, cell engineering targets were selected. Our working hypothesis that increasing intracellular amino acid levels could help unburden cellular metabolism and improve recombinant protein production was examined by constitutive overexpression of genes related to amino acid metabolism. In addition to 12 genes involved in specific amino acid biosynthetic pathways, the transcription factor GCN4 responsible for regulation of amino acid biosynthetic genes was overexpressed. The production of the used model protein, a secreted carboxylesterase (CES) from Sphingopyxis macrogoltabida, was increased by overexpression of pathway genes for alanine and for aromatic amino acids, and most pronounced, when overexpressing the regulator GCN4. The analysis of intracellular amino acid levels of selected clones indicated a direct linkage of improved recombinant protein production to the increased availability of intracellular amino acids. Finally, fed batch cultures showed that overexpression of GCN4 increased CES titers 2.6-fold, while the positive effect of other amino acid synthesis genes could not be transferred from screening to bioreactor cultures.
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Affiliation(s)
- Hannes Rußmayer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Markus Buchetics
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Matthias Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Copenhagen University, Copenhagen, Denmark
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Matthias Steiger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- School of Bioengineering, University of Applied Sciences FH Campus Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
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2
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Wang R, Sun J, Lassabliere B, Yu B, Liu SQ. Green tea fermentation with Saccharomyces boulardii CNCM I-745 and Lactiplantibacillus plantarum 299V. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Munasinghe M, Afshari R, Heydarian D, Almotayri A, Dias DA, Thomas J, Jois M. Effects of cocoa on altered metabolite levels in purine metabolism pathways and urea cycle in Alzheimer's disease in C. elegans. TRANSLATIONAL MEDICINE OF AGING 2022. [DOI: 10.1016/j.tma.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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4
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Gorospe CM, Jemiseye OT, Lee SK. Leucine supplementation mimics the effects of caloric restriction on yeast chronological lifespan. Mol Cell Toxicol 2021. [DOI: 10.1007/s13273-021-00166-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Lourenço AB, Artal-Sanz M. The Mitochondrial Prohibitin (PHB) Complex in C. elegans Metabolism and Ageing Regulation. Metabolites 2021; 11:metabo11090636. [PMID: 34564452 PMCID: PMC8472356 DOI: 10.3390/metabo11090636] [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: 07/31/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
The mitochondrial prohibitin (PHB) complex, composed of PHB-1 and PHB-2, is an evolutionarily conserved context-dependent modulator of longevity. This extremely intriguing phenotype has been linked to alterations in mitochondrial function and lipid metabolism. The true biochemical function of the mitochondrial PHB complex remains elusive, but it has been shown to affect membrane lipid composition. Recent work, using large-scale biochemical approaches, has highlighted a broad effect of PHB on the C. elegans metabolic network. Collectively, the biochemical data support the notion that PHB modulates, at least partially, worm longevity through the moderation of fat utilisation and energy production via the mitochondrial respiratory chain. Herein, we review, in a systematic manner, recent biochemical insights into the impact of PHB on the C. elegans metabolome.
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Affiliation(s)
- Artur B. Lourenço
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km 1, 41013 Seville, Spain
- Correspondence: (A.B.L.); (M.A.-S.)
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km 1, 41013 Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013 Seville, Spain
- Correspondence: (A.B.L.); (M.A.-S.)
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6
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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.
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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
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7
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Mukherjee S, Kundu I, Askari M, Barai RS, Venkatesh KV, Idicula-Thomas S. Exploring the druggable proteome of Candida species through comprehensive computational analysis. Genomics 2021; 113:728-739. [PMID: 33484798 DOI: 10.1016/j.ygeno.2020.12.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
Candida albicans and non-albicans Candida spp. are major cause of systemic mycoses. Antifungal drugs such as azoles and polyenes are not efficient to successfully eradicate Candida infection owing to their fungistatic nature or low bioavailability. Here, we have adopted a comprehensive computational workflow for identification, prioritization and validation of targets from proteomes of Candida albicans and Candida tropicalis. The protocol involves identification of essential drug-target candidates using subtractive genomics, protein-protein interaction network properties and systems biology based methods. The essentiality of the novel metabolic and non-metabolic targets was established by performing in silico gene knockouts, under aerobic as well as anaerobic conditions, and in vitro drug inhibition assays respectively. Deletion of twelve genes that are involved in amino acid, secondary metabolite, and carbon metabolism showed zero growth in metabolic model under simulated conditions. The algorithm, used in this study, can be downloaded from http://pbit.bicnirrh.res.in/offline.php and executed locally.
