1
|
Ehrmann AK, Wronska AK, Perli T, de Hulster EAF, Luttik MAH, van den Broek M, Carqueija Cardoso C, Pronk JT, Daran JM. Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth. Metab Eng 2024; 82:201-215. [PMID: 38364997 DOI: 10.1016/j.ymben.2024.01.010] [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: 09/26/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Chemically defined media for cultivation of Saccharomyces cerevisiae strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this study, suboptimal growth rates of S. cerevisiae CEN.PK113-7D in the absence of pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and/or biotin were corrected by single or combined overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and Cyberlindnera fabianii BIO1, respectively. Several strategies were explored to improve growth of S. cerevisiae CEN.PK113-7D in thiamine-free medium. Overexpression of ScTHI4 and/or ScTHI5 enabled thiamine-independent growth at 83% of the maximum specific growth rate of the reference strain in vitamin-supplemented medium. Combined overexpression of seven native S. cerevisiae genes and CfBIO1 enabled a maximum specific growth rate of 0.33 ± 0.01 h-1 in vitamin-free synthetic medium. This growth rate was only 17 % lower than that of a congenic reference strain in vitamin-supplemented medium. Physiological parameters of the engineered vitamin-independent strain in aerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) grown on vitamin-free synthetic medium were similar to those of similar cultures of the parental strain grown on vitamin-supplemented medium. Transcriptome analysis revealed only few differences in gene expression between these cultures, which primarily involved genes with roles in Class-B vitamin metabolism. These results pave the way for development of fast-growing vitamin-independent industrial strains of S. cerevisiae.
Collapse
Affiliation(s)
- Anja K Ehrmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Anna K Wronska
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Clara Carqueija Cardoso
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| |
Collapse
|
2
|
Pijuan J, Moreno DF, Yahya G, Moisa M, Ul Haq I, Krukiewicz K, Mosbah R, Metwally K, Cavalu S. Regulatory and pathogenic mechanisms in response to iron deficiency and excess in fungi. Microb Biotechnol 2023; 16:2053-2071. [PMID: 37804207 PMCID: PMC10616654 DOI: 10.1111/1751-7915.14346] [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: 07/12/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023] Open
Abstract
Iron is an essential element for all eukaryote organisms because of its redox properties, which are important for many biological processes such as DNA synthesis, mitochondrial respiration, oxygen transport, lipid, and carbon metabolism. For this reason, living organisms have developed different strategies and mechanisms to optimally regulate iron acquisition, transport, storage, and uptake in different environmental responses. Moreover, iron plays an essential role during microbial infections. Saccharomyces cerevisiae has been of key importance for decrypting iron homeostasis and regulation mechanisms in eukaryotes. Specifically, the transcription factors Aft1/Aft2 and Yap5 regulate the expression of genes to control iron metabolism in response to its deficiency or excess, adapting to the cell's iron requirements and its availability in the environment. We also review which iron-related virulence factors have the most common fungal human pathogens (Aspergillus fumigatus, Cryptococcus neoformans, and Candida albicans). These factors are essential for adaptation in different host niches during pathogenesis, including different fungal-specific iron-uptake mechanisms. While being necessary for virulence, they provide hope for developing novel antifungal treatments, which are currently scarce and usually toxic for patients. In this review, we provide a compilation of the current knowledge about the metabolic response to iron deficiency and excess in fungi.
Collapse
Affiliation(s)
- Jordi Pijuan
- Laboratory of Neurogenetics and Molecular MedicineInstitut de Recerca Sant Joan de DéuBarcelonaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIIIMadridSpain
| | - David F. Moreno
- Department of Molecular Cellular and Developmental BiologyYale UniversityNew HavenConnecticutUSA
- Systems Biology InstituteYale UniversityWest HavenConnecticutUSA
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of PharmacyZagazig UniversityAl SharqiaEgypt
| | - Mihaela Moisa
- Faculty of Medicine and PharmacyUniversity of OradeaOradeaRomania
| | - Ihtisham Ul Haq
- Department of Physical Chemistry and Polymers TechnologySilesian University of TechnologyGliwicePoland
- Programa de Pós‐graduação em Inovação TecnológicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Polymers TechnologySilesian University of TechnologyGliwicePoland
- Centre for Organic and Nanohybrid ElectronicsSilesian University of TechnologyGliwicePoland
| | - Rasha Mosbah
- Infection Control UnitHospitals of Zagazig UniversityZagazigEgypt
| | - Kamel Metwally
- Department of Medicinal Chemistry, Faculty of PharmacyUniversity of TabukTabukSaudi Arabia
- Department of Pharmaceutical Medicinal Chemistry, Faculty of PharmacyZagazig UniversityZagazigEgypt
| | - Simona Cavalu
- Faculty of Medicine and PharmacyUniversity of OradeaOradeaRomania
| |
Collapse
|
3
|
Makeeva AS, Sidorin AV, Ishtuganova VV, Padkina MV, Rumyantsev AM. Effect of Biotin Starvation on Gene Expression in Komagataella phaffii Cells. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1368-1377. [PMID: 37770403 DOI: 10.1134/s000629792309016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 09/30/2023]
Abstract
Methylotrophic yeast Komagataella phaffii is widely used in biotechnology for recombinant protein production. Due to the practical significance of these yeasts, it is extremely important to properly select cultivation conditions and optimize the media composition. In this study the effect of biotin starvation on gene expression in K. phaffii at transcriptome level was investigated. It was demonstrated, that the response of K. phaffii cell to biotin deficiency strongly depends on the carbon source in the medium. In the media containing glycerol, biotin deficiency led to activation of the genes involved in biotin metabolism, glyoxylate cycle, and synthesis of acetyl-CoA in cytoplasm, as well as repression of the genes, involved in lipo- and gluconeogenesis. In the methanol-containing media, biotin deficiency primarily led to repression of the genes, involved in protein synthesis, and activation of cell response to oxidative stress.
Collapse
Affiliation(s)
- Anastasiya S Makeeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Anton V Sidorin
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Valeria V Ishtuganova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Marina V Padkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrey M Rumyantsev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
| |
Collapse
|
4
|
Liu J, Shen Y, Cao H, He K, Chu Z, Li N. OsbHLH057 targets the AATCA cis-element to regulate disease resistance and drought tolerance in rice. PLANT CELL REPORTS 2022; 41:1285-1299. [PMID: 35278106 DOI: 10.1007/s00299-022-02859-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/28/2022] [Indexed: 05/27/2023]
Abstract
The AATCA motif was identified to respond pathogens infection in the promoter of defense-related gene Os2H16. OsbHLH057 bound to the motif to positively regulate rice disease resistance and drought tolerance. Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani, is a devastating disease in rice (Oryza sativa L.). The transcriptional regulation of host defense-related genes in response to R. solani infection is poorly understood. In this study, we identified a cis-element, AATCA, in the promoter of Os2H16, a previously identified multifaceted defense-related gene in rice that responded to fungal attack. Using a DNA pull-down assay coupled with mass spectrometry, a basic helix-loop-helix (bHLH) transcription factor OsbHLH057 was determined to interact with the AATCA cis-element. OsbHLH057 was rapidly induced by R. solani, Xanthomonas oryzae pv. oryzae (Xoo), and osmotic stress. Furthermore, overexpressing OsbHLH057 enhanced rice disease resistance and drought tolerance, while knocking out OsbHLH057 made rice more susceptible to pathogens and drought. Overall, our results uncovered an OsbHLH057 and AATCA module that synergistically regulates the expression of Os2H16 in response to R. solani, Xoo, and drought in conjunction with the previously identified stress-related OsASR2 and GT-1 module.
Collapse
Affiliation(s)
- Jiazong Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yanting Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongxiang Cao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Kang He
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Zhaohui Chu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Ning Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| |
Collapse
|
5
|
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.
Collapse
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.)
