1
|
Barlit H, Romero AM, Gülhan A, Patnaik PK, Tyshkovskiy A, Martínez-Pastor MT, Gladyshev VN, Puig S, Labunskyy VM. Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation. iScience 2024; 27:109868. [PMID: 38779483 PMCID: PMC11109004 DOI: 10.1016/j.isci.2024.109868] [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: 09/28/2023] [Revised: 03/12/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels.
Collapse
Affiliation(s)
- Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Antonia M. Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Ali Gülhan
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Praveen K. Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - María T. Martínez-Pastor
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Vyacheslav M. Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| |
Collapse
|
2
|
Muñoz-Miranda LA, Zepeda-Peña AC, Casas-Godoy L, Pereira-Santana A, Méndez-Zamora A, Barrera-Martínez I, Rodríguez-Zapata L, Gschaedler-Mathis AC, Figueroa-Yáñez LJ. CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3. World J Microbiol Biotechnol 2024; 40:121. [PMID: 38441729 DOI: 10.1007/s11274-023-03811-0] [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: 07/31/2023] [Accepted: 10/18/2023] [Indexed: 03/07/2024]
Abstract
Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.
Collapse
Affiliation(s)
- Luis A Muñoz-Miranda
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Andrea Catalina Zepeda-Peña
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Leticia Casas-Godoy
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Subsede Zapopan, Zapopan, Jalisco, México
| | - Alejandro Pereira-Santana
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. Subsede Sureste, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
| | - Andrés Méndez-Zamora
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Iliana Barrera-Martínez
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Subsede Zapopan, Zapopan, Jalisco, México
| | - Luis Rodríguez-Zapata
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, México
| | - Anne Christine Gschaedler-Mathis
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México.
| | - Luis J Figueroa-Yáñez
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México.
| |
Collapse
|
3
|
Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 2022; 74:139-149. [DOI: 10.1016/j.ymben.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
|
4
|
Liu Y, Song D, Hu H, Yang R, Lyu X. De Novo Production of Hydroxytyrosol by Saccharomyces cerevisiae-Escherichia coli Coculture Engineering. ACS Synth Biol 2022; 11:3067-3077. [PMID: 35952699 DOI: 10.1021/acssynbio.2c00300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hydroxytyrosol is a valuable plant-derived phenolic compound with excellent pharmacological activities for application in the food and health care industries. Microbial biosynthesis provides a promising approach for sustainable production of hydroxytyrosol via metabolic engineering. However, its efficient production is limited by the machinery and resources available in the commonly used individual microbial platform, for example, Escherichia coli, Saccharomyces cerevisiae. In this study, a S. cerevisiae-E. coli coculture system was designed for de novo biosynthesis of hydroxytyrosol by taking advantage of their inherent metabolic properties, whereby S. cerevisiae was engineered for de novo production of tyrosol based on an endogenous Ehrlich pathway, and E. coli was dedicated to converting tyrosol to hydroxytyrosol by use of native hydroxyphenylacetate 3-monooxygenase (EcHpaBC). To enhance hydroxytyrosol production, intra- and intermodule engineering was employed in this microbial consortium: (I) in the upstream S. cerevisiae strain, multipath regulations combining with a glucose-sensitive GAL regulation system were engineered to enhance the precursor supply, resulting in significant increase of tyrosol production (from 17.60 mg/L to 461.07 mg/L); (II) Echpabc was overexpressed in the downstream E. coli strain, improving the conversion rate of tyrosol to hydroxytyrosol from 0.03% to 86.02%; (III) and last, intermodule engineering with this coculture system was performed by optimization of the initial inoculation ratio of each population and fermentation conditions, achieving 435.32 mg/L of hydroxytyrosol. This S. cerevisiae-E. coli coculture strategy provides a new opportunity for de novo production of hydroxytyrosol from inexpensive feedstock.