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Affiliation(s)
- Shuvechha Mukherjee
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Indra Kundu
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Mehdi Askari
- Department of Bioinformatics, Guru Nanak Khalsa College, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Ram Shankar Barai
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India.
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India.
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8
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Canfield CA, Bradshaw PC. Amino acids in the regulation of aging and aging-related diseases. TRANSLATIONAL MEDICINE OF AGING 2019. [DOI: 10.1016/j.tma.2019.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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9
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Chronological lifespan regulation of Saccharomyces cerevisiae by leucine biosynthesis pathway genes via TOR1 and COX2 expression regulation. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-019-0008-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Bach EE, Hi EMB, Martins AMC, Nascimento PAM, Wadt NSY. Hypoglicemic and Hypolipedimic Effects of Ganoderma lucidum in Streptozotocin-Induced Diabetic Rats. MEDICINES 2018; 5:medicines5030078. [PMID: 30060545 PMCID: PMC6163537 DOI: 10.3390/medicines5030078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 11/16/2022]
Abstract
Background:Ganoderma lucidum (Leyss. Ex. Fr) Karst is a basidiomycete mushroom that has been used for many years as a food supplement and medicine. In Brazil, National Health Surveillance Agency (ANVISA) classified Ganoderma lucidum as a nutraceutical product. The objective of the present work was to observe the effects of an extract from Ganoderma lucidum in rats treated with streptozotocin, and an agent that induces diabetes. Method: Male Wistar rats were obtained from the animal lodging facilities of both University Nove de Julho (UNINOVE) and Lusiada Universitary Center (UNILUS) with approval from the Ethics Committee for Animal Research. Animals were separated into groups: (1) C: Normoglycemic control water; (2) CE: Normoglycemic control group that received hydroethanolic extract (GWA); (3) DM1 + GWA: Diabetic group that received extract GWA; and (4) DM1: Diabetic group that received water. The treatment was evaluated over a 30-day period. Food and water were weighted, and blood plasma biochemical analysis performed. Results: G. lucidum extract contained beta-glucan, proteins and phenols. Biochemical analysis indicated a decrease of plasma glycemic and lipid levels in DM rats induced with streptozotocin and treated with GWA extract. Histopathological analysis from pancreas of GWA-treated DM animals showed preservation of up to 50% of pancreatic islet total area when compared to the DM control group. In plasma, Kyn was present in diabetic rats, while in treated diabetic rats more Trp was detected. Conclusion: Evaluation from G. lucidum extract in STZ-hyperglycemic rats indicated that the extract possesses hypoglycemic and hypolipidemic activities. Support: Proj. CNPq 474681/201.
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Affiliation(s)
- Erna Elisabeth Bach
- Biomedical Sciences, Health Department, UNINOVE (Universidade Nove de Julho), São Paulo 01156-050, São Paulo, Brazil.
| | - Edgar Matias Bach Hi
- Experimental Biochemistry Academic Nucleum (NABEX), UNILUS (Lusiada University Center), Santos 11050-071, São Paulo, Brazil.
| | | | - Paloma A M Nascimento
- Biomedical Sciences, Health Department, Scientific Research Student, UNINOVE (Universidade Nove de Julho), São Paulo 01156-050, São Paulo, Brazil.
| | - Nilsa Sumie Yamashita Wadt
- Pharmacy, Health Department, Sciences, UNIP (Universidade Paulista), Jundiaí 13214-525, São Paulo, Brazil.
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11
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Khatun MM, Yu X, Kondo A, Bai F, Zhao X. Improved ethanol production at high temperature by consolidated bioprocessing using Saccharomyces cerevisiae strain engineered with artificial zinc finger protein. BIORESOURCE TECHNOLOGY 2017; 245:1447-1454. [PMID: 28554523 DOI: 10.1016/j.biortech.2017.05.088] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/14/2017] [Accepted: 05/15/2017] [Indexed: 05/28/2023]
Abstract
In this work, the consolidated bioprocessing (CBP) yeast Saccharomyces cerevisiae MNII/cocδBEC3 was transformed by an artificial zinc finger protein (AZFP) library to improve its thermal tolerance, and the strain MNII-AZFP with superior growth at 42°C was selected. Improved degradation of acid swollen cellulose by 45.9% led to an increase in ethanol production, when compared to the control strain. Moreover, the fermentation of Jerusalem artichoke stalk (JAS) by MNII-AZFP was shortened by 12h at 42°C with a concomitant improvement in ethanol production. Comparative transcriptomics analysis suggested that the AZFP in the mutant exerted beneficial effect by modulating the expression of multiple functional genes. These results provide a feasible strategy for efficient ethanol production from JAS and other cellulosic biomass through CBP based-fermentation at elevated temperatures.