| |
Collapse
|
6
|
Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
Collapse
Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| |
Collapse
|
7
|
Sprenger M, Hartung TS, Allert S, Wisgott S, Niemiec MJ, Graf K, Jacobsen ID, Kasper L, Hube B. Fungal biotin homeostasis is essential for immune evasion after macrophage phagocytosis and virulence. Cell Microbiol 2020; 22:e13197. [PMID: 32083801 DOI: 10.1111/cmi.13197] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/05/2023]
Abstract
Biotin is an important cofactor for multiple enzymes in central metabolic processes. While many bacteria and most fungi are able to synthesise biotin de novo, Candida spp. are auxotrophic for this vitamin and thus require efficient uptake systems to facilitate biotin acquisition during infection. Here we show that Candida glabrata and Candida albicans use a largely conserved system for biotin uptake and regulation, consisting of the high-affinity biotin transporter Vht1 and the transcription factor Vhr1. Both species induce expression of biotin-metabolic genes upon in vitro biotin depletion and following phagocytosis by macrophages, indicating low biotin levels in the Candida-containing phagosome. In line with this, we observed reduced intracellular proliferation of both Candida cells pre-starved of biotin and deletion mutants lacking VHR1 or VHT1 genes. VHT1 was essential for the full virulence of C. albicans during systemic mouse infections, and the lack of VHT1 led to reduced fungal burden in C. glabrata-infected brains and C. albicans-infected brains and kidneys. Together, our data suggest a critical role of Vht1-mediated biotin acquisition for C. glabrata and C. albicans during intracellular growth in macrophages and systemic infections.
Collapse
Affiliation(s)
- Marcel Sprenger
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Teresa S Hartung
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Stephanie Wisgott
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Maria J Niemiec
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Katja Graf
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
8
|
Daicho K, Koike N, Ott RG, Daum G, Ushimaru T. TORC1 ensures membrane trafficking of Tat2 tryptophan permease via a novel transcriptional activator Vhr2 in budding yeast. Cell Signal 2020; 68:109542. [PMID: 31954176 DOI: 10.1016/j.cellsig.2020.109542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
The target of rapamycin complex 1 (TORC1) protein kinase is activated by nutrients and controls nutrient uptake via the membrane trafficking of various nutrient permeases. However, its molecular mechanisms remain elusive. Cholesterol (ergosterol in yeast) in conjunction with sphingolipids forms tight-packing microdomains, "lipid rafts", which are critical for intracellular protein sorting. Here we show that a novel target of rapamycin (TOR)-interacting transcriptional activator Vhr2 is required for full expression of some ERG genes for ergosterol biogenesis and for proper sorting of the tryptophan permease Tat2 in budding yeast. Loss of Vhr2 caused sterol biogenesis disturbance and Tat2 missorting. TORC1 activity maintained VHR2 transcript and protein levels, and total sterol levels. Vhr2 was not involved in regulation of the TORC1-downstream protein kinase Npr1, which regulates Tat2 sorting. This study suggests that TORC1 regulates nutrient uptake via sterol biogenesis.
Collapse
Affiliation(s)
- Katsue Daicho
- Biological Science, Graduate School of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Naoki Koike
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - René Georg Ott
- Institut für Biochemie, Technische Universität Graz, Petersgasse 12/2, A-8010 Graz, Austria
| | - Günther Daum
- Institut für Biochemie, Technische Universität Graz, Petersgasse 12/2, A-8010 Graz, Austria
| | - Takashi Ushimaru
- Biological Science, Graduate School of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan.
| |
Collapse
|
9
|
Sun ZG, Wang MQ, Wang YP, Xing S, Hong KQ, Chen YF, Guo XW, Xiao DG. Identification by comparative transcriptomics of core regulatory genes for higher alcohol production in a top-fermenting yeast at different temperatures in beer fermentation. Appl Microbiol Biotechnol 2019; 103:4917-4929. [DOI: 10.1007/s00253-019-09807-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/29/2022]
|
10
|
Michel S, Keller MA, Wamelink MMC, Ralser M. A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genet 2015; 16:13. [PMID: 25887987 PMCID: PMC4331311 DOI: 10.1186/s12863-015-0171-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Studying the survival of yeast in stationary phase, known as chronological lifespan, led to the identification of molecular ageing factors conserved from yeast to higher organisms. To identify functional interactions among yeast chronological ageing genes, we conducted a haploproficiency screen on the basis of previously identified long-living mutants. For this, we created a library of heterozygous Saccharomyces cerevisiae double deletion strains and aged them in a competitive manner. RESULTS Stationary phase survival was prolonged in a double heterozygous mutant of the metabolic enzyme non-quiescent mutant 1 (NQM1), a paralogue to the pentose phosphate pathway enzyme transaldolase (TAL1), and the transcription factor vitamin H response transcription factor 1 (VHR1). We find that cells deleted for the two genes possess increased clonogenicity at late stages of stationary phase survival, but find no indication that the mutations delay initial mortality upon reaching stationary phase, canonically defined as an extension of chronological lifespan. We show that both genes influence the concentration of metabolites of glycolysis and the pentose phosphate pathway, central metabolic players in the ageing process, and affect osmolality of growth media in stationary phase cultures. Moreover, NQM1 is glucose repressed and induced in a VHR1 dependent manner upon caloric restriction, on non-fermentable carbon sources, as well as under osmotic and oxidative stress. Finally, deletion of NQM1 is shown to confer resistance to oxidizing substances. CONCLUSIONS The transaldolase paralogue NQM1 and the transcription factor VHR1 interact haploproficiently and affect yeast stationary phase survival. The glucose repressed NQM1 gene is induced under various stress conditions, affects stress resistance and this process is dependent on VHR1. While NQM1 appears not to function in the pentose phosphate pathway, the interplay of NQM1 with VHR1 influences the yeast metabolic homeostasis and stress tolerance during stationary phase, processes associated with yeast ageing.
Collapse
Affiliation(s)
- Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestr 73, Berlin, 14195, Germany.
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, Amsterdam, The Netherlands.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.
| |
Collapse
|
11
|
Abstract
The term “transcriptional network” refers to the mechanism(s) that underlies coordinated expression of genes, typically involving transcription factors (TFs) binding to the promoters of multiple genes, and individual genes controlled by multiple TFs. A multitude of studies in the last two decades have aimed to map and characterize transcriptional networks in the yeast Saccharomyces cerevisiae. We review the methodologies and accomplishments of these studies, as well as challenges we now face. For most yeast TFs, data have been collected on their sequence preferences, in vivo promoter occupancy, and gene expression profiles in deletion mutants. These systematic studies have led to the identification of new regulators of numerous cellular functions and shed light on the overall organization of yeast gene regulation. However, many yeast TFs appear to be inactive under standard laboratory growth conditions, and many of the available data were collected using techniques that have since been improved. Perhaps as a consequence, comprehensive and accurate mapping among TF sequence preferences, promoter binding, and gene expression remains an open challenge. We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms.
Collapse
|
12
|
Philpott CC, Leidgens S, Frey AG. Metabolic remodeling in iron-deficient fungi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1509-20. [PMID: 22306284 DOI: 10.1016/j.bbamcr.2012.01.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/13/2012] [Accepted: 01/18/2012] [Indexed: 01/12/2023]
Abstract
Eukaryotic cells contain dozens, perhaps hundreds, of iron-dependent proteins, which perform critical functions in nearly every major cellular process. Nutritional iron is frequently available to cells in only limited amounts; thus, unicellular and higher eukaryotes have evolved mechanisms to cope with iron scarcity. These mechanisms have been studied at the molecular level in the model eukaryotes Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as in some pathogenic fungi. Each of these fungal species exhibits metabolic adaptations to iron deficiency that serve to reduce the cell's reliance on iron. However, the regulatory mechanisms that accomplish these adaptations differ greatly between fungal species. This article is part of a Special Issue entitled: Cell Biology of Metals.
Collapse
Affiliation(s)
- Caroline C Philpott
- Genetics and Metabolism Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 10, Rm. 9B-16, 10 Center Drive, Bethesda, MD 20892, USA.
| | | | | |
Collapse
|
13
|
Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 2011; 12:R125. [PMID: 22189060 PMCID: PMC3334620 DOI: 10.1186/gb-2011-12-12-r125] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/09/2011] [Accepted: 12/21/2011] [Indexed: 11/24/2022] Open
Abstract
Background Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. Results We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. Conclusions The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles.
Collapse
Affiliation(s)
- Raluca Gordân
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
14
|
Weider M, Schröder A, Klebl F, Sauer N. A novel mechanism for target gene-specific SWI/SNF recruitment via the Snf2p N-terminus. Nucleic Acids Res 2011; 39:4088-98. [PMID: 21278159 PMCID: PMC3105400 DOI: 10.1093/nar/gkr004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Chromatin-remodeling complexes regulate the expression of genes in all eukaryotic genomes. The SWI/SNF complex of Saccharomyces cerevisiae is recruited to its target promoters via interactions with selected transcription factors. Here, we show that the N-terminus of Snf2p, the chromatin remodeling core unit of the SWI/SNF complex, is essential for the expression of VHT1, the gene of the plasma membrane H+/biotin symporter, and of BIO5, the gene of a 7-keto-8-aminopelargonic acid transporter, biotin biosynthetic precursor. chromatin immunoprecipitation (ChIP) analyses demonstrate that Vhr1p, the transcriptional regulator of VHT1 and BIO5 expression, is responsible for the targeting of Snf2p to the VHT1 promoter at low biotin. We identified an Snf2p mutant, Snf2p-R15C, that specifically abolishes the induction of VHT1 and BIO5 but not of other Snf2p-regulated genes, such as GAL1, SUC2 or INO1. We present a novel mechanism of target gene-specific SWI/SNF recruitment via Vhr1p and a conserved N-terminal Snf2p domain.
Collapse
Affiliation(s)
| | | | | | - N. Sauer
- *To whom correspondence should be addressed. Tel: + 49 9131 85 28212; Fax: + 49 9131 85 28751;
| |
Collapse
|
15
|
Ju S, Tardiff DF, Han H, Divya K, Zhong Q, Maquat LE, Bosco DA, Hayward LJ, Brown RH, Lindquist S, Ringe D, Petsko GA. A yeast model of FUS/TLS-dependent cytotoxicity. PLoS Biol 2011; 9:e1001052. [PMID: 21541368 PMCID: PMC3082520 DOI: 10.1371/journal.pbio.1001052] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 03/17/2011] [Indexed: 12/12/2022] Open
Abstract
FUS/TLS is a nucleic acid binding protein that, when mutated, can cause a subset
of familial amyotrophic lateral sclerosis (fALS). Although FUS/TLS is normally
located predominantly in the nucleus, the pathogenic mutant forms of FUS/TLS
traffic to, and form inclusions in, the cytoplasm of affected spinal motor
neurons or glia. Here we report a yeast model of human FUS/TLS expression that
recapitulates multiple salient features of the pathology of the disease-causing
mutant proteins, including nuclear to cytoplasmic translocation, inclusion
formation, and cytotoxicity. Protein domain analysis indicates that the
carboxyl-terminus of FUS/TLS, where most of the ALS-associated mutations are
clustered, is required but not sufficient for the toxicity of the protein. A
genome-wide genetic screen using a yeast over-expression library identified five
yeast DNA/RNA binding proteins, encoded by the yeast genes
ECM32, NAM8, SBP1,
SKO1, and VHR1, that rescue the toxicity
of human FUS/TLS without changing its expression level, cytoplasmic
translocation, or inclusion formation. Furthermore, hUPF1, a
human homologue of ECM32, also rescues the toxicity of FUS/TLS
in this model, validating the yeast model and implicating a possible
insufficiency in RNA processing or the RNA quality control machinery in the
mechanism of FUS/TLS mediated toxicity. Examination of the effect of FUS/TLS
expression on the decay of selected mRNAs in yeast indicates that the
nonsense-mediated decay pathway is probably not the major determinant of either
toxicity or suppression. Of all the thousand natural shocks that flesh is heir to, one of the most
devastating is amyotrophic lateral sclerosis (ALS), commonly known as Lou
Gehrig's Disease. This disorder, which comes in both inherited and random
forms, is characterized by degeneration of spinal motor neurons, leading to
paralysis and death. The cause of the sporadic form is unknown, but new insight
has come from studying the genetic variations that lead to the rarer familial
forms. One such gene, accounting for 5%–10% of inherited
ALS, is FUS/TLS, which encodes a protein that normally lives in the nucleus of
the cell and is involved in the life-cycle of messenger RNA (mRNA).
ALS-associated mutations in FUS/TLS cause the protein to mislocalize outside the
nucleus into stress granules. Understanding the basis for the toxicity of
mislocalized FUS/TLS could lead to new approaches to the treatment of ALS. We
have made a yeast model for FUS/TLS cellular toxicity that recapitulates the
mislocalization, granular accumulation, and cell death. We have exploited the
yeast model to obtain information about what part of the protein is required for
proper localization and what part is essential for toxicity. We have also
identified several human genes that, when over-expressed in yeast, are able to
rescue the cell from the toxicity of mislocalized FUS/TLS. These genes all have
functions in mRNA quality control, implicating changes in this pathway in the
pathology of ALS.
Collapse
Affiliation(s)
- Shulin Ju
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
- Department of Neurology and Center for Neurologic Diseases, Harvard
Medical School and Brigham & Women's Hospital, Cambridge,
Massachusetts, United States of America
| | - Daniel F. Tardiff
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Haesun Han
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Kanneganti Divya
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
| | - Quan Zhong
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston,
Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts,
United States of America
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics and Center for RNA Biology,
School of Medicine and Dentistry, University of Rochester, Rochester, New York,
United States of America
| | - Daryl A. Bosco
- Department of Neurology, University of Massachusetts Medical School,
Worcester, Massachusetts, United States of America
| | - Lawrence J. Hayward
- Department of Neurology, University of Massachusetts Medical School,
Worcester, Massachusetts, United States of America
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School,
Worcester, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Dagmar Ringe
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
- Department of Neurology and Center for Neurologic Diseases, Harvard
Medical School and Brigham & Women's Hospital, Cambridge,
Massachusetts, United States of America
- * E-mail: (DR); (GAP)
| | - Gregory A. Petsko
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
- Department of Neurology and Center for Neurologic Diseases, Harvard
Medical School and Brigham & Women's Hospital, Cambridge,
Massachusetts, United States of America
- * E-mail: (DR); (GAP)
| |
Collapse
|
16
|
Weirauch MT, Hughes TR. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell Biochem 2011; 52:25-73. [PMID: 21557078 DOI: 10.1007/978-90-481-9069-0_3] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Transcription factors (TFs) play key roles in the regulation of gene expression by binding in a sequence-specific manner to genomic DNA. In eukaryotes, DNA binding is achieved by a wide range of structural forms and motifs. TFs are typically classified by their DNA-binding domain (DBD) type. In this chapter, we catalogue and survey 91 different TF DBD types in metazoa, plants, fungi, and protists. We briefly discuss well-characterized TF families representing the major DBD superclasses. We also examine the species distributions and inferred evolutionary histories of the various families, and the potential roles played by TF family expansion and dimerization.
Collapse
Affiliation(s)
- Matthew T Weirauch
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada,
| | | |
Collapse
|
17
|
Verwaal R, Jiang Y, Wang J, Daran JM, Sandmann G, van den Berg JA, van Ooyen AJJ. Heterologous carotenoid production in Saccharomyces cerevisiae induces the pleiotropic drug resistance stress response. Yeast 2010; 27:983-98. [DOI: 10.1002/yea.1807] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
18
|
Gasser B, Dragosits M, Mattanovich D. Engineering of biotin-prototrophy in Pichia pastoris for robust production processes. Metab Eng 2010; 12:573-80. [DOI: 10.1016/j.ymben.2010.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 06/30/2010] [Accepted: 07/27/2010] [Indexed: 10/19/2022]
|
19
|
Hoth S, Niedermeier M, Feuerstein A, Hornig J, Sauer N. An ABA-responsive element in the AtSUC1 promoter is involved in the regulation of AtSUC1 expression. PLANTA 2010; 232:911-23. [PMID: 20635094 DOI: 10.1007/s00425-010-1228-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 07/06/2010] [Indexed: 05/24/2023]
Abstract
Abscisic acid (ABA) and sugars regulate many aspects of plant growth and development, and we are only just beginning to understand the complex interactions between ABA and sugar signaling networks. Here, we show that ABA-dependent transcription factors bind to the promoter of the Arabidopsis thaliana AtSUC1 (At1g71880) sucrose transporter gene in vitro. We present the characterization of a cis-regulatory element by truncation of the AtSUC1 promoter and by electrophoretic mobility shift assays that is identical to a previously characterized ABA-responsive element (ABRE). In yeast 1-hybrid analyses we identified ABI5 (AtbZIP39; At2g36270) and AREB3 (AtbZIP66; At3g56850) as potential interactors. Analyses of plants expressing the beta-glucuronidase reporter gene under the control of ABI5 or AREB3 promoter sequences demonstrated that both transcription factor genes are co-expressed with AtSUC1 in pollen and seedlings, the primary sites of AtSUC1 action. Mutational analyses of the identified cis-regulatory element verified its importance for AtSUC1 expression in young seedlings. In abi5-4 seedlings, we observed an increase of sucrose-dependent anthocyanin accumulation and AtSUC1 mRNA levels. This suggests that ABI5 prevents an overshoot of sucrose-induced AtSUC1 expression and confirmed a novel cross-link between sugar and ABA signaling.
Collapse
Affiliation(s)
- Stefan Hoth
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | | | | |
Collapse
|
20
|
Characterization of the Aspergillus nidulans biotin biosynthetic gene cluster and use of the bioDA gene as a new transformation marker. Fungal Genet Biol 2010; 48:208-15. [PMID: 20713166 DOI: 10.1016/j.fgb.2010.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Revised: 08/06/2010] [Accepted: 08/09/2010] [Indexed: 11/23/2022]
Abstract
The genes involved in the biosynthesis of biotin were identified in the hyphal fungus Aspergillus nidulans through homology searches and complementation of Escherichia coli biotin-auxotrophic mutants. Whereas the 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase are encoded by distinct genes in bacteria and the yeast Saccharomyces cerevisiae, both activities are performed in A. nidulans by a single enzyme, encoded by the bifunctional gene bioDA. Such a bifunctional bioDA gene is a genetic feature common to numerous members of the ascomycete filamentous fungi and basidiomycetes, as well as in plants and oömycota. However, unlike in other eukaryota, the three bio genes contributing to the four enzymatic steps from pimeloyl-CoA to biotin are organized in a gene cluster in pezizomycotina. The A. nidulans auxotrophic mutants biA1, biA2 and biA3 were all found to have mutations in the 7,8-diaminopelargonic acid synthase domain of the bioDA gene. Although biotin auxotrophy is an inconvenient marker in classical genetic manipulations due to cross-feeding of biotin, transformation of the biA1 mutant with the bioDA gene from either A. nidulans or Aspergillus fumigatus led to the recovery of well-defined biotin-prototrophic colonies. The usefulness of bioDA gene as a novel and robust transformation marker was demonstrated in co-transformation experiments with a green fluorescent protein reporter, and in the efficient deletion of the laccase (yA) gene via homologous recombination in a mutant lacking non-homologous end-joining activity.
Collapse
|
21
|
Pendini NR, Bailey LM, Booker GW, Wilce MC, Wallace JC, Polyak SW. Microbial biotin protein ligases aid in understanding holocarboxylase synthetase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:973-82. [DOI: 10.1016/j.bbapap.2008.03.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/16/2008] [Accepted: 03/26/2008] [Indexed: 11/16/2022]
|
22
|
Giancaspero TA, Wait R, Boles E, Barile M. Succinate dehydrogenase flavoprotein subunit expression in Saccharomyces cerevisiae--involvement of the mitochondrial FAD transporter, Flx1p. FEBS J 2008; 275:1103-17. [PMID: 18279395 DOI: 10.1111/j.1742-4658.2008.06270.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The mitochondrial FAD transporter, Flx1p, is a member of the mitochondrial carrier family responsible for FAD transport in Saccharomyces cerevisiae. It has also been suggested that it has a role in maintaining the normal activity of mitochondrial FAD-binding enzymes, including lipoamide dehydrogenase and succinate dehydrogenase flavoprotein subunit Sdh1p. A decrease in the amount of Sdh1p in the flx1Delta mutant strain has been determined here to be due to a post-transcriptional control that involves regulatory sequences located upstream of the SDH1 coding sequence. The SDH1 coding sequence and the regulatory sequences located downstream of the SDH1 coding region, as well as protein import and cofactor attachment, seem to be not involved in the decrease in the amount of protein.
Collapse
Affiliation(s)
- Teresa A Giancaspero
- Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università degli Studi di Bari, Via Orabona 4, Bari, Italy
| | | | | | | |
Collapse
|
23
|
Abstract
Although the role of biotin in metabolic reactions has long been recognized, its influence on transcription has only recently been discovered. A key protein in biotin-mediated transcription regulation is the biotin protein ligase, the enzyme responsible for catalyzing covalent linkage of the vitamin to biotin-dependent carboxylases. In the biotin regulatory system of Escherichia coli, the best characterized of the biotin-sensing systems, the biotin protein ligase functions both as the biotinylating enzyme and as a transcription repressor. Detailed mechanistic studies of this system are reviewed. In addition, recent studies have revealed other biotin-sensing systems in organisms ranging from bacteria to humans. These systems and the central role of the biotin protein ligase in each are also reviewed.
Collapse
Affiliation(s)
- Dorothy Beckett
- Department of Chemistry and Biochemistry, College of Chemical and Life Sciences, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
24
|
Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|