1
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Martinez KP, Gasmi N, Jeronimo C, Klimova N, Robert F, Turcotte B. Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition. Nucleic Acids Res 2024; 52:2242-2259. [PMID: 38109318 PMCID: PMC10954478 DOI: 10.1093/nar/gkad1185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers.
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Affiliation(s)
- Karla Páez Martinez
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - Najla Gasmi
- Department of Biochemistry, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Natalia Klimova
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Bernard Turcotte
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
- Department of Biochemistry, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
- Department of Microbiology and Immunology, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
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2
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Sunder S, Bauman JS, Decker SJ, Lifton AR, Kumar A. The yeast AMP-activated protein kinase Snf1 phosphorylates the inositol polyphosphate kinase Kcs1. J Biol Chem 2024; 300:105657. [PMID: 38224949 PMCID: PMC10851228 DOI: 10.1016/j.jbc.2024.105657] [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: 11/03/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
The yeast Snf1/AMP-activated kinase (AMPK) maintains energy homeostasis, controlling metabolic processes and glucose derepression in response to nutrient levels and environmental cues. Under conditions of nitrogen or glucose limitation, Snf1 regulates pseudohyphal growth, a morphological transition characterized by the formation of extended multicellular filaments. During pseudohyphal growth, Snf1 is required for wild-type levels of inositol polyphosphate (InsP), soluble phosphorylated species of the six-carbon cyclitol inositol that function as conserved metabolic second messengers. InsP levels are established through the activity of a family of inositol kinases, including the yeast inositol polyphosphate kinase Kcs1, which principally generates pyrophosphorylated InsP7. Here, we report that Snf1 regulates Kcs1, affecting Kcs1 phosphorylation and inositol kinase activity. A snf1 kinase-defective mutant exhibits decreased Kcs1 phosphorylation, and Kcs1 is phosphorylated in vivo at Ser residues 537 and 646 during pseudohyphal growth. By in vitro analysis, Snf1 directly phosphorylates Kcs1, predominantly at amino acids 537 and 646. A yeast strain carrying kcs1 encoding Ser-to-Ala point mutations at these residues (kcs1-S537A,S646A) shows elevated levels of pyrophosphorylated InsP7, comparable to InsP7 levels observed upon deletion of SNF1. The kcs1-S537A,S646A mutant exhibits decreased pseudohyphal growth, invasive growth, and cell elongation. Transcriptional profiling indicates extensive perturbation of metabolic pathways in kcs1-S537A,S646A. Growth of kcs1-S537A,S646A is affected on medium containing sucrose and antimycin A, consistent with decreased Snf1p signaling. This work identifies Snf1 phosphorylation of Kcs1, collectively highlighting the interconnectedness of AMPK activity and InsP signaling in coordinating nutrient availability, energy homoeostasis, and cell growth.
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Affiliation(s)
- Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joshua S Bauman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stuart J Decker
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandra R Lifton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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3
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Shrivastava M, Kouyoumdjian GS, Kirbizakis E, Ruiz D, Henry M, Vincent AT, Sellam A, Whiteway M. The Adr1 transcription factor directs regulation of the ergosterol pathway and azole resistance in Candida albicans. mBio 2023; 14:e0180723. [PMID: 37791798 PMCID: PMC10653825 DOI: 10.1128/mbio.01807-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Research often relies on well-studied orthologs within related species, with researchers using a well-studied gene or protein to allow prediction of the function of the ortholog. In the opportunistic pathogen Candida albicans, orthologs are usually compared with Saccharomyces cerevisiae, and this approach has been very fruitful. Many transcription factors (TFs) do similar jobs in the two species, but many do not, and typically changes in function are driven not by modifications in the structures of the TFs themselves but in the connections between the transcription factors and their regulated genes. This strategy of changing TF function has been termed transcription factor rewiring. In this study, we specifically looked for rewired transcription factors, or Candida-specific TFs, that might play a role in drug resistance. We investigated 30 transcription factors that were potentially rewired or were specific to the Candida clade. We found that the Adr1 transcription factor conferred resistance to drugs like fluconazole, amphotericin B, and terbinafine when activated. Adr1 is known for fatty acid and glycerol utilization in Saccharomyces, but our study reveals that it has been rewired and is connected to ergosterol biosynthesis in Candida albicans.
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Affiliation(s)
- Manjari Shrivastava
- Department of Biology, Concordia University, Montréal, Quebec, Canada
- Center for research, Montreal Heart Institute, Montréal, Quebec, Canada
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | | | | | - Daniel Ruiz
- Department of Biology, Concordia University, Montréal, Quebec, Canada
| | - Manon Henry
- Center for research, Montreal Heart Institute, Montréal, Quebec, Canada
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Antony T. Vincent
- Department of Animal Sciences, Université Laval, Quebec City, Canada
| | - Adnane Sellam
- Center for research, Montreal Heart Institute, Montréal, Quebec, Canada
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, Quebec, Canada
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4
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Li K, Mocciaro G, Griffin JL, Zhang N. The Saccharomyces cerevisiae acetyltransferase Gcn5 exerts antagonistic pleiotropic effects on chronological ageing. Aging (Albany NY) 2023; 15:10915-10937. [PMID: 37874684 PMCID: PMC10637828 DOI: 10.18632/aging.205109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023]
Abstract
Compared to replicative lifespan, epigenetic regulation of chronological lifespan (CLS) is less well understood in yeast. Here, by screening all the viable mutants of histone acetyltransferase (HAT) and histone deacetylase (HDAC), we demonstrate that Gcn5, functioning in the HAT module of the SAGA/SLIK complex, exhibits an epistatic relationship with the HDAC Hda1 to control the expression of starvation-induced stress response and respiratory cell growth. Surprisingly, the gcn5Δ mutants lose their colony-forming potential early in the stationary phase but display a longer maximum CLS than their WT counterparts, suggesting the contradictory roles of Gcn5 in lifespan regulation. Integrative analyses of the transcriptome, metabolome and ChIP assays reveal that Gcn5 is necessary for the activation of two regulons upon glucose starvation: the Msn2/4-/Gis1-dependent stress response and the Cat8-/Adr1-mediated metabolic reprogramming, to enable pro-longevity characteristics, including redox homeostasis, stress resistance and maximal storage of carbohydrates. The activation of Cat8-/Adr1-dependent regulon also promotes the pyruvate dehydrogenase (PDH) bypass, leading to acetyl-CoA synthesis, global and targeted H3K9 acetylation. Global H3K9 acetylation levels mediated by Gcn5 and Hda1 during the transition into stationary phase are positively correlated with senescent cell populations accumulated in the aged cell cultures. These data suggest that Gcn5 lies in the centre of a feed-forward loop between histone acetylation and starvation-induced gene expression, enabling stress resistance and homeostasis but also promoting chronological ageing concomitantly.
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Affiliation(s)
- Kaiqiang Li
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Gabriele Mocciaro
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jules L. Griffin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- The Rowett Institute, University of Aberdeen, Foresterhill Campus, Aberdeen AB25 2ZD, UK
| | - Nianshu Zhang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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5
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Vijjamarri AK, Gupta N, Onu C, Niu X, Zhang F, Kumar R, Lin Z, Greenberg M, Hinnebusch AG. mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability. Nucleic Acids Res 2023; 51:9314-9336. [PMID: 37439347 PMCID: PMC10516646 DOI: 10.1093/nar/gkad584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/17/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023] Open
Abstract
We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1Δ and pat1Δ mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in wild-type cells. These mRNAs show both reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
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Affiliation(s)
- Anil Kumar Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Xiao Niu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Fan Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rakesh Kumar
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Gutiérrez-Corona JF, González-Hernández GA, Padilla-Guerrero IE, Olmedo-Monfil V, Martínez-Rocha AL, Patiño-Medina JA, Meza-Carmen V, Torres-Guzmán JC. Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential. Cells 2023; 12:2239. [PMID: 37759461 PMCID: PMC10526403 DOI: 10.3390/cells12182239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Fungal alcohol dehydrogenases (ADHs) participate in growth under aerobic or anaerobic conditions, morphogenetic processes, and pathogenesis of diverse fungal genera. These processes are associated with metabolic operation routes related to alcohol, aldehyde, and acid production. The number of ADH enzymes, their metabolic roles, and their functions vary within fungal species. The most studied ADHs are associated with ethanol metabolism, either as fermentative enzymes involved in the production of this alcohol or as oxidative enzymes necessary for the use of ethanol as a carbon source; other enzymes participate in survival under microaerobic conditions. The fast generation of data using genome sequencing provides an excellent opportunity to determine a correlation between the number of ADHs and fungal lifestyle. Therefore, this review aims to summarize the latest knowledge about the importance of ADH enzymes in the physiology and metabolism of fungal cells, as well as their structure, regulation, evolutionary relationships, and biotechnological potential.
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Affiliation(s)
- J. Félix Gutiérrez-Corona
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Gloria Angélica González-Hernández
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Israel Enrique Padilla-Guerrero
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Vianey Olmedo-Monfil
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Ana Lilia Martínez-Rocha
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - J. Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Víctor Meza-Carmen
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Juan Carlos Torres-Guzmán
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
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7
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Deng H, Du Z, Lu S, Wang Z, He X. Regulation of Cat8 in energy metabolic balance and glucose tolerance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12593-2. [PMID: 37249587 DOI: 10.1007/s00253-023-12593-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023]
Abstract
Cat8 is a C6 zinc cluster transcription activator in yeast. It is generally recognized that the transcription of CAT8 is inhibited and that Cat8 is inactive in the presence of high concentrations of glucose. However, our recent study found that constitutively overexpressed Cat8 played a regulatory role in Saccharomyces cerevisiae in the presence of 20 g/L glucose. To explore the regulatory network of Cat8 at high glucose concentrations, CAT8 was both overexpressed and deleted in this study. Cell growth and glucose consumption in different media were significantly accelerated by the deletion of CAT8, while the lag period was greatly shortened. RNA-seq and genetic modification showed that the deletion of CAT8 changed the type of energy metabolism in yeast cells. Many genes related to the mitochondrial respiratory chain were downregulated, resulting in a reduction in aerobic respiration and the tricarboxylic acid cycle. Meanwhile, both the energy supply of anaerobic ethanol fermentation and the Crabtree effect of S. cerevisiae were enhanced by the deletion of CAT8. CAT8 knockout cells show a higher sugar uptake rate, a higher cell growth rate, and higher tolerance to glucose than the wild-type strain YS58. This study expands the understanding of the regulatory network of Cat8 and provides guidance for modulating yeast cell growth. KEY POINTS: • The deletion of CAT8 promoted cell growth of S. cerevisiae. • Transcriptome analysis revealed the regulation network of Cat8 under 1% glucose condition. • CAT8 deletion increases the glucose tolerance of cells by enhancing the Crabtree effect.