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Affiliation(s)
- M Mahfuza Khatun
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Xinshui Yu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Kobe University, Kobe 657-8501, Japan
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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12
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Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes. Genetics 2017; 208:419-431. [PMID: 29127264 DOI: 10.1534/genetics.117.300377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
A single gene can partake in several biological processes, and therefore gene deletions can lead to different-sometimes unexpected-phenotypes. However, it is not always clear whether such pleiotropy reflects the loss of a unique molecular activity involved in different processes or the loss of a multifunctional protein. Here, using Saccharomyces cerevisiae metabolism as a model, we systematically test the null hypothesis that enzyme phenotypes depend on a single annotated molecular function, namely their catalysis. We screened a set of carefully selected genes by quantifying the contribution of catalysis to gene deletion phenotypes under different environmental conditions. While most phenotypes were explained by loss of catalysis, slow growth was readily rescued by a catalytically inactive protein in about one-third of the enzymes tested. Such noncatalytic phenotypes were frequent in the Alt1 and Bat2 transaminases and in the isoleucine/valine biosynthetic enzymes Ilv1 and Ilv2, suggesting novel "moonlighting" activities in these proteins. Furthermore, differential genetic interaction profiles of gene deletion and catalytic mutants indicated that ILV1 is functionally associated with regulatory processes, specifically to chromatin modification. Our systematic study shows that gene loss phenotypes and their genetic interactions are frequently not driven by the loss of an annotated catalytic function, underscoring the moonlighting nature of cellular metabolism.
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13
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Tambellini NP, Zaremberg V, Krishnaiah S, Turner RJ, Weljie AM. Primary Metabolism and Medium-Chain Fatty Acid Alterations Precede Long-Chain Fatty Acid Changes Impacting Neutral Lipid Metabolism in Response to an Anticancer Lysophosphatidylcholine Analogue in Yeast. J Proteome Res 2017; 16:3741-3752. [PMID: 28849941 DOI: 10.1021/acs.jproteome.7b00430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The nonmetabolizable lysophosphatidylcholine (LysoPC) analogue edelfosine is the prototype of a class of compounds being investigated for their potential as selective chemotherapeutic agents. Edelfosine targets membranes, disturbing cellular homeostasis. Is not clear at this point how membrane alterations are communicated between intracellular compartments leading to growth inhibition and eventual cell death. In the present study, a combined metabolomics/lipidomics approach for the unbiased identification of metabolic pathways altered in yeast treated with sublethal concentrations of the LysoPC analogue was employed. Mass spectrometry of polar metabolites, fatty acids, and lipidomic profiling was used to study the effects of edelfosine on yeast metabolism. Amino acid and sugar metabolism, the Krebs cycle, and fatty acid profiles were most disrupted, with polar metabolites and short-medium chain fatty acid changes preceding long and very long-chain fatty acid variations. Initial increases in metabolites such as trehalose, proline, and γ-amino butyric acid with a concomitant decrease in metabolites of the Krebs cycle, citrate and fumarate, are interpreted as a cellular attempt to offset oxidative stress in response to mitochondrial dysfunction induced by the treatment. Notably, alanine, inositol, and myristoleic acid showed a steady increase during the period analyzed (2, 4, and 6 h after treatment). Of importance was the finding that edelfosine induced significant alterations in neutral glycerolipid metabolism resulting in a significant increase in the signaling lipid diacylglycerol.
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Affiliation(s)
- Nicolas P Tambellini
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada.,Metabolomics Research Centre, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Saikumari Krishnaiah
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104-5158, United States of America
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Aalim M Weljie
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada.,Metabolomics Research Centre, University of Calgary , Calgary, Alberta T2N 1N4, Canada.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104-5158, United States of America
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14
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Luo X, Zhao S, Huan T, Sun D, Friis RMN, Schultz MC, Li L. High-Performance Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast. J Proteome Res 2016; 15:1602-12. [PMID: 26947805 DOI: 10.1021/acs.jproteome.6b00070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downstream sample analysis and differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) for in-depth yeast metabolome profiling. Using (12)C- and (13)C-dansylation (Dns) labeling to analyze the amine/phenol submetabolome, we detected and quantified a total of 5719 peak pairs or metabolites. Among them, 120 metabolites were positively identified using a library of 275 Dns-metabolite standards, and 2980 metabolites were putatively identified based on accurate mass matches to metabolome databases. We also applied (12)C- and (13)C-dimethylaminophenacyl (DmPA) labeling to profile the carboxylic acid submetabolome and detected over 2286 peak pairs, from which 33 metabolites were positively identified using a library of 188 DmPA-metabolite standards, and 1595 metabolites were putatively identified. Using this workflow for metabolomic profiling of cells challenged by ammonium limitation revealed unexpected links between ammonium assimilation and pantothenate accumulation that might be amenable to engineering for better acetyl-CoA production in yeast. We anticipate that efforts to improve other schemes of metabolic engineering will benefit from application of this workflow to multiple cell types.
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Affiliation(s)
- Xian Luo
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Shuang Zhao
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Tao Huan
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Difei Sun
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - R Magnus N Friis
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Michael C Schultz
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Liang Li
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
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15
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Lourenço AB, Muñoz-Jiménez C, Venegas-Calerón M, Artal-Sanz M. Analysis of the effect of the mitochondrial prohibitin complex, a context-dependent modulator of longevity, on the C. elegans metabolome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1457-68. [PMID: 26092086 PMCID: PMC4580209 DOI: 10.1016/j.bbabio.2015.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/11/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022]
Abstract
The mitochondrial prohibitin complex, composed of two proteins, PHB-1 and PHB-2, is a context-dependent modulator of longevity. Specifically, prohibitin deficiency shortens the lifespan of otherwise wild type worms, while it dramatically extends the lifespan under compromised metabolic conditions. This extremely intriguingly phenotype has been linked to alterations in mitochondrial function and in fat metabolism. However, the true function of the mitochondrial prohibitin complex remains elusive. Here, we used gas chromatography coupled to a flame ionization detector (GC/FID) and 1H NMR spectroscopy to gain molecular insights into the effect of prohibitin depletion on the Caenorhabditis elegans metabolome. We analysed the effect of prohibitin deficiency in two different developmental stages and under two different conditions, which result in opposing longevity phenotypes, namely wild type worms and daf-2(e1370) insulin signalling deficient mutants. Prohibitin depletion was shown to alter the fatty acid (GC/FID) and 1H NMR metabolic profiles of wild type animals both at the fourth larval stage of development (L4) and at the young adult (YA) stage, while being more pronounced at the later stage. Furthermore, wild type and the diapause mutant daf-2(e1370), either expressing or not prohibitin, were clearly distinguishable based on their metabolic profiles, revealing changes in fatty acid composition, as well as in carbohydrate and amino acid metabolism. Moreover, the metabolic data indicate that daf-2(e1370) mutants are more robust than the wild type animals to changes induced by prohibitin depletion. The impact of prohibitin depletion on the C. elegans metabolome will be discussed herein in the scope of its effect on longevity. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging. Guest Editor: Aleksandra Trifunovic Impact of the mitochondrial prohibitin (PHB) complex on the C. elegans metabolome Depletion of individual PHB subunits results in similar metabolic profiles. PHB affects fatty acid composition, amino acid and carbohydrate metabolism. daf-2 mutants are more robust than wild type worms to the effect of PHB depletion. Modulation of fermentation may contribute to the longevity of PHB-depleted worms.
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Affiliation(s)
- Artur B Lourenço
- Andalusian Centre for Developmental Biology (CABD), CSIC, Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera, km 1, 41013 Sevilla, Spain
| | - Celia Muñoz-Jiménez
- Andalusian Centre for Developmental Biology (CABD), CSIC, Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera, km 1, 41013 Sevilla, Spain
| | - Mónica Venegas-Calerón
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (IG-CSIC), Ctra. Utrera Km 1, Campus Universitario Pablo de Olavide, 41013, Sevilla, Spain
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology (CABD), CSIC, Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera, km 1, 41013 Sevilla, Spain.
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16
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Wan C, Zhang M, Fang Q, Xiong L, Zhao X, Hasunuma T, Bai F, Kondo A. The impact of zinc sulfate addition on the dynamic metabolic profiling of Saccharomyces cerevisiae subjected to long term acetic acid stress treatment and identification of key metabolites involved in the antioxidant effect of zinc. Metallomics 2015; 7:322-32. [DOI: 10.1039/c4mt00275j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc modulates cellular amino acid metabolism and redox balance to exert its antioxidant effect.