Collapse
Affiliation(s)
- Yingjie Liu
- School of Food Science and Technology, Jiangnan University, 214122, Wuxi, P. R. China
| | - Dong Song
- Jiangxi Baiyue Food Co. Ltd, Pingxiang, Jiangxi 337000, P. R. China
| | - Haitao Hu
- School of Food Science and Technology, Jiangnan University, 214122, Wuxi, P. R. China
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, 214122, Wuxi, P. R. China.,Jiangnan University (Rugao) Institute of Food Biotechnology, 226503, Nantong, P. R. China
| | - Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, 214122, Wuxi, P. R. China.,Jiangnan University (Rugao) Institute of Food Biotechnology, 226503, Nantong, P. R. China
| |
Collapse
|
5
|
Liu Y, Liu H, Hu H, Ng KR, Yang R, Lyu X. De Novo Production of Hydroxytyrosol by Metabolic Engineering of Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7490-7499. [PMID: 35649155 DOI: 10.1021/acs.jafc.2c02137] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hydroxytyrosol is an olive-derived phenolic compound of increasing commercial interest due to its health-promoting properties. In this study, a high-yield hydroxytyrosol-producing Saccharomyces cerevisiae cell factory was established via a comprehensive metabolic engineering scheme. First, de novo biosynthetic pathway of hydroxytyrosol was constructed in yeast by gene screening and overexpression of different phenol hydroxylases, among which paHD (from Pseudomonas aeruginosa) displayed the best catalytic performance. Next, hydroxytyrosol precursor supply was enhanced via a multimodular engineering approach: elimination of tyrosine feedback inhibition through genomic integration of aro4K229L and aro7G141S, construction of an aromatic aldehyde synthase (AAS)-based tyrosine metabolic pathway, and redistribution of metabolic flux between glycolytic pathway and pentose phosphate pathway (PPP) by introducing the exogenous gene Bbxfpkopt. As a result, the titer of hydroxytyrosol was improved by 6.88-fold. Finally, a glucose-responsive dynamic regulation system based on GAL80 deletion was implemented, resulting in the final hydroxytyrosol yields of 308.65 mg/L and 167.98 mg/g cell mass, the highest known from de novo production in S. cerevisiae to date.
Collapse
Affiliation(s)
- Yingjie Liu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Han Liu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Haitao Hu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Kuan Rei Ng
- Food Science and Technology Programme, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| |
Collapse
|
6
|
Farkas Á, Urlaub H, Bohnsack KE, Schwappach B. Regulated targeting of the monotopic hairpin membrane protein Erg1 requires the GET pathway. J Biophys Biochem Cytol 2022; 221:213228. [PMID: 35587358 PMCID: PMC9123286 DOI: 10.1083/jcb.202201036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 02/08/2023] Open
Abstract
The guided entry of tail-anchored proteins (GET) pathway targets C-terminally anchored transmembrane proteins and protects cells from lipotoxicity. Here, we reveal perturbed ergosterol production in ∆get3 cells and demonstrate the sensitivity of GET pathway mutants to the sterol synthesis inhibiting drug terbinafine. Our data uncover a key enzyme of sterol synthesis, the hairpin membrane protein squalene monooxygenase (Erg1), as a non-canonical GET pathway client, thus rationalizing the lipotoxicity phenotypes of GET pathway mutants. Get3 recognizes the hairpin targeting element of Erg1 via its classical client-binding pocket. Intriguingly, we find that the GET pathway is especially important for the acute upregulation of Erg1 induced by low sterol conditions. We further identify several other proteins anchored to the endoplasmic reticulum (ER) membrane exclusively via a hairpin as putative clients of the GET pathway. Our findings emphasize the necessity of dedicated targeting pathways for high-efficiency targeting of particular clients during dynamic cellular adaptation and highlight hairpin proteins as a potential novel class of GET clients.