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Affiliation(s)
- Hong Deng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Surui Lu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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8
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Wolf IR, Marques LF, de Almeida LF, Lázari LC, de Moraes LN, Cardoso LH, Alves CCDO, Nakajima RT, Schnepper AP, Golim MDA, Cataldi TR, Nijland JG, Pinto CM, Fioretto MN, Almeida RO, Driessen AJM, Simōes RP, Labate MV, Grotto RMT, Labate CA, Fernandes Junior A, Justulin LA, Coan RLB, Ramos É, Furtado FB, Martins C, Valente GT. Integrative Analysis of the Ethanol Tolerance of Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065646. [PMID: 36982719 PMCID: PMC10051466 DOI: 10.3390/ijms24065646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Ethanol (EtOH) alters many cellular processes in yeast. An integrated view of different EtOH-tolerant phenotypes and their long noncoding RNAs (lncRNAs) is not yet available. Here, large-scale data integration showed the core EtOH-responsive pathways, lncRNAs, and triggers of higher (HT) and lower (LT) EtOH-tolerant phenotypes. LncRNAs act in a strain-specific manner in the EtOH stress response. Network and omics analyses revealed that cells prepare for stress relief by favoring activation of life-essential systems. Therefore, longevity, peroxisomal, energy, lipid, and RNA/protein metabolisms are the core processes that drive EtOH tolerance. By integrating omics, network analysis, and several other experiments, we showed how the HT and LT phenotypes may arise: (1) the divergence occurs after cell signaling reaches the longevity and peroxisomal pathways, with CTA1 and ROS playing key roles; (2) signals reaching essential ribosomal and RNA pathways via SUI2 enhance the divergence; (3) specific lipid metabolism pathways also act on phenotype-specific profiles; (4) HTs take greater advantage of degradation and membraneless structures to cope with EtOH stress; and (5) our EtOH stress-buffering model suggests that diauxic shift drives EtOH buffering through an energy burst, mainly in HTs. Finally, critical genes, pathways, and the first models including lncRNAs to describe nuances of EtOH tolerance are reported here.
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Affiliation(s)
- Ivan Rodrigo Wolf
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Lucas Farinazzo Marques
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Lauana Fogaça de Almeida
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Lucas Cardoso Lázari
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil
| | - Leonardo Nazário de Moraes
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Luiz Henrique Cardoso
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Camila Cristina de Oliveira Alves
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Rafael Takahiro Nakajima
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Amanda Piveta Schnepper
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Marjorie de Assis Golim
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Thais Regiani Cataldi
- Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil
| | - Jeroen G. Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Camila Moreira Pinto
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Matheus Naia Fioretto
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Rodrigo Oliveira Almeida
- Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais–Campus Muriaé, Muriaé 36884-036, Brazil
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Rafael Plana Simōes
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Mônica Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil
| | - Rejane Maria Tommasini Grotto
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil
| | - Ary Fernandes Junior
- Laboratory of Bacteriology, Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Luis Antonio Justulin
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Rafael Luiz Buogo Coan
- Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Érica Ramos
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Fabiana Barcelos Furtado
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
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9
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Transcriptional Response of Multi-Stress-Tolerant Saccharomyces cerevisiae to Sequential Stresses. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
During the fermentation process, yeast cells face different stresses, and their survival and fermentation efficiency depend on their adaptation to these challenging conditions. Yeast cells must tolerate not only a single stress but also multiple simultaneous and sequential stresses. However, the adaptation and cellular response when cells are sequentially stressed are not completely understood. To explore this, we exposed a multi-stress-tolerant strain (BT0510) to different consecutive stresses to globally explore a common response, focusing on the genes induced in both stresses. Gene Ontology, pathway analyses, and common transcription factor motifs identified many processes linked to this common response. A metabolic shift to the pentose phosphate pathway, peroxisome activity, and the oxidative stress response were some of the processes found. The SYM1, STF2, and HSP genes and the transcription factors Adr1 and Usv1 may play a role in this response. This study presents a global view of the transcriptome of a multi-resistance yeast and provides new insights into the response to sequential stresses. The identified response genes can indicate future directions for the genetic engineering of yeast strains, which could improve many fermentation processes, such as those used for bioethanol production and beverages.
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10
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Vijjamarri AK, Niu X, Vandermeulen MD, Onu C, Zhang F, Qiu H, Gupta N, Gaikwad S, Greenberg ML, Cullen PJ, Lin Z, Hinnebusch AG. Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522830. [PMID: 36711592 PMCID: PMC9881900 DOI: 10.1101/2023.01.05.522830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, in coupling codon non-optimality to enhanced degradation, and as a translational repressor, but its functions in cells are incompletely understood. RNA-Seq analyses coupled with CAGE sequencing of all capped mRNAs revealed increased abundance of hundreds of mRNAs in dcp2 Δ cells that appears to result directly from impaired decapping rather than elevated transcription, which was confirmed by ChIP-Seq analysis of RNA Polymerase II occupancies genome-wide. Interestingly, only a subset of mRNAs requires Dhh1 for targeting by Dcp2, and also generally requires the other decapping activators Pat1, Lsm2, Edc3 or Scd6; whereas most of the remaining transcripts utilize NMD factors for Dcp2-mediated turnover. Neither inefficient translation initiation nor stalled elongation appears to be a major driver of Dhh1-enhanced mRNA degradation. Surprisingly, ribosome profiling revealed that dcp2 Δ confers widespread changes in relative TEs that generally favor well-translated mRNAs. Because ribosome biogenesis is reduced while capped mRNA abundance is increased by dcp2 Δ, we propose that an increased ratio of mRNA to ribosomes increases competition among mRNAs for limiting ribosomes to favor efficiently translated mRNAs in dcp2 Δ cells. Interestingly, genes involved in respiration or utilization of alternative carbon or nitrogen sources are derepressed, and both mitochondrial function and cell filamentation (a strategy for nutrient foraging) are elevated by dcp2 Δ, suggesting that mRNA decapping sculpts gene expression post-transcriptionally to fine-tune metabolic pathways and morphological transitions according to nutrient availability.
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Affiliation(s)
- Anil Kumar Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Xiao Niu
- Department of Biology, Saint Louis University, St. Louis, MO
| | | | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Fan Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Hongfang Qiu
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | | | - Paul J Cullen
- Department of Biological Sciences, State University of Buffalo, Buffalo, NY
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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11
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Rewiring regulation on respiro-fermentative metabolism relieved Crabtree effects in Saccharomyces cerevisiae. Synth Syst Biotechnol 2022; 7:1034-1043. [PMID: 35801089 PMCID: PMC9241035 DOI: 10.1016/j.synbio.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 11/20/2022] Open
Abstract
The respiro-fermentative metabolism in the yeast Saccharomyces cerevisiae, also called the Crabtree effect, results in lower energy efficiency and biomass yield which can impact yields of chemicals to be produced using this cell factory. Although it can be engineered to become Crabtree negative, the slow growth and glucose consumption rate limit its industrial application. Here the Crabtree effect in yeast can be alleviated by engineering the transcription factor Mth1 involved in glucose signaling and a subunit of the RNA polymerase II mediator complex Med2. It was found that the mutant with the MTH1A81D&MED2*432Y allele could grow in glucose rich medium with a specific growth rate of 0.30 h−1, an ethanol yield of 0.10 g g−1, and a biomass yield of 0.21 g g−1, compared with a specific growth rate of 0.40 h−1, an ethanol yield of 0.46 g g−1, and a biomass yield of 0.11 g g−1 in the wild-type strain CEN.PK 113-5D. Transcriptome analysis revealed significant downregulation of the glycolytic process, as well as the upregulation of the TCA cycle and the electron transfer chain. Significant expression changes of several reporter transcription factors were also identified, which might explain the higher energy efficiencies in the engineered strain. We further demonstrated the potential of the engineered strain with the production of 3-hydroxypropionic acid at a titer of 2.04 g L−1, i.e., 5.4-fold higher than that of a reference strain, indicating that the alleviated glucose repression could enhance the supply of mitochondrial acetyl-CoA. These results suggested that the engineered strain could be used as an efficient cell factory for mitochondrial production of acetyl-CoA derived chemicals.