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Affiliation(s)
- Chun Wan
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Mingming Zhang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Qing Fang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Liang Xiong
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Xinqing Zhao
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
- School of Life Science and Biotechnology
- Shanghai Jiaotong University
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology
- Kobe University
- Kobe 657-8501, Japan
| | - Fengwu Bai
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
- School of Life Science and Biotechnology
- Shanghai Jiaotong University
| | - Akihiko Kondo
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501, Japan
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17
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Han WB, Lu YH, Zhang AH, Zhang GF, Mei YN, Jiang N, Lei X, Song YC, Ng SW, Tan RX. Curvulamine, a new antibacterial alkaloid incorporating two undescribed units from a Curvularia species. Org Lett 2014; 16:5366-9. [PMID: 25286294 DOI: 10.1021/ol502572g] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The white croaker (Argyrosomus argentatus) derived Curvularia sp. IFB-Z10 produces curvulamine as a skeletally unprecedented alkaloid incorporating two undescribed extender units. Curvulamine is more selectively antibacterial than tinidazole and biosynthetically unique in the new extenders formed through a decarboxylative condensation between an oligoketide motif and alanine.
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Affiliation(s)
- Wen Bo Han
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, China
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18
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Mitochondrial proteomic analysis reveals the molecular mechanisms underlying reproductive toxicity of zearalenone in MLTC-1 cells. Toxicology 2014; 324:55-67. [PMID: 25058043 DOI: 10.1016/j.tox.2014.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/03/2014] [Accepted: 07/18/2014] [Indexed: 02/07/2023]
Abstract
Zearalenone (ZEA), a Fusarium mycotoxin that contaminates cereal crops worldwide, has been shown to affect the male reproductive system and trigger reactive oxygen species (ROS) generation. However, the mechanisms of its toxicity have not been fully understood. Because mitochondrion is a key organelle involved in producing ROS and generating metabolic intermediates for biosynthesis, an iTRAQ-based mitoproteomics approach was employed to identify the molecular mechanism of zearalenone toxicity using mitochondria of mouse Leydig tumor cells (MLTC-1). A total of 2014 nonredundant proteins were identified, among which 1401 proteins (69.56%) were overlapped. There were 52 differentially expressed proteins in response to ZEA, and they were primarily involved in energy metabolism, molecular transport and endocrine-related functions. Consistent with mitochondrial proteomic analysis, the ATP and intracellular Ca(2+) levels increased after ZEA treatment. The results suggest that lipid metabolism changed significantly after low-dose ZEA exposure, resulting in two alterations. One is the increase in energy production through promoted fatty acid uptake and β-oxidation, along with excessive oxidative stress; the other is an inhibition of steroidogenesis and esterification, possibly resulting in reduced hormone secretion. A hypothetical model of ZEA-induced mitochondrial damage is proposed to provide a framework for the mechanism of ZEA toxicity.
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19
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N-acetylglucosamine (GlcNAc)-inducible gene GIG2 is a novel component of GlcNAc metabolism in Candida albicans. EUKARYOTIC CELL 2013; 13:66-76. [PMID: 24186949 DOI: 10.1128/ec.00244-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Candida albicans is an opportunistic fungal pathogen that resides in the human body as a commensal and can turn pathogenic when the host is immunocompromised. Adaptation of C. albicans to host niche-specific conditions is important for the establishment of pathogenicity, where the ability of C. albicans to utilize multiple carbon sources provides additional flexibility. One alternative sugar is N-acetylglucosamine (GlcNAc), which is now established as an important carbon source for many pathogens and can also act as a signaling molecule. Although GlcNAc catabolism has been well studied in many pathogens, the importance of several enzymes involved in the formation of metabolic intermediates still remains elusive. In this context, microarray analysis was carried out to investigate the transcriptional responses induced by GlcNAc under different conditions. A novel gene that was highly upregulated immediately following the GlcNAc catabolic genes was identified and was named GIG2 (GlcNAc-induced gene 2). This gene is regulated in a manner distinct from that of the GlcNAc-induced genes described previously in that GlcNAc metabolism is essential for its induction. Furthermore, this gene is involved in the metabolism of N-acetylneuraminate (sialic acid), a molecule equally important for initial host-pathogen recognition. Mutant cells showed a considerable decrease in fungal burden in mouse kidneys and were hypersensitive to oxidative stress conditions. Since GIG2 is also present in many other fungal and enterobacterial genomes, targeted inhibition of its activity would offer insight into the treatment of candidiasis and other fungal or enterobacterial infections.
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