Collapse
Affiliation(s)
- Ákos Farkas
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytic Mass Spectrometry, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| |
Collapse
|
7
|
Analysing intracellular isoprenoid metabolites in diverse prokaryotic and eukaryotic microbes. Methods Enzymol 2022; 670:235-284. [DOI: 10.1016/bs.mie.2022.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
8
|
Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress. mSystems 2021; 6:e0118921. [PMID: 34874779 PMCID: PMC8651089 DOI: 10.1128/msystems.01189-21] [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] [Indexed: 12/02/2022] Open
Abstract
It is known that organisms have developed various mechanisms to cope with cadmium (Cd) stress, while we still lack a system-level understanding of the functional isomorphy among them. In the present study, a cross-kingdom comparison was conducted among Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, through toxicological tests, comparative transcriptomics, as well as conventional functional genomics. An equivalent level of Cd stress was determined via inhibition tests. Through transcriptome comparison, the three organisms exhibited differential gene expression under the same Cd stress relative to the corresponding no-treatment control. Results from functional enrichment analysis of differentially expressed genes (DEGs) showed that four metabolic pathways responsible for combating Cd stress were commonly regulated in the three organisms, including antioxidant reactions, sulfur metabolism, cell wall remodeling, and metal transport. In vivo expression patterns of 43 DEGs from the four pathways were further examined using quantitative PCR and resulted in a relatively comparable dynamic of gene expression patterns with transcriptome sequencing (RNA-seq). Cross-kingdom comparison of typical Cd stress-responding proteins resulted in the detection of 12 groups of homologous proteins in the three species. A class of potential metal transporters were subjected to cross-transformation to test their functional complementation. An ABC transporter gene in E. coli, possibly homologous to the yeast ycf1, was heterologously expressed in S. cerevisiae, resulting in enhanced Cd tolerance. Overall, our findings indicated that conserved genetic modules against Cd toxicity were commonly regulated among distantly related microbial species, which will be helpful for utilizing them in modifying microbial traits for bioremediation. IMPORTANCE Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms. A transcriptomic comparison was done among model microbes, leading to the identification of a conserved cellular model pinpointing the generic strategies utilized by microbes for combating Cd stress. A novel E. coli transporter gene substantially increased yeast’s Cd tolerance. Knowledge on systems understanding of the cellular response to metals provides the basis for developing bioengineering remediation technology.
Collapse
|
9
|
Höler S, Bertl A, Degreif D. Novel auto-selection systems for transformation selection of Saccharomyces cerevisiae in rich complex media. FEMS Yeast Res 2021; 21:6316778. [PMID: 34232310 DOI: 10.1093/femsyr/foab039] [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: 04/15/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022] Open
Abstract
The most widely used strategy for selection of yeast transformed with episomal plasmids comprises the use of auxotrophic yeast strains in combination with vectors containing complementing prototrophic marker genes. Another approach uses heterologous genes or cassettes which, if present in the vector, render the otherwise sensitive yeast strain resistant to antibiotics. In addition, auto-selection systems for Saccharomyces cerevisiae have been developed that eliminate the requirement for synthetic drop-out media or the use of antibiotics for transformation selection and subsequent plasmid maintenance in expression cultures. Here we describe a combination of host strain and vector system introducing a novel concept of auto-selection systems that allows for easy and robust propagation of host cells deleted in essential genes in supplemented media before being transformed with rescuing plasmids. With that, our approach is favorable over commonly used selection strategies and has major advantage over other auto-selection systems. Our approach complements the auto-selection toolbox already available for S. cerevisiae, thus contributing a novel system that enables the use of complex peptone-based media for protein expression and metabolic engineering approaches. We therefore expect that this new strategy will be of general interest to the yeast research community in academia and industry.
Collapse
Affiliation(s)
- Sebastian Höler
- Department of Biology, Yeast Membrane Biology, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Adam Bertl
- Department of Biology, Yeast Membrane Biology, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Daniel Degreif
- Department of Biology, Yeast Membrane Biology, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| |
Collapse
|
10
|
Chen K, Zhu Y, Zhang Y, Hamza T, Yu H, Saint Fleur A, Galen J, Yang Z, Feng H. A probiotic yeast-based immunotherapy against Clostridioides difficile infection. Sci Transl Med 2021; 12:12/567/eaax4905. [PMID: 33115949 DOI: 10.1126/scitranslmed.aax4905] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 02/12/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
Antibiotic-resistant Clostridioides difficile is an anaerobic Gram-positive bacterium that colonizes the colon and is responsible for more than 29,000 deaths in the United States each year. Hence, C. difficile infection (CDI) poses an urgent threat to public health. Antibody-mediated neutralization of TcdA and TcdB toxins, the major virulence factors of CDI, represents an effective strategy to combat the disease without invoking antibiotic resistance. However, current antitoxin approaches are mostly based on parenteral infusion of monoclonal antibodies that are costly, narrow spectrum, and not optimized against the intestinal disease. Here, we engineered probiotic Saccharomyces boulardii to constitutively secrete a single tetra-specific antibody that potently and broadly neutralized both toxins and demonstrated protection against primary and recurrent CDI in both prophylactic and therapeutic mouse models of disease. This yeast immunotherapy is orally administered, can be used concurrently with antibiotics, and may have potential as a prophylactic against CDI risk and as a therapeutic for patients with CDI.
Collapse
Affiliation(s)
- Kevin Chen
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Yixuan Zhu
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yongrong Zhang
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Therwa Hamza
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Hua Yu
- FZata Inc., Halethorpe, MD 21227, USA
| | - Ashley Saint Fleur
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - James Galen
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Hanping Feng
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA.
| |
Collapse
|
11
|
Prins RC, Billerbeck S. A buffered media system for yeast batch culture growth. BMC Microbiol 2021; 21:127. [PMID: 33892647 PMCID: PMC8063419 DOI: 10.1186/s12866-021-02191-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/11/2021] [Indexed: 11/24/2022] Open
Abstract
Background Fungi are premier hosts for the high-yield secretion of proteins for biomedical and industrial applications. The stability and activity of these secreted proteins is often dependent on the culture pH. As yeast acidifies the commonly used synthetic complete drop-out (SD) media that contains ammonium sulfate, the pH of the media needs to be buffered in order to maintain a desired extracellular pH during biomass production. At the same time, many buffering agents affect growth at the concentrations needed to support a stable pH. Although the standard for biotechnological research and development is shaken batch cultures or microtiter plate cultures that cannot be easily automatically pH-adjusted during growth, there is no comparative study that evaluates the buffering capacity and growth effects of different media types across pH-values in order to develop a pH-stable batch culture system. Results We systematically test the buffering capacity and growth effects of a citrate-phosphate buffer (CPB) from acidic to neutral pH across different media types. These media types differ in their nitrogen source (ammonium sulfate, urea or both). We find that the widely used synthetic drop-out media that uses ammonium sulfate as nitrogen source can only be effectively buffered at buffer concentrations that also affect growth. At lower concentrations, yeast biomass production still acidifies the media. When replacing the ammonium sulfate with urea, the media alkalizes. We then develop a medium combining ammonium sulfate and urea which can be buffered at low CPB concentrations that do not affect growth. In addition, we show that a buffer based on Tris/HCl is not effective in maintaining any of our media types at neutral pH even at relatively high concentrations. Conclusion Here we show that the buffering of yeast batch cultures is not straight-forward and addition of a buffering agent to set a desired starting pH does not guarantee pH-maintenance during growth. In response, we present a buffered media system based on an ammonium sulfate/urea medium that enables relatively stable pH-maintenance across a wide pH-range without affecting growth. This buffering system is useful for protein-secretion-screenings, antifungal activity assays, as well as for other pH-dependent basic biology or biotechnology projects. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02191-5.
Collapse
Affiliation(s)
- Rianne C Prins
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
12
|
Thiol Peroxidases as Major Regulators of Intracellular Levels of Peroxynitrite in Live Saccharomyces cerevisiae Cells. Antioxidants (Basel) 2020; 9:antiox9050434. [PMID: 32429358 PMCID: PMC7278867 DOI: 10.3390/antiox9050434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/27/2022] Open
Abstract
Thiol peroxidases (TP) are ubiquitous and abundant antioxidant proteins of the peroxiredoxin and glutathione peroxidase families that can catalytically and rapidly reduce biologically relevant peroxides, such as hydrogen peroxide and peroxynitrite. However, the TP catalytic cycle is complex, depending on multiple redox reactions and partners, and is subjected to branching and competition points that may limit their peroxide reductase activity in vivo. The goals of the present study were to demonstrate peroxynitrite reductase activity of TP members in live cells in real time and to evaluate its catalytic characteristics. To these ends, we developed a simple fluorescence assay using coumarin boronic acid (CBA), exploiting that fact that TP and CBA compete for peroxynitrite, with the expectation that higher TP peroxynitrite reductase activity will lower the CBA oxidation. TP peroxynitrite reductase activity was evaluated by comparing CBA oxidation in live wild type and genetically modified Δ8 (TP-deficient strain) and Δ8+TSA1 (Δ8 strain that expresses only one TP member, the TSA1 gene) Saccharomyces cerevisiae strains. The results showed that CBA oxidation decreased with cell density and increased with increasing peroxynitrite availability. