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Du MM, Zhang GG, Zhu ZT, Zhao YQ, Gao B, Tao XY, Wang FQ, Wei DZ. Boosting the epoxidation of squalene to produce triterpenoids in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:76. [PMID: 37143155 PMCID: PMC10161426 DOI: 10.1186/s13068-023-02310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/24/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Polycyclic triterpenoids (PTs) are common in plants, and have attracted considerable interest due to their remarkable biological activities. Currently, engineering the ergosterol synthesis pathway in Saccharomyces cerevisiae is a safe and cost-competitive way to produce triterpenoids. However, the strict regulation of ERG1 involved in the epoxidation of squalene limits the triterpenoid production. RESULTS In this study, we found that the decrease in ERG7 protein level could dramatically boost the epoxidation of squalene by improving the protein stability of ERG1. We next explored the potential factors that affected the degradation process of ERG1 and confirmed that ERG7 was involved in the degradation process of ERG1. Subsequently, expression of four different triterpene cyclases utilizing either 2,3-oxidosqualene or 2,3:22,23-dioxidosqualene as the substrate in ERG7-degraded strains showed that the degradation of ERG7 to prompt the epoxidation of squalene could significantly increase triterpenoid production. To better display the potential of the strategy, we increased the supply of 2,3-oxidosqualene, optimized flux distribution between ergosterol synthesis pathway and β-amyrin synthesis pathway, and modified the GAL-regulation system to separate the growth stage from the production stage. The best-performing strain ultimately produced 4216.6 ± 68.4 mg/L of β-amyrin in a two-stage fed-fermentation (a 47-fold improvement over the initial strain). CONCLUSIONS This study showed that deregulation of the native restriction in ergosterol pathway was an effective strategy to increase triterpenoid production in yeast, which provided a new insight into triterpenoids biosynthesis.
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Affiliation(s)
- Meng-Meng Du
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China
| | - Ge-Ge Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China
| | - Zhan-Tao Zhu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China
| | - Yun-Qiu Zhao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China
| | - Xin-Yi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B.311, Shanghai, 200237, China.
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Monitoring of switches in heterochromatin-induced silencing shows incomplete establishment and developmental instabilities. Proc Natl Acad Sci U S A 2019; 116:20043-20053. [PMID: 31527269 DOI: 10.1073/pnas.1909724116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Position effect variegation (PEV) in Drosophila results from new juxtapositions of euchromatic and heterochromatic chromosomal regions, and manifests as striking bimodal patterns of gene expression. The semirandom patterns of PEV, reflecting clonal relationships between cells, have been interpreted as gene-expression states that are set in development and thereafter maintained without change through subsequent cell divisions. The rate of instability of PEV is almost entirely unexplored beyond the final expression of the modified gene; thus the origin of the expressivity and patterns of PEV remain unexplained. Many properties of PEV are not predicted from currently accepted biochemical and theoretical models. In this work we investigate the time at which expressivity of silencing is set, and find that it is determined before heterochromatin exists. We employ a mathematical simulation and a corroborating experimental approach to monitor switching (i.e., gains and losses of silencing) through development. In contrast to current views, we find that gene silencing is incompletely set early in embryogenesis, but nevertheless is repeatedly lost and gained in individual cells throughout development. Our data support an alternative to locus-specific "epigenetic" silencing at variegating gene promoters that more fully accounts for the final patterns of PEV.
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Rodrigues-Pousada C, Devaux F, Caetano SM, Pimentel C, da Silva S, Cordeiro AC, Amaral C. Yeast AP-1 like transcription factors (Yap) and stress response: a current overview. MICROBIAL CELL 2019; 6:267-285. [PMID: 31172012 PMCID: PMC6545440 DOI: 10.15698/mic2019.06.679] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Yeast adaptation to stress has been extensively studied. It involves large reprogramming of genome expression operated by many, more or less specific, transcription factors. Here, we review our current knowledge on the function of the eight Yap transcription factors (Yap1 to Yap8) in Saccharomyces cerevisiae, which were shown to be involved in various stress responses. More precisely, Yap1 is activated under oxidative stress, Yap2/Cad1 under cadmium, Yap4/Cin5 and Yap6 under osmotic shock, Yap5 under iron overload and Yap8/Arr1 by arsenic compounds. Yap3 and Yap7 seem to be involved in hydroquinone and nitrosative stresses, respectively. The data presented in this article illustrate how much knowledge on the function of these Yap transcription factors is advanced. The evolution of the Yap family and its roles in various pathogenic and non-pathogenic fungal species is discussed in the last section.
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Affiliation(s)
- Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Soraia M Caetano
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Sofia da Silva
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Ana Carolina Cordeiro
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
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Leshets M, Ramamurthy D, Lisby M, Lehming N, Pines O. Fumarase is involved in DNA double-strand break resection through a functional interaction with Sae2. Curr Genet 2017; 64:697-712. [DOI: 10.1007/s00294-017-0786-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/19/2017] [Accepted: 11/22/2017] [Indexed: 11/28/2022]
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Mediator, SWI/SNF and SAGA complexes regulate Yap8-dependent transcriptional activation of ACR2 in response to arsenate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:472-481. [DOI: 10.1016/j.bbagrm.2017.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/12/2023]
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Howard GC, Tansey WP. Interaction of Gcn4 with target gene chromatin is modulated by proteasome function. Mol Biol Cell 2016; 27:2735-41. [PMID: 27385344 PMCID: PMC5007093 DOI: 10.1091/mbc.e16-03-0192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/28/2016] [Indexed: 12/18/2022] Open
Abstract
The yeast transcription factor Gcn4 requires a ubiquitin ligase and the proteasome in order to function. Inhibiting proteasome function prevents the interaction of Gcn4 with target gene chromatin, and this activity is suppressed by inactivation of the ubiquitin-selective chaperone Cdc48. Thus proteolysis of Gcn4 is not required for its function. The ubiquitin–proteasome system (UPS) influences gene transcription in multiple ways. One way in which the UPS affects transcription centers on transcriptional activators, the function of which can be stimulated by components of the UPS that also trigger their destruction. Activation of transcription by the yeast activator Gcn4, for example, is attenuated by mutations in the ubiquitin ligase that mediates Gcn4 ubiquitylation or by inhibition of the proteasome, leading to the idea that ubiquitin-mediated proteolysis of Gcn4 is required for its activity. Here we probe the steps in Gcn4 activity that are perturbed by disruption of the UPS. We show that the ubiquitylation machinery and the proteasome control different steps in Gcn4 function and that proteasome activity is required for the ability of Gcn4 to bind to its target genes in the context of chromatin. Curiously, the effect of proteasome inhibition on Gcn4 activity is suppressed by mutations in the ubiquitin-selective chaperone Cdc48, revealing that proteolysis per se is not required for Gcn4 activity. Our data highlight the role of Cdc48 in controlling promoter occupancy by Gcn4 and support a model in which ubiquitylation of activators—not their destruction—is important for function.
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Affiliation(s)
- Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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Kalderon B, Kogan G, Bubis E, Pines O. Cytosolic Hsp60 can modulate proteasome activity in yeast. J Biol Chem 2014; 290:3542-51. [PMID: 25525272 DOI: 10.1074/jbc.m114.626622] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hsp60, an essential oligomeric molecular mitochondrial chaperone, has been subject to rigorous basic and clinical research. With yeast as a model system, we provide evidence for the ability of cytosolic yHsp60 to inhibit the yeast proteasome. (i) Following biological turnover of murine Bax (a proteasome substrate), we show that co-expression of cytosolic yHsp60 stabilizes Bax, enhances its association with mitochondria, and enhances its killing capacity. (ii) Expression of yHsp60 in the yeast cytosol (yHsp60c) inhibits degradation of a cytosolic protein ΔMTS-Aco1 tagged with the degron SL17 (a ubiquitin-proteasome substrate). (iii) Conditions under which Hsp60 accumulates in the cytosol (elevated Hsp60c or growth at 37 °C) correlate with reduced 20 S peptidase activity in proteasomes purified from cell extracts. (iv) Elevated yHsp60 in the cytosol correlate with accumulation of polyubiquitinated proteins. (v) According to 20 S proteasome pulldown experiments, Hsp60 is physically associated with proteasomes in extracts of cells expressing Hsp60c or grown at 37 °C. Even mutant Hsp60 proteins, lacking chaperone activity, were still capable of proteasome inhibition. The results support the hypothesis that localization of Hsp60 to the cytosol may modulate proteasome activity according to cell need.
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Affiliation(s)
- Bella Kalderon
- From the Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel and
| | - Gleb Kogan
- From the Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel and
| | - Ettel Bubis
- From the Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel and
| | - Ophry Pines
- From the Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel and the CREATE-NUS-HUJ Program, National University of Singapore, 138602 Singapore
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Conrad M, Schothorst J, Kankipati HN, Van Zeebroeck G, Rubio-Texeira M, Thevelein JM. Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 2014; 38:254-99. [PMID: 24483210 PMCID: PMC4238866 DOI: 10.1111/1574-6976.12065] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 02/04/2023] Open
Abstract
The yeast Saccharomyces cerevisiae has been a favorite organism for pioneering studies on nutrient-sensing and signaling mechanisms. Many specific nutrient responses have been elucidated in great detail. This has led to important new concepts and insight into nutrient-controlled cellular regulation. Major highlights include the central role of the Snf1 protein kinase in the glucose repression pathway, galactose induction, the discovery of a G-protein-coupled receptor system, and role of Ras in glucose-induced cAMP signaling, the role of the protein synthesis initiation machinery in general control of nitrogen metabolism, the cyclin-controlled protein kinase Pho85 in phosphate regulation, nitrogen catabolite repression and the nitrogen-sensing target of rapamycin pathway, and the discovery of transporter-like proteins acting as nutrient sensors. In addition, a number of cellular targets, like carbohydrate stores, stress tolerance, and ribosomal gene expression, are controlled by the presence of multiple nutrients. The protein kinase A signaling pathway plays a major role in this general nutrient response. It has led to the discovery of nutrient transceptors (transporter receptors) as nutrient sensors. Major shortcomings in our knowledge are the relationship between rapid and steady-state nutrient signaling, the role of metabolic intermediates in intracellular nutrient sensing, and the identity of the nutrient sensors controlling cellular growth.
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Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Marta Rubio-Texeira
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
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Durairaj G, Lahudkar S, Bhaumik SR. A new regulatory pathway of mRNA export by an F-box protein, Mdm30. RNA (NEW YORK, N.Y.) 2014; 20:133-42. [PMID: 24327750 PMCID: PMC3895266 DOI: 10.1261/rna.042325.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mdm30, an F-box protein in yeast, has been recently shown to promote mRNA export. However, it remains unknown how Mdm30 facilitates mRNA export. Here, we show that Mdm30 targets the Sub2 component of the TREX (Transcription/Export) complex for ubiquitylation and subsequent proteasomal degradation. Such a targeted degradation of Sub2 enhances the recruitment of the mRNA export adaptor, Yra1, to the active genes to promote mRNA export. Together, these results elucidate that Mdm30 promotes mRNA export by lowering Sub2's stability and consequently enhancing Yra1 recruitment, thus illuminating new regulatory mechanisms of mRNA export by Mdm30.
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Ansari SA, Morse RH. Mechanisms of Mediator complex action in transcriptional activation. Cell Mol Life Sci 2013; 70:2743-56. [PMID: 23361037 PMCID: PMC11113466 DOI: 10.1007/s00018-013-1265-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 12/14/2022]
Abstract
Mediator is a large multisubunit complex that plays a central role in the regulation of RNA Pol II transcribed genes. Conserved in overall structure and function among eukaryotes, Mediator comprises 25-30 protein subunits that reside in four distinct modules, termed head, middle, tail, and CDK8/kinase. Different subunits of Mediator contact other transcriptional regulators including activators, co-activators, general transcription factors, subunits of RNA Pol II, and specifically modified histones, leading to the regulated expression of target genes. This review is focused on the interactions of specific Mediator subunits with diverse transcription regulators and how those interactions contribute to Mediator function in transcriptional activation.
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Affiliation(s)
- Suraiya A. Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
- Department of Biomedical Science, University at Albany School of Public Health, Albany, NY USA
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Mechanisms of antisense transcription initiation from the 3' end of the GAL10 coding sequence in vivo. Mol Cell Biol 2013; 33:3549-67. [PMID: 23836882 DOI: 10.1128/mcb.01715-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In spite of the important regulatory functions of antisense transcripts in gene expression, it remains unknown how antisense transcription is initiated. Recent studies implicated RNA polymerase II in initiation of antisense transcription. However, how RNA polymerase II is targeted to initiate antisense transcription has not been elucidated. Here, we have analyzed the association of RNA polymerase II with the antisense initiation site at the 3' end of the GAL10 coding sequence in dextrose-containing growth medium that induces antisense transcription. We find that RNA polymerase II is targeted to the antisense initiation site at GAL10 by Reb1p activator as well as general transcription factors (e.g., TFIID, TFIIB, and Mediator) for antisense transcription initiation. Intriguingly, while GAL10 antisense transcription is dependent on TFIID, its sense transcription does not require TFIID. Further, the Gal4p activator that promotes GAL10 sense transcription is dispensable for antisense transcription. Moreover, the proteasome that facilitates GAL10 sense transcription does not control its antisense transcription. Taken together, our results reveal that GAL10 sense and antisense transcriptions are regulated differently and shed much light on the mechanisms of antisense transcription initiation.
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Ee G, Lehming N. How the ubiquitin proteasome system regulates the regulators of transcription. Transcription 2012; 3:235-9. [PMID: 22885980 DOI: 10.4161/trns.21249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The ubiquitin proteasome system plays an important role in transcription. Monoubiquitination of activators is believed to aid their function, while the 26S proteasomal degradation of repressors is believed to restrict their function. What remains controversial is the question of whether the degradation of activators aids or restricts their function.
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Affiliation(s)
- Gary Ee
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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