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12
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Chen H, Chai X, Wang Y, Liu J, Zhou G, Wei P, Song Y, Ma L. The multiple effects of REG1 deletion and SNF1 overexpression improved the production of S-adenosyl-L-methionine in Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:174. [PMID: 36030199 PMCID: PMC9419380 DOI: 10.1186/s12934-022-01900-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is often used as a cell factory for the production of S-adenosyl-L-methionine (SAM) for diverse pharmaceutical applications. However, SAM production by S. cerevisiae is negatively influenced by glucose repression, which is regulated by a serine/threonine kinase SNF1 complex. Here, a strategy of alleviating glucose repression by deleting REG1 (encodes the regulatory subunit of protein phosphatase 1) and overexpressing SNF1 (encodes the catalytic subunit of the SNF1 complex) was applied to improve SAM production in S. cerevisiae. SAM production, growth conditions, glucose consumption, ethanol accumulation, lifespan, glycolysis and amino acid metabolism were analyzed in the mutant strains. RESULTS The results showed that the multiple effects of REG1 deletion and/or SNF1 overexpression exhibited a great potential for improving the SAM production in yeast. Enhanced the expression levels of genes involved in glucose transport and glycolysis, which improved the glucose utilization and then elevated the levels of glycolytic intermediates. The expression levels of ACS1 (encoding acetyl-CoA synthase I) and ALD6 (encoding aldehyde dehydrogenase), and the activity of alcohol dehydrogenase II (ADH2) were enhanced especially in the presence of excessive glucose levels, which probably promoted the conversion of ethanol in fermentation broth into acetyl-CoA. The gene expressions involved in sulfur-containing amino acids were also enhanced for the precursor amino acid biosynthesis. In addition, the lifespan of yeast was extended by REG1 deletion and/or SNF1 overexpression. As expected, the final SAM yield of the mutant YREG1ΔPSNF1 reached 8.28 g/L in a 10-L fermenter, which was 51.6% higher than the yield of the parent strain S. cerevisiae CGMCC 2842. CONCLUSION This study showed that the multiple effects of REG1 deletion and SNF1 overexpression improved SAM production in S. cerevisiae, providing new insight into the application of the SNF1 complex to abolish glucose repression and redirect carbon flux to nonethanol products in S. cerevisiae.
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Affiliation(s)
- Hailong Chen
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Xiaoqin Chai
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Yan Wang
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Jing Liu
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Guohai Zhou
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Pinghe Wei
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Yuhe Song
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China.
| | - Lingman Ma
- School of Life Science and Technology, China Pharmaceutical University, 211198, Nanjing, Jiangsu, People's Republic of China.
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Li S, Yang J, Mohamed H, Wang X, Pang S, Wu C, López-García S, Song Y. Identification and Functional Characterization of Adenosine Deaminase in Mucor circinelloides: A Novel Potential Regulator of Nitrogen Utilization and Lipid Biosynthesis. J Fungi (Basel) 2022; 8:jof8080774. [PMID: 35893142 PMCID: PMC9332508 DOI: 10.3390/jof8080774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 02/05/2023] Open
Abstract
Adenosine deaminase (ADA) is an enzyme distributed in a wide variety of organisms that cleaves adenosine into inosine. Since inosine plays an important role in nitrogen metabolism, ADA may have a critical function in the regulation of fatty acid synthesis. However, the role of ADA in oleaginous fungi has not been reported so far. Therefore, in this study, we identified one ada gene encoding ADA (with ID scaffold0027.9) in the high lipid-producing fungus, Mucor circinelloides WJ11, and investigated its role in cell growth, lipid production, and nitrogen metabolism by overexpressing and knockout of this gene. The results showed that knockout of the ada altered the efficiency of nitrogen consumption, which led to a 20% increment in the lipid content (25% of cell dry weight) of the engineered strain, while overexpression of the ada showed no significant differences compared with the control strain at the final growth stage; however, interestingly, it increased lipid accumulation at the early growth stage. Additionally, transcriptional analysis was conducted by RT-qPCR and our findings indicated that the deletion of ada activated the committed steps of lipid biosynthesis involved in acetyl-CoA carboxylase (acc1 gene), cytosolic malic acid enzyme (cme1 gene), and fatty acid synthases (fas1 gene), while it suppressed the expression of AMP-activated protein kinase (ampk α1 and ampk β genes), which plays a role in lipolysis, whereas the ada-overexpressed strain displayed reverse trends. Conclusively, this work unraveled a novel role of ADA in governing lipid biosynthesis and nitrogen metabolism in the oleaginous fungus, M. circinelloides.
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Affiliation(s)
- Shaoqi Li
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China; (S.L.); (H.M.); (X.W.); (S.P.); (C.W.)
| | - Junhuan Yang
- Department of Food Sciences, College of Food Science and Engineering, Lingnan Normal University, Zhanjiang 524048, China;
| | - Hassan Mohamed
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China; (S.L.); (H.M.); (X.W.); (S.P.); (C.W.)
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Xiuwen Wang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China; (S.L.); (H.M.); (X.W.); (S.P.); (C.W.)
| | - Shuxian Pang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China; (S.L.); (H.M.); (X.W.); (S.P.); (C.W.)
| | - Chen Wu
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China; (S.L.); (H.M.); (X.W.); (S.P.); (C.W.)
| | - Sergio López-García
- Department of Genetics and Microbiology (Associated Unit to IQFR-CSIC), Faculty of Biology, University of Murcia, 3100 Murcia, Spain;
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China; (S.L.); (H.M.); (X.W.); (S.P.); (C.W.)
- Correspondence: ; Tel.: +86-13964463099
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14
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Du Z, Deng H, Cheng Y, Zhai Z, Guo X, Wang Z, He X. Cat8 Response to Nutritional Changes and Interaction With Ehrlich Pathway Related Factors. Front Microbiol 2022; 13:898938. [PMID: 35783377 PMCID: PMC9245043 DOI: 10.3389/fmicb.2022.898938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cat8 is an important transcription factor regulating the utilization of non-fermentative carbon sources in Saccharomyces cerevisiae. However, our previous studies found that Cat8 may play a critical role in nitrogen metabolism, but the regulatory mechanism has not been elucidated. In this study, the nuclear localization and analysis of regulatory activity showed that the Cat8 function relies on Snf1 kinase. In the fermentation with glucose or glycerol as carbon sources under phenylalanine (Phe) induction, by comparing the changes of cellular gene expression and Cat8 target gene binding profiles after Cat8 overexpression, enhanced transcription was shown among key genes involved in the Ehrlich pathway (e.g., ARO9, ARO10, and ADH2) and its upstream and downstream related factors (e.g., GAP1, AGP1, GAT1, PDR12, and ESPB6), indicating that Cat8 participated in the regulation of nitrogen metabolism. Moreover, highly active Cat8 interacts with transcriptional activator Aro80 and GATA activator Gat1 coordinately to regulate the transcription of ARO10. Altogether, our results showed that Cat8 may act as a global transcription factor in response to nutritional changes, regulating both carbon and nitrogen utilization. This provides a new insight for us to explore the regulation of cell nutrient metabolism networks in yeast.
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Affiliation(s)
- Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Hong Deng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Yanfei Cheng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiguang Zhai
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Zhaoyue Wang,
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
- Xiuping He,
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15
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Two homologs of the Cat8 transcription factor are involved in the regulation of ethanol utilization in Komagataella phaffii. Curr Genet 2021; 67:641-661. [PMID: 33725138 PMCID: PMC8254726 DOI: 10.1007/s00294-021-01165-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/26/2022]
Abstract
The transcription factors Cat8 and Sip4 were described in Saccharomyces cerevisiae and Kluyveromyces lactis to have very similar DNA binding domains and to be necessary for derepression of a variety of genes under non-fermentative growth conditions via binding to the carbon source responsive elements (CSREs). The methylotrophic yeast Komagataella phaffii (syn Pichia pastoris) has two transcription factors (TFs), which are putative homologs of Cat8 based on sequence similarity, termed Cat8-1 and Cat8-2. It is yet unclear in which cellular processes they are involved and if one of them is actually the homolog of Sip4. To study the roles of the Cat8 homologs in K. phaffii, overexpression or deletion strains were generated for the two TFs. The ability of these mutant strains to grow on different carbon sources was tested, and transcript levels of selected genes from the carbon metabolism were quantified. Our experiments showed that the TFs are required for the growth of K. phaffii on C2 carbon sources, but not on glucose, glycerol or methanol. K. phaffii deleted for Cat8-1 showed impaired growth on acetate, while both Cat8-1 and Cat8-2 are involved in the growth of K. phaffii on ethanol. Correspondingly, both TFs are participating in the activation of ADH2, ALD4 and ACS1, three genes encoding enzymes important for the assimilation of ethanol. Different from S. cerevisiae and K. lactis, Cat8-1 is not regulating the transcription of the putative Sip4-family member Cat8-2 in K. phaffii. Furthermore, Cat8-1 is necessary for the activation of genes from the glyoxylate cycle, whereas Cat8-2 is necessary for the activation of genes from the carnitine shuttle. Neither Cat8-1 nor Cat8-2 are required for the activation of gluconeogenesis genes. Finally, the CAT8-2 gene is repressed by the Mig1-2 transcription factor on glucose and autorepressed by the Cat8-2 protein on all tested carbon sources. Our study identified the involvement of K. phaffii Cat8-1 and Cat8-2 in C2-metabolism, and highlighted similarities and differences to their homologs in other yeast species.
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16
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Tang H, Wu Y, Deng J, Chen N, Zheng Z, Wei Y, Luo X, Keasling JD. Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae. Metabolites 2020; 10:metabo10080320. [PMID: 32781665 PMCID: PMC7466126 DOI: 10.3390/metabo10080320] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 12/23/2022] Open
Abstract
Promoters play an essential role in the regulation of gene expression for fine-tuning genetic circuits and metabolic pathways in Saccharomyces cerevisiae (S. cerevisiae). However, native promoters in S. cerevisiae have several limitations which hinder their applications in metabolic engineering. These limitations include an inadequate number of well-characterized promoters, poor dynamic range, and insufficient orthogonality to endogenous regulations. Therefore, it is necessary to perform promoter engineering to create synthetic promoters with better properties. Here, we review recent advances related to promoter architecture, promoter engineering and synthetic promoter applications in S. cerevisiae. We also provide a perspective of future directions in this field with an emphasis on the recent advances of machine learning based promoter designs.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Jiliang Deng
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Nanzhu Chen
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Zhaohui Zheng
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China;
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
- Correspondence: (X.L.); (J.D.K.)
| | - Jay D. Keasling
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Correspondence: (X.L.); (J.D.K.)
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17
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Raghavendran V, Webb JP, Cartron ML, Springthorpe V, Larson TR, Hines M, Mohammed H, Zimmerman WB, Poole RK, Green J. A microbubble-sparged yeast propagation-fermentation process for bioethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:104. [PMID: 32523617 PMCID: PMC7281951 DOI: 10.1186/s13068-020-01745-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Industrial biotechnology will play an increasing role in creating a more sustainable global economy. For conventional aerobic bioprocesses supplying O2 can account for 15% of total production costs. Microbubbles (MBs) are micron-sized bubbles that are widely used in industry and medical imaging. Using a fluidic oscillator to generate energy-efficient MBs has the potential to decrease the costs associated with aeration. However, little is understood about the effect of MBs on microbial physiology. To address this gap, a laboratory-scale MB-based Saccharomyces cerevisiae Ethanol Red propagation-fermentation bioethanol process was developed and analysed. RESULTS Aeration with MBs increased O2 transfer to the propagation cultures. Titres and yields of bioethanol in subsequent anaerobic fermentations were comparable for MB-propagated and conventional, regular bubble (RB)-propagated yeast. However, transcript profiling showed significant changes in gene expression in the MB-propagated yeast compared to those propagated using RB. These changes included up-regulation of genes required for ergosterol biosynthesis. Ergosterol contributes to ethanol tolerance, and so the performance of MB-propagated yeast in fed-batch fermentations sparged with 1% O2 as either RBs or MBs were tested. The MB-sparged yeast retained higher levels of ergosteryl esters during the fermentation phase, but this did not result in enhanced viability or ethanol production compared to ungassed or RB-sparged fermentations. CONCLUSIONS The performance of yeast propagated using energy-efficient MB technology in bioethanol fermentations is comparable to that of those propagated conventionally. This should underpin the future development of MB-based commercial yeast propagation.
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Affiliation(s)
| | - Joseph P. Webb
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Michaël L. Cartron
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | | | - Tony R. Larson
- Department of Biology, University of York, York, YO10 5DD UK
| | - Michael Hines
- Perlemax Ltd, Kroto Innovation Centre, 318 Broad Lane, Sheffield, S3 7HQ UK
| | - Hamza Mohammed
- Perlemax Ltd, Kroto Innovation Centre, 318 Broad Lane, Sheffield, S3 7HQ UK
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, S1 3JD UK
| | - William B. Zimmerman
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, S1 3JD UK
| | - Robert K. Poole
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Jeffrey Green
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
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18
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Bergman A, Vitay D, Hellgren J, Chen Y, Nielsen J, Siewers V. Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome. FEMS Yeast Res 2019; 19:5423327. [PMID: 30924859 PMCID: PMC6755256 DOI: 10.1093/femsyr/foz027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
Microbial conversion of biomass to fatty acids (FA) and products derived thereof is an attractive alternative to the traditional oleochemical production route from animal and plant lipids. This study examined if NADPH-costly FA biosynthesis could be enhanced by overexpressing the transcription factor Stb5 in Saccharomyces cerevisiae. Stb5 activates expression of multiple genes encoding enzymes within the pentose phosphate pathway (PPP) and other NADPH-producing reactions. Overexpression of STB5 led to a decreased growth rate and an increased free fatty acid (FFA) production during growth on glucose. The improved FFA synthetic ability in the glucose phase was shown to be independent of flux through the oxidative PPP. RNAseq analysis revealed that STB5 overexpression had wide-ranging effects on the transcriptome in the batch phase, and appeared to cause a counterintuitive phenotype with reduced flux through the oxidative PPP. During glucose limitation, when an increased NADPH supply is likely less harmful, an overall induction of the proposed target genes of Stb5 (eg. GND1/2, TAL1, ALD6, YEF1) was observed. Taken together, the strategy of utilizing STB5 overexpression to increase NADPH supply for reductive biosynthesis is suggested to have potential in strains engineered to have strong ability to consume excess NADPH, alleviating a potential redox imbalance.
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Affiliation(s)
- Alexandra Bergman
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| | - Dóra Vitay
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden
| | - John Hellgren
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, DK2800 Kgs. Lyngby, Denmark
| | - Verena Siewers
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
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19
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Zhang Q, Huang Q, Fang Q, Li H, Tang H, Zou G, Wang D, Li S, Bei W, Chen H, Li L, Zhou R. Identification of genes regulated by the two-component system response regulator NarP of Actinobacillus pleuropneumoniae via DNA-affinity-purified sequencing. Microbiol Res 2019; 230:126343. [PMID: 31539852 DOI: 10.1016/j.micres.2019.126343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 01/21/2023]
Abstract
Identifying the direct target genes of response regulators (RRs) of a bacterial two-component system (TCS) is critical to understand the roles of TCS in bacterial environmental adaption and pathogenesis. Actinobacillus pleuropneumoniae is an important respiratory bacterial pathogen that causes considerable economic losses to swine industry worldwide. The targets of A. pleuropneumoniae NarP (nitrate/nitrite RR), which is the cognate RR of the nitrate/nitrite sensor histidine kinase NarQ, are still unknown. In the present study, a DNA-affinity-purified sequencing (DAP-Seq) approach was established. The upstream regions of a total of 131 candidate genes from the genome of A. pleuropneumoniae were co-purified with the activated NarP protein. Electrophoretic mobility shift assay (EMSA) results confirmed the interactions of NarP with the promoter regions of five selected target genes, including dmsA, pgaA, ftpA, cstA and ushA. The EMSA-confirmed target genes were significantly up-regulated in the narP-deleted mutant in the presence of additional nitrate, whilst the transcriptional changes were restored in the complemented strain. The NarP binding motif in the upstream regions of the target genes dmsA and ftpA were further identified and confirmed by EMSA using the truncated binding motif. The NarP binding sites were present in a total of 25.2% of the DNA fragments captured by DAP-Seq. These results demonstrated that the established DAP-Seq method is effective for exploring the direct targets of RRs of bacterial TCSs and that the A. pleuropneumoniae NarP could be a repressor in response to nitrate.
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Affiliation(s)
- Qiuhong Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Qiong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Haotian Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Hao Tang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Dong Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Siqi Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China.
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China.
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20
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Ergün BG, Gasser B, Mattanovich D, Çalık P. Engineering of
alcohol dehydrogenase 2
hybrid‐promoter architectures in
Pichia pastoris
to enhance recombinant protein expression on ethanol. Biotechnol Bioeng 2019; 116:2674-2686. [DOI: 10.1002/bit.27095] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical EngineeringMiddle East Technical University Ankara Turkey
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied SciencesMiddle East Technical University Ankara Turkey
| | - Brigitte Gasser
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences Vienna Austria
- Austrian Centre of Industrial Biotechnology (ACIB) Vienna Austria
| | - Diethard Mattanovich
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences Vienna Austria
- Austrian Centre of Industrial Biotechnology (ACIB) Vienna Austria
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical EngineeringMiddle East Technical University Ankara Turkey
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied SciencesMiddle East Technical University Ankara Turkey
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21
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Xiberras J, Klein M, Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses - Knowledge gaps regarding the central carbon catabolism of this 'non-fermentable' carbon source. Biotechnol Adv 2019; 37:107378. [PMID: 30930107 DOI: 10.1016/j.biotechadv.2019.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022]
Abstract
Glycerol is an interesting alternative carbon source in industrial bioprocesses due to its higher degree of reduction per carbon atom compared to sugars. During the last few years, significant progress has been made in improving the well-known industrial platform organism Saccharomyces cerevisiae with regard to its glycerol utilization capability, particularly in synthetic medium. This provided a basis for future metabolic engineering focusing on the production of valuable chemicals from glycerol. However, profound knowledge about the central carbon catabolism in synthetic glycerol medium is a prerequisite for such incentives. As a matter of fact, the current assumptions about the actual in vivo fluxes active on glycerol as the sole carbon source have mainly been based on omics data collected in complex media or were even deduced from studies with other non-fermentable carbon sources, such as ethanol or acetate. A number of uncertainties have been identified which particularly regard the role of the glyoxylate cycle, the subcellular localization of the respective enzymes, the contributions of mitochondrial transporters and the active anaplerotic reactions under these conditions. The review scrutinizes the current knowledge, highlights the necessity to collect novel experimental data using cells growing in synthetic glycerol medium and summarizes the current state of the art with regard to the production of valuable fermentation products from a carbon source that has been considered so far as 'non-fermentable' for the yeast S. cerevisiae.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany.
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22
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Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P. A resource of variant effect predictions of single nucleotide variants in model organisms. Mol Syst Biol 2018; 14:e8430. [PMID: 30573687 PMCID: PMC6301329 DOI: 10.15252/msb.20188430] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022] Open
Abstract
The effect of single nucleotide variants (SNVs) in coding and noncoding regions is of great interest in genetics. Although many computational methods aim to elucidate the effects of SNVs on cellular mechanisms, it is not straightforward to comprehensively cover different molecular effects. To address this, we compiled and benchmarked sequence and structure-based variant effect predictors and we computed the impact of nearly all possible amino acid and nucleotide variants in the reference genomes of Homo sapiens, Saccharomyces cerevisiae and Escherichia coli Studied mechanisms include protein stability, interaction interfaces, post-translational modifications and transcription factor binding sites. We apply this resource to the study of natural and disease coding variants. We also show how variant effects can be aggregated to generate protein complex burden scores that uncover protein complex to phenotype associations based on a set of newly generated growth profiles of 93 sequenced S. cerevisiae strains in 43 conditions. This resource is available through mutfunc (www.mutfunc.com), a tool by which users can query precomputed predictions by providing amino acid or nucleotide-level variants.
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Affiliation(s)
- Omar Wagih
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Marco Galardini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Bede P Busby
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Danish Memon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
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23
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Alsina D, Ros J, Tamarit J. Nitric oxide prevents Aft1 activation and metabolic remodeling in frataxin-deficient yeast. Redox Biol 2018; 14:131-141. [PMID: 28918000 PMCID: PMC5602528 DOI: 10.1016/j.redox.2017.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/25/2017] [Accepted: 09/02/2017] [Indexed: 11/30/2022] Open
Abstract
Yeast frataxin homolog (Yfh1) is the orthologue of human frataxin, a mitochondrial protein whose deficiency causes Friedreich Ataxia. Yfh1 deficiency activates Aft1, a transcription factor governing iron homeostasis in yeast cells. Although the mechanisms causing this activation are not completely understood, it is assumed that it may be caused by iron-sulfur deficiency. However, several evidences indicate that activation of Aft1 occurs in the absence of iron-sulfur deficiency. Besides, Yfh1 deficiency also leads to metabolic remodeling (mainly consisting in a shift from respiratory to fermentative metabolism) and to induction of Yhb1, a nitric oxide (NO) detoxifying enzyme. In this work, we have used conditional Yfh1 mutant yeast strains to investigate the relationship between NO, Aft1 activation and metabolic remodeling. We have observed that NO prevents Aft1 activation caused by Yfh1 deficiency. This phenomenon is not observed when Aft1 is activated by iron scarcity or impaired iron-sulfur biogenesis. In addition, analyzing key metabolic proteins by a targeted proteomics approach, we have observed that NO prevents the metabolic remodeling caused by Yfh1 deficiency. We conclude that Aft1 activation in Yfh1-deficient yeasts is not caused by iron-sulfur deficiency or iron scarcity. Our hypothesis is that Yfh1 deficiency leads to the presence of anomalous iron species that can compromise iron bioavailability and activate a signaling cascade that results in Aft1 activation and metabolic remodeling.
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Affiliation(s)
- David Alsina
- Departament de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Lleida, Spain
| | - Joaquim Ros
- Departament de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Lleida, Spain
| | - Jordi Tamarit
- Departament de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Lleida, Spain.
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24
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Simpson-Lavy K, Xu T, Johnston M, Kupiec M. The Std1 Activator of the Snf1/AMPK Kinase Controls Glucose Response in Yeast by a Regulated Protein Aggregation. Mol Cell 2017; 68:1120-1133.e3. [PMID: 29249654 DOI: 10.1016/j.molcel.2017.11.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/10/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
The ability to respond to available nutrients is critical for all living cells. The AMP-activated protein kinase (SNF1 in yeast) is a central regulator of metabolism that is activated when energy is depleted. We found that SNF1 activity in the nucleus is regulated by controlled relocalization of the SNF1 activator Std1 into puncta. This process is regulated by glucose through the activity of the previously uncharacterized protein kinase Vhs1 and its substrate Sip5, a protein of hitherto unknown function. Phosphorylation of Sip5 prevents its association with Std1 and triggers Std1 accretion. Reversible Std1 puncta formation occurs under non-stressful, ambient conditions, creating non-amyloid inclusion bodies at the nuclear-vacuolar junction, and it utilizes cellular chaperones similarly to the aggregation of toxic or misfolded proteins such as those associated with Parkinson's, Alzheimer's, and CJD diseases. Our results reveal a controlled, non-pathological, physiological role of protein aggregation in the regulation of a major metabolic cellular pathway.
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Affiliation(s)
- Kobi Simpson-Lavy
- Dept of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Tianchang Xu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mark Johnston
- Dept of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Martin Kupiec
- Dept of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel.
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25
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Caloric Restriction Extends Yeast Chronological Life Span by Optimizing the Snf1 (AMPK) Signaling Pathway. Mol Cell Biol 2017; 37:MCB.00562-16. [PMID: 28373292 DOI: 10.1128/mcb.00562-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/29/2017] [Indexed: 11/20/2022] Open
Abstract
AMP-activated protein kinase (AMPK) and the homologous yeast SNF1 complex are key regulators of energy metabolism that counteract nutrient deficiency and ATP depletion by phosphorylating multiple enzymes and transcription factors that maintain energetic homeostasis. AMPK/SNF1 also promotes longevity in several model organisms, including yeast. Here we investigate the role of yeast SNF1 in mediating the extension of chronological life span (CLS) by caloric restriction (CR). We find that SNF1 activity is required throughout the transition of log phase to stationary phase (diauxic shift) for effective CLS extension. CR expands the period of maximal SNF1 activation beyond the diauxic shift, as indicated by Sak1-dependent T210 phosphorylation of the Snf1 catalytic α-subunit. A concomitant increase in ADP is consistent with SNF1 activation by ADP in vivo Downstream of SNF1, the Cat8 and Adr1 transcription factors are required for full CR-induced CLS extension, implicating an alternative carbon source utilization for acetyl coenzyme A (acetyl-CoA) production and gluconeogenesis. Indeed, CR increased acetyl-CoA levels during the diauxic shift, along with expression of both acetyl-CoA synthetase genes ACS1 and ACS2 We conclude that CR maximizes Snf1 activity throughout and beyond the diauxic shift, thus optimizing the coordination of nucleocytosolic acetyl-CoA production with massive reorganization of the transcriptome and respiratory metabolism.
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26
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Zhan C, Yang Y, Zhang Z, Li X, Liu X, Bai Z. Transcription factor Mxr1 promotes the expression of Aox1 by repressing glycerol transporter 1 in Pichia pastoris. FEMS Yeast Res 2017; 17:3061371. [DOI: 10.1093/femsyr/fox015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/02/2017] [Indexed: 11/14/2022] Open
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27
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Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PLoS Comput Biol 2017; 13:e1005297. [PMID: 28072816 PMCID: PMC5224888 DOI: 10.1371/journal.pcbi.1005297] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/07/2016] [Indexed: 11/19/2022] Open
Abstract
Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to in silico estimate the enzymatic activity of signalling kinases. Our approach identified informative associations between kinases and metabolic enzymes capable of predicting metabolic changes. We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism. Changes in activity of transcription factors, kinases and phosphatases were estimated in silico and these were capable of building predictive models to infer the metabolic adaptations of previously unseen conditions across different dynamic experiments. Time-resolved experiments were significantly more informative than genetic perturbations to infer metabolic adaptation. This difference may be due to the indirect nature of the associations and of general cellular states that can hinder the identification of causal relationships. This work provides a novel genome-scale integrative analysis to propose putative transcriptional and post-translational regulatory mechanisms of metabolic processes. Phosphorylation is a broad regulatory mechanism with implications in nearly all processes of the cell. However, a global understanding of possible regulatory mechanisms remains elusive. In this study, we examined the potential regulatory role of kinases, phosphatases and transcription-factors in yeast metabolism across a variety of steady-state and dynamic conditions. The main novelty of our analysis was to infer putative regulatory interactions from in silico estimated activity of transcription-factors and kinases/phosphatases. This provided functional information about the proteins important for the experimental conditions at hand that had not been uncovered before. We showed that activity profiles are predictive features to estimate metabolite changes in dynamic experiments, while the same was not visible in steady-state conditions. We also showed that dynamic experiments could be used to recapitulate and provide novel TFs-metabolite and K/Ps-metabolite regulatory associations. We believe these findings illustrates the usefulness of this approach for future integrative studies interested in studying metabolic regulation.
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Affiliation(s)
- Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Zrinka Raguz Nakic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Mattia Zampieri
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Omar Wagih
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail: (PB); (JSR)
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine (JRC-COMBINE), Aachen
- * E-mail: (PB); (JSR)
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28
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Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:170. [PMID: 28690679 PMCID: PMC5496416 DOI: 10.1186/s13068-017-0825-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/22/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Trichoderma reesei (Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis, and plant-fungal interactions. The genomes of QM6a and its high enzyme-producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute. While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture, and genetic modification or engineering. RESULTS We integrated Pacific Biosciences and Illumina sequencing platforms for the highest-quality genome assembly yet achieved, revealing seven telomere-to-telomere chromosomes (34,922,528 bp; 10877 genes) with 1630 newly predicted genes and >1.5 Mb of new sequences. Most new sequences are located on AT-rich blocks, including 7 centromeres, 14 subtelomeres, and 2329 interspersed AT-rich blocks. The seven QM6a centromeres separately consist of 24 conserved repeats and 37 putative centromere-encoded genes. These findings open up a new perspective for future centromere and chromosome architecture studies. Next, we demonstrate that sexual crossing readily induced cytosine-to-thymine point mutations on both tandem and unlinked duplicated sequences. We also show by bioinformatic analysis that T. reesei has evolved a robust repeat-induced point mutation (RIP) system to accumulate AT-rich sequences, with longer AT-rich blocks having more RIP mutations. The widespread distribution of AT-rich blocks correlates genome-wide partitions with gene clusters, explaining why clustering of genes has been reported to not influence gene expression in T. reesei. CONCLUSION Compartmentation of ancestral gene clusters by AT-rich blocks might promote flexibilities that are evolutionarily advantageous in this fungus' soil habitats and other natural environments. Our analyses, together with the complete genome sequence, provide a better blueprint for biotechnological and industrial applications.
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Affiliation(s)
- Wan-Chen Li
- Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Life Sciences, National Defense Medical Center, Taipei, 115 Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Chien-Hao Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Genome Sciences, National Yang-Ming University, Taipei, 112 Taiwan
| | - Chia-Ling Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Shu-Yun Tung
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Ting-Fang Wang
- Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
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29
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Laera L, Guaragnella N, Ždralević M, Marzulli D, Liu Z, Giannattasio S. The transcription factors ADR1 or CAT8 are required for RTG pathway activation and evasion from yeast acetic acid-induced programmed cell death in raffinose. ACTA ACUST UNITED AC 2016; 3:621-631. [PMID: 28357334 PMCID: PMC5348981 DOI: 10.15698/mic2016.12.549] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Yeast Saccharomyces cerevisiae grown on glucose undergoes programmed cell death (PCD) induced by acetic acid (AA-PCD), but evades PCD when grown in raffinose. This is due to concomitant relief of carbon catabolite repression (CCR) and activation of mitochondrial retrograde signaling, a mitochondria-to-nucleus communication pathway causing up-regulation of various nuclear target genes, such as CIT2, encoding peroxisomal citrate synthase, dependent on the positive regulator RTG2 in response to mitochondrial dysfunction. CCR down-regulates genes mainly involved in mitochondrial respiratory metabolism. In this work, we investigated the relationships between the RTG and CCR pathways in the modulation of AA-PCD sensitivity under glucose repression or de-repression conditions. Yeast single and double mutants lacking RTG2 and/or certain factors regulating carbon source utilization, including MIG1, HXK2, ADR1, CAT8, and HAP4, have been analyzed for their survival and CIT2 expression after acetic acid treatment. ADR1 and CAT8 were identified as positive regulators of RTG-dependent gene transcription. ADR1 and CAT8 interact with RTG2 and with each other in inducing cell resistance to AA-PCD in raffinose and controlling the nature of cell death. In the absence of ADR1 and CAT8, AA-PCD evasion is acquired through activation of an alternative factor/pathway repressed by RTG2, suggesting that RTG2 may play a function in promoting necrotic cell death in repressing conditions when RTG pathway is inactive. Moreover, our data show that simultaneous mitochondrial retrograde pathway activation and SNF1-dependent relief of CCR have a key role in central carbon metabolism reprogramming which modulates the yeast acetic acid-stress response.
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Affiliation(s)
- Luna Laera
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Nicoletta Guaragnella
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Maša Ždralević
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Domenico Marzulli
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Sergio Giannattasio
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
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Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast. Proc Natl Acad Sci U S A 2016; 113:E7428-E7437. [PMID: 27810962 DOI: 10.1073/pnas.1603577113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ability to rationally manipulate the transcriptional states of cells would be of great use in medicine and bioengineering. We have developed an algorithm, NetSurgeon, which uses genome-wide gene-regulatory networks to identify interventions that force a cell toward a desired expression state. We first validated NetSurgeon extensively on existing datasets. Next, we used NetSurgeon to select transcription factor deletions aimed at improving ethanol production in Saccharomyces cerevisiae cultures that are catabolizing xylose. We reasoned that interventions that move the transcriptional state of cells using xylose toward that of cells producing large amounts of ethanol from glucose might improve xylose fermentation. Some of the interventions selected by NetSurgeon successfully promoted a fermentative transcriptional state in the absence of glucose, resulting in strains with a 2.7-fold increase in xylose import rates, a 4-fold improvement in xylose integration into central carbon metabolism, or a 1.3-fold increase in ethanol production rate. We conclude by presenting an integrated model of transcriptional regulation and metabolic flux that will enable future efforts aimed at improving xylose fermentation to prioritize functional regulators of central carbon metabolism.
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31
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Wang Z, Bai X, Guo X, He X. Regulation of crucial enzymes and transcription factors on 2-phenylethanol biosynthesis via Ehrlich pathway in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2016; 44:129-139. [PMID: 27770224 DOI: 10.1007/s10295-016-1852-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/06/2016] [Indexed: 11/26/2022]
Abstract
2-Phenylethanol (2-PE) is widely used in food, perfume and pharmaceutical industry, but lower production in microbes and less known regulatory mechanisms of 2-PE make further study necessary. In this study, crucial genes like ARO8 and ARO10 of Ehrlich pathway for 2-PE synthesis and key transcription factor ARO80 in Saccharomyces cerevisiae were re-regulated using constitutive promoter; in the meantime, the effect of nitrogen source in synthetic complete (SC) medium with L-phenylalanine (L-Phe) on Aro8/Aro9 and Aro10 was investigated. The results showed that aromatic aminotransferase activities of ARO8 over-expressing strains were seriously inhibited by ammonia sulfate in SC + Phe medium. Flask fermentation test demonstrated that over-expressing ARO8 or ARO10 led to about 42 % increase in 2-PE production when compared with the control strain. Furthermore, influence of transcription factors Cat8 and Mig1 on 2-PE biosynthesis was explored. CAT8 over-expression or MIG1 deletion increased in the transcription of ARO9 and ARO10. 2-PE production of CAT8 over-expressing strain was 62 % higher than that of control strain. Deletion of MIG1 also led to 2-PE biosynthesis enhancement. The strain of CAT8 over-expression and MIG1 deletion was most effective in regulating expression of ARO9 and ARO10. Analysis of mRNA levels and enzyme activities indicates that transaminase in Ehrlich pathway is the crucial target of Nitrogen Catabolize Repression (NCR). Among the engineering strains, the higher 3.73 g/L 2-PE production in CAT8 over-expressing strain without in situ product recovery suggests that the robust strain has potentiality for commercial exploitation.
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Affiliation(s)
- Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xuejing Bai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.
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Cardarelli S, D'Amici S, Tassone P, Tramonti A, Uccelletti D, Mancini P, Saliola M. Characterization of the transcription factor encoding gene, KlADR1: metabolic role in Kluyveromyces lactis and expression in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2016; 162:1933-1944. [PMID: 27655407 DOI: 10.1099/mic.0.000374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In Saccharomyces cerevisiae, Adr1 is a zinc-finger transcription factor involved in the transcriptional activation of ADH2. Deletion of KlADR1, its putative ortholog in Kluyveromyces lactis, led to reduced growth in glycerol, oleate and yeast extract-peptone medium suggesting, as in S. cerevisiae, its requirement for glycerol, fatty acid and nitrogen utilization. Moreover, growth comparison on yeast extract and peptone plates showed in K. lactis a KlAdr1-dependent growth trait not present in S. cerevisiae, indicating different metabolic roles of the two factors in their environmental niches. KlADR1 is required for growth under respiratory and fermentative conditions like KlADH, alcohol dehydrogenase genes necessary for metabolic adaptation during the growth transition. Using in-gel native alcohol dehydrogenase assay, we showed that this factor affected the Adh pattern by altering the balance between these activities. Since the activity most affected by KlAdr1 is KlAdh3, a deletion analysis of the KlADH3 promoter allowed the isolation of a DNA fragment through which KlAdr1 modulated its expression. The expression of the KlADR1-GFP gene allowed the intracellular localization of the factor in K. lactis and S. cerevisiae, suggesting in the two yeasts a common mechanism of KlAdr1 translocation under fermentative and respiratory conditions. Finally, the chimeric Kl/ScADR1 gene encoding the zinc-finger domains of KlAdr1 fused to the transactivating domains of the S. cerevisiae factor activated in Scadr1Δ the transcription of ADH2 in a ScAdr1-dependent fashion.
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Affiliation(s)
- Silvia Cardarelli
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sirio D'Amici
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Paola Tassone
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Angela Tramonti
- CNR Department of Biochemical Sciences 'Rossi Fanelli', Istituto di Biologia e Patologia Molecolari, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Uccelletti
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Patrizia Mancini
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
| | - Michele Saliola
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Deroover S, Ghillebert R, Broeckx T, Winderickx J, Rolland F. Trehalose-6-phosphate synthesis controls yeast gluconeogenesis downstream and independent of SNF1. FEMS Yeast Res 2016; 16:fow036. [PMID: 27189362 DOI: 10.1093/femsyr/fow036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2016] [Indexed: 11/12/2022] Open
Abstract
Trehalose-6-P (T6P), an intermediate of trehalose biosynthesis, was identified as an important regulator of yeast sugar metabolism and signaling. tps1Δ mutants, deficient in T6P synthesis (TPS), are unable to grow on rapidly fermentable medium with uncontrolled influx in glycolysis, depletion of ATP and accumulation of sugar phosphates. However, the exact molecular mechanisms involved are not fully understood. We show that SNF1 deletion restores the tps1Δ growth defect on glucose, suggesting that lack of TPS hampers inactivation of SNF1 or SNF1-regulated processes. In addition to alternative, non-fermentable carbon metabolism, SNF1 controls two major processes: respiration and gluconeogenesis. The tps1Δ defect appears to be specifically associated with deficient inhibition of gluconeogenesis, indicating more downstream effects. Consistently, Snf1 dephosphorylation and inactivation on glucose medium are not affected, as confirmed with an in vivo Snf1 activity reporter. Detailed analysis shows that gluconeogenic Pck1 and Fbp1 expression, protein levels and activity are not repressed upon glucose addition to tps1Δ cells, suggesting a link between the metabolic defect and persistent gluconeogenesis. While SNF1 is essential for induction of gluconeogenesis, T6P/TPS is required for inactivation of gluconeogenesis in the presence of glucose, downstream and independent of SNF1 activity and the Cat8 and Sip4 transcription factors.
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Affiliation(s)
- Sofie Deroover
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Ruben Ghillebert
- Laboratory of Functional Biology, Department of Biology, KU Leuven, B-3001 Leuven, Belgium
| | - Tom Broeckx
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Joris Winderickx
- Laboratory of Functional Biology, Department of Biology, KU Leuven, B-3001 Leuven, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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Abstract
Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs) controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1) chromatin immunoprecipitation data for colocalization of transcription factors, (2) gene expression data for coexpression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF) occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1) combinatorial cis-regulation can be inferred by multi-genome analysis and (2) combinatorial cis-regulation can explain differences in gene expression between species.
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35
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Natural Diversity in Pentose Fermentation Is Explained by Variations in Histone Deacetylases. Cell Rep 2016; 14:458-463. [DOI: 10.1016/j.celrep.2015.12.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/13/2015] [Accepted: 12/07/2015] [Indexed: 11/17/2022] Open
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Sanz P, Viana R, Garcia-Gimeno MA. AMPK in Yeast: The SNF1 (Sucrose Non-fermenting 1) Protein Kinase Complex. EXPERIENTIA SUPPLEMENTUM (2012) 2016; 107:353-374. [PMID: 27812987 DOI: 10.1007/978-3-319-43589-3_14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In yeast, SNF1 protein kinase is the orthologue of mammalian AMPK complex. It is a trimeric complex composed of Snf1 protein kinase (orthologue of AMPKα catalytic subunit), Snf4 (orthologue of AMPKγ regulatory subunit), and a member of the Gal83/Sip1/Sip2 family of proteins (orthologues of AMPKβ subunit) that act as scaffolds and also regulate the subcellular localization of the complex. In this chapter, we review the recent literature on the characteristics of SNF1 complex subunits, the structure and regulation of the activity of the SNF1 complex, its role at the level of transcriptional regulation of relevant target genes and also at the level of posttranslational modification of targeted substrates. We also review the crosstalk of SNF1 complex activity with other key protein kinase pathways such as cAMP-PKA, TORC1, and PAS kinase.
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Affiliation(s)
- Pascual Sanz
- Instituto de Biomedicina de Valencia, CSIC and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCiii), Jaime Roig 11, 46010, Valencia, Spain.
| | - Rosa Viana
- Instituto de Biomedicina de Valencia, CSIC and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCiii), Jaime Roig 11, 46010, Valencia, Spain
| | - Maria Adelaida Garcia-Gimeno
- Department of Biotecnología, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politécnica de Valencia, Valencia, Spain
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Casal M, Queirós O, Talaia G, Ribas D, Paiva S. Carboxylic Acids Plasma Membrane Transporters in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:229-251. [PMID: 26721276 DOI: 10.1007/978-3-319-25304-6_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This chapter covers the functionally characterized plasma membrane carboxylic acids transporters Jen1, Ady2, Fps1 and Pdr12 in the yeast Saccharomyces cerevisiae, addressing also their homologues in other microorganisms, as filamentous fungi and bacteria. Carboxylic acids can either be transported into the cells, to be used as nutrients, or extruded in response to acid stress conditions. The secondary active transporters Jen1 and Ady2 can mediate the uptake of the anionic form of these substrates by a H(+)-symport mechanism. The undissociated form of carboxylic acids is lipid-soluble, crossing the plasma membrane by simple diffusion. Furthermore, acetic acid can also be transported by facilitated diffusion via Fps1 channel. At the cytoplasmic physiological pH, the anionic form of the acid prevails and it can be exported by the Pdr12 pump. This review will highlight the mechanisms involving carboxylic acids transporters, and the way they operate according to the yeast cell response to environmental changes, as carbon source availability, extracellular pH and acid stress conditions.
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Affiliation(s)
- Margarida Casal
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Odília Queirós
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra, 1317, 4585-116, Gandra, PRD, Portugal
| | - Gabriel Talaia
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - David Ribas
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sandra Paiva
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Tangsombatvichit P, Semkiv MV, Sibirny AA, Jensen LT, Ratanakhanokchai K, Soontorngun N. Zinc cluster protein Znf1, a novel transcription factor of non-fermentative metabolism in Saccharomyces cerevisiae. FEMS Yeast Res 2015; 15:fou002. [PMID: 25673751 DOI: 10.1093/femsyr/fou002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The ability to rapidly respond to nutrient changes is a fundamental requirement for cell survival. Here, we show that the zinc cluster regulator Znf1 responds to altered nutrient signals following glucose starvation through the direct control of genes involved in non-fermentative metabolism, including those belonged to the central pathways of gluconeogenesis (PCK1, FBP1 and MDH2), glyoxylate shunt (MLS1 and ICL1) and the tricarboxylic acid cycle (ACO1), which is demonstrated by Znf1-binding enrichment at these promoters during the glucose-ethanol shift. Additionally, reduced Pck1 and Fbp1 enzymatic activities correlate well with the data obtained from gene transcription analysis. Cells deleted for ZNF1 also display defective mitochondrial morphology with unclear structures of the inner membrane cristae when grown in ethanol, in agreement with the substantial reduction in the ATP content, suggesting for roles of Znf1 in maintaining mitochondrial morphology and function. Furthermore, Znf1 also plays a role in tolerance to pH and osmotic stress, especially during the oxidative metabolism. Taken together, our results clearly suggest that Znf1 is a critical transcriptional regulator for stress adaptation during non-fermentative growth with some partial overlapping targets with previously reported regulators in Saccharomyces cerevisiae.
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Affiliation(s)
- Pitchya Tangsombatvichit
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Marta V Semkiv
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow 35-601, Poland
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Nitnipa Soontorngun
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
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Mehlgarten C, Krijger JJ, Lemnian I, Gohr A, Kasper L, Diesing AK, Grosse I, Breunig KD. Divergent Evolution of the Transcriptional Network Controlled by Snf1-Interacting Protein Sip4 in Budding Yeasts. PLoS One 2015; 10:e0139464. [PMID: 26440109 PMCID: PMC4634231 DOI: 10.1371/journal.pone.0139464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/14/2015] [Indexed: 11/19/2022] Open
Abstract
Cellular responses to starvation are of ancient origin since nutrient limitation has always been a common challenge to the stability of living systems. Hence, signaling molecules involved in sensing or transducing information about limiting metabolites are highly conserved, whereas transcription factors and the genes they regulate have diverged. In eukaryotes the AMP-activated protein kinase (AMPK) functions as a central regulator of cellular energy homeostasis. The yeast AMPK ortholog SNF1 controls the transcriptional network that counteracts carbon starvation conditions by regulating a set of transcription factors. Among those Cat8 and Sip4 have overlapping DNA-binding specificity for so-called carbon source responsive elements and induce target genes upon SNF1 activation. To analyze the evolution of the Cat8-Sip4 controlled transcriptional network we have compared the response to carbon limitation of Saccharomyces cerevisiae to that of Kluyveromyces lactis. In high glucose, S. cerevisiae displays tumor cell-like aerobic fermentation and repression of respiration (Crabtree-positive) while K. lactis has a respiratory-fermentative life-style, respiration being regulated by oxygen availability (Crabtree-negative), which is typical for many yeasts and for differentiated higher cells. We demonstrate divergent evolution of the Cat8-Sip4 network and present evidence that a role of Sip4 in controlling anabolic metabolism has been lost in the Saccharomyces lineage. We find that in K. lactis, but not in S. cerevisiae, the Sip4 protein plays an essential role in C2 carbon assimilation including induction of the glyoxylate cycle and the carnitine shuttle genes. Induction of KlSIP4 gene expression by KlCat8 is essential under these growth conditions and a primary function of KlCat8. Both KlCat8 and KlSip4 are involved in the regulation of lactose metabolism in K. lactis. In chromatin-immunoprecipitation experiments we demonstrate binding of both, KlSip4 and KlCat8, to selected CSREs and provide evidence that KlSip4 counteracts KlCat8-mediated transcription activation by competing for binding to some but not all CSREs. The finding that the hierarchical relationship of these transcription factors differs between K. lactis and S. cerevisiae and that the sets of target genes have diverged contributes to explaining the phenotypic differences in metabolic life-style.
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Affiliation(s)
| | - Jorrit-Jan Krijger
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ioana Lemnian
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - André Gohr
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Lydia Kasper
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | | | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Karin D. Breunig
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
- * E-mail:
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40
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Simpson-Lavy KJ, Bronstein A, Kupiec M, Johnston M. Cross-Talk between Carbon Metabolism and the DNA Damage Response in S. cerevisiae. Cell Rep 2015; 12:1865-75. [PMID: 26344768 DOI: 10.1016/j.celrep.2015.08.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/29/2015] [Accepted: 08/07/2015] [Indexed: 12/20/2022] Open
Abstract
Yeast cells with DNA damage avoid respiration, presumably because products of oxidative metabolism can be harmful to DNA. We show that DNA damage inhibits the activity of the Snf1 (AMP-activated) protein kinase (AMPK), which activates expression of genes required for respiration. Glucose and DNA damage upregulate SUMOylation of Snf1, catalyzed by the SUMO E3 ligase Mms21, which inhibits SNF1 activity. The DNA damage checkpoint kinases Mec1/ATR and Tel1/ATM, as well as the nutrient-sensing protein kinase A (PKA), regulate Mms21 activity toward Snf1. Mec1 and Tel1 are required for two SNF1-regulated processes-glucose sensing and ADH2 gene expression-even without exogenous genotoxic stress. Our results imply that inhibition of Snf1 by SUMOylation is a mechanism by which cells lower their respiration in response to DNA damage. This raises the possibility that activation of DNA damage checkpoint mechanisms could contribute to aerobic fermentation (Warburg effect), a hallmark of cancer cells.
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Affiliation(s)
- Kobi J Simpson-Lavy
- University of Colorado School of Medicine, Department of Biochemistry and Molecular Genetics, 12801 E 17(th) Avenue, Aurora, CO 80045, USA; Tel Aviv University, Department of Molecular Microbiology and Biotechnology, Haim Levanon Street, Tel Aviv 6997801, Israel.
| | - Alex Bronstein
- Tel Aviv University, Department of Molecular Microbiology and Biotechnology, Haim Levanon Street, Tel Aviv 6997801, Israel
| | - Martin Kupiec
- Tel Aviv University, Department of Molecular Microbiology and Biotechnology, Haim Levanon Street, Tel Aviv 6997801, Israel
| | - Mark Johnston
- University of Colorado School of Medicine, Department of Biochemistry and Molecular Genetics, 12801 E 17(th) Avenue, Aurora, CO 80045, USA.
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Gemayel R, Chavali S, Pougach K, Legendre M, Zhu B, Boeynaems S, van der Zande E, Gevaert K, Rousseau F, Schymkowitz J, Babu MM, Verstrepen KJ. Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity. Mol Cell 2015; 59:615-27. [PMID: 26257283 PMCID: PMC4543046 DOI: 10.1016/j.molcel.2015.07.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/26/2015] [Accepted: 07/01/2015] [Indexed: 12/15/2022]
Abstract
Excessive expansions of glutamine (Q)-rich repeats in various human proteins are known to result in severe neurodegenerative disorders such as Huntington's disease and several ataxias. However, the physiological role of these repeats and the consequences of more moderate repeat variation remain unknown. Here, we demonstrate that Q-rich domains are highly enriched in eukaryotic transcription factors where they act as functional modulators. Incremental changes in the number of repeats in the yeast transcriptional regulator Ssn6 (Cyc8) result in systematic, repeat-length-dependent variation in expression of target genes that result in direct phenotypic changes. The function of Ssn6 increases with its repeat number until a certain threshold where further expansion leads to aggregation. Quantitative proteomic analysis reveals that the Ssn6 repeats affect its solubility and interactions with Tup1 and other regulators. Thus, Q-rich repeats are dynamic functional domains that modulate a regulator's innate function, with the inherent risk of pathogenic repeat expansions.
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Affiliation(s)
- Rita Gemayel
- Laboratory of Systems Biology, VIB, Gaston Geenslaan 1, 3001 Heverlee, Belgium; Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Heverlee, Belgium
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ksenia Pougach
- Laboratory of Systems Biology, VIB, Gaston Geenslaan 1, 3001 Heverlee, Belgium; Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Heverlee, Belgium
| | - Matthieu Legendre
- Structural and Genomic Information Laboratory, IGS UMR7256, Centre National de la Recherche Scientifique, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (IMM), 13288 Marseille Cedex 9, France
| | - Bo Zhu
- Laboratory of Systems Biology, VIB, Gaston Geenslaan 1, 3001 Heverlee, Belgium; Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Heverlee, Belgium
| | - Steven Boeynaems
- Laboratory of Systems Biology, VIB, Gaston Geenslaan 1, 3001 Heverlee, Belgium; Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Heverlee, Belgium
| | - Elisa van der Zande
- Laboratory of Systems Biology, VIB, Gaston Geenslaan 1, 3001 Heverlee, Belgium; Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Heverlee, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB, Campus Gasthuisberg, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB, Campus Gasthuisberg, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kevin J Verstrepen
- Laboratory of Systems Biology, VIB, Gaston Geenslaan 1, 3001 Heverlee, Belgium; Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Heverlee, Belgium.
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Schaefke B, Wang TY, Wang CY, Li WH. Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus. Genome Biol Evol 2015. [PMID: 26220934 PMCID: PMC4558856 DOI: 10.1093/gbe/evv138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains).
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Affiliation(s)
- Bernhard Schaefke
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan National Yang-Ming University, Taipei, Taiwan Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | | | | | - Wen-Hsiung Li
- National Yang-Ming University, Taipei, Taiwan China Medical University Hospital, Taichung, Taiwan Department of Ecology and Evolution, University of Chicago
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Abstract
Glucose is the primary source of energy for the budding yeast Saccharomyces cerevisiae. Although yeast cells can utilize a wide range of carbon sources, presence of glucose suppresses molecular activities involved in the use of alternate carbon sources as well as it represses respiration and gluconeogenesis. This dominant effect of glucose on yeast carbon metabolism is coordinated by several signaling and metabolic interactions that mainly regulate transcriptional activity but are also effective at post-transcriptional and post-translational levels. This review describes effects of glucose repression on yeast carbon metabolism with a focus on roles of the Snf3/Rgt2 glucose-sensing pathway and Snf1 signal transduction in establishment and relief of glucose repression. The role of Snf1 signaling in glucose repression and carbon metabolism in Saccharomyces cerevisae.
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Affiliation(s)
- Ömur Kayikci
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE41296 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE41296 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
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44
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Mast FD, Rachubinski RA, Aitchison JD. Signaling dynamics and peroxisomes. Curr Opin Cell Biol 2015; 35:131-6. [PMID: 26042681 DOI: 10.1016/j.ceb.2015.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/09/2015] [Indexed: 02/08/2023]
Abstract
Peroxisomes are remarkably responsive organelles. Their composition, abundance and even their mechanism of biogenesis are influenced strongly by cell type and the environment. This plasticity underlies peroxisomal functions in metabolism and the detoxification of dangerous reactive oxygen species. However, peroxisomes are integrated into the cellular system as a whole such that they communicate intimately with other organelles, control signaling dynamics as in the case of innate immune responses to infectious disease, and contribute to processes as fundamental as longevity. The increasing evidence for peroxisomes having roles in various cellular and organismal functions, combined with their malleability, suggests complex mechanisms operate to control cellular dynamics and the specificity of cellular responses and functions extending well beyond the peroxisome itself. A deeper understanding of the functions of peroxisomes and the mechanisms that control their plasticity could offer opportunities for exploiting changes in peroxisome abundance to control cellular function.
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Affiliation(s)
- Fred D Mast
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA
| | | | - John D Aitchison
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA.
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45
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Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. mBio 2015; 6:mBio.00427-15. [PMID: 25873380 PMCID: PMC4453552 DOI: 10.1128/mbio.00427-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca2+ takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca2+. These results unify the generally accepted lectin hypothesis with the historically first-proposed “Ca2+-bridge” hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.
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46
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Prielhofer R, Cartwright SP, Graf AB, Valli M, Bill RM, Mattanovich D, Gasser B. Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level. BMC Genomics 2015; 16:167. [PMID: 25887254 PMCID: PMC4408588 DOI: 10.1186/s12864-015-1393-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
Background The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1393-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roland Prielhofer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Stephanie P Cartwright
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria. .,School of Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria.
| | - Minoska Valli
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Brigitte Gasser
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
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47
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Transcriptional response of Saccharomyces cerevisiae to low temperature during wine fermentation. Antonie van Leeuwenhoek 2015; 107:1029-48. [DOI: 10.1007/s10482-015-0395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/22/2015] [Indexed: 01/31/2023]
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48
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Parua PK, Dombek KM, Young ET. Yeast 14-3-3 protein functions as a comodulator of transcription by inhibiting coactivator functions. J Biol Chem 2014; 289:35542-60. [PMID: 25355315 PMCID: PMC4271238 DOI: 10.1074/jbc.m114.592287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/22/2014] [Indexed: 01/23/2023] Open
Abstract
In eukaryotes combinatorial activation of transcription is an important component of gene regulation. In the budding yeast Saccharomyces cerevisiae, Adr1-Cat8 and Adr1-Oaf1/Pip2 are pairs of activators that act together to regulate two diverse sets of genes. Transcription activation of both sets is regulated positively by the yeast AMP-activated protein kinase homolog, Snf1, in response to low glucose or the presence of a non-fermentable carbon source and negatively by two redundant 14-3-3 isoforms, Bmh1 and Bmh2. Bmh regulates the function of these pairs at a post-promoter binding step by direct binding to Adr1. However, how Bmh regulates transcription after activator binding remains unknown. In the present study we analyzed Bmh-mediated regulation of two sets of genes activated independently by these pairs of activators. We report that Bmh inhibits mRNA synthesis when the second activator is absent. Using gene fusions we show that Bmh binding to the Adr1 regulatory domain inhibits an Adr1 activation domain but not a heterologous activation domain or artificially recruited Mediator, consistent with Bmh acting at a step in transcription downstream of activator binding. Bmh inhibits the assembly and the function of a preinitiation complex (PIC). Gene expression studies suggest that Bmh regulates Adr1 activity through the coactivators Mediator and Swi/Snf. Mediator recruitment appeared to occur normally, but PIC formation and function were defective, suggesting that Bmh inhibits a step between Mediator recruitment and PIC activation.
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Affiliation(s)
- Pabitra K Parua
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Kenneth M Dombek
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Elton T Young
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
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Dutta A, Gogol M, Kim JH, Smolle M, Venkatesh S, Gilmore J, Florens L, Washburn MP, Workman JL. Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions. Genes Dev 2014; 28:2314-30. [PMID: 25319830 PMCID: PMC4201291 DOI: 10.1101/gad.243584.114] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. Dutta et al. find that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. The intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. The presence of histone acetylation and activator-dependent recruitment and retention of Swi/Snf is important for its efficient function. It is not understood, however, why such mechanisms are required to enhance Swi/Snf activity on nucleosomes. Snf2, the catalytic subunit of the Swi/Snf remodeling complex, has been shown to be a target of the Gcn5 acetyltransferase. Our study found that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. Also, the intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Interestingly, the presence of transcription activators mitigates the effects of the reduced affinity of acetylated Snf2 for acetylated nucleosomes. Supporting our in vitro results, we found that activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. Our studies demonstrate that competing effects of (1) Swi/Snf retention by activators or high levels of histone acetylation and (2) Snf2 acetylation-mediated release regulate dynamics of Swi/Snf occupancy at target genes.
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Affiliation(s)
- Arnob Dutta
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeong-Hoon Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, Korea
| | - Michaela Smolle
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | - Joshua Gilmore
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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50
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Protein acetylation and acetyl coenzyme a metabolism in budding yeast. EUKARYOTIC CELL 2014; 13:1472-83. [PMID: 25326522 DOI: 10.1128/ec.00189-14] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells sense and appropriately respond to the physical conditions and availability of nutrients in their environment. This sensing of the environment and consequent cellular responses are orchestrated by a multitude of signaling pathways and typically involve changes in transcription and metabolism. Recent discoveries suggest that the signaling and transcription machineries are regulated by signals which are derived from metabolism and reflect the metabolic state of the cell. Acetyl coenzyme A (CoA) is a key metabolite that links metabolism with signaling, chromatin structure, and transcription. Acetyl-CoA is produced by glycolysis as well as other catabolic pathways and used as a substrate for the citric acid cycle and as a precursor in synthesis of fatty acids and steroids and in other anabolic pathways. This central position in metabolism endows acetyl-CoA with an important regulatory role. Acetyl-CoA serves as a substrate for lysine acetyltransferases (KATs), which catalyze the transfer of acetyl groups to the epsilon-amino groups of lysines in histones and many other proteins. Fluctuations in the concentration of acetyl-CoA, reflecting the metabolic state of the cell, are translated into dynamic protein acetylations that regulate a variety of cell functions, including transcription, replication, DNA repair, cell cycle progression, and aging. This review highlights the synthesis and homeostasis of acetyl-CoA and the regulation of transcriptional and signaling machineries in yeast by acetylation.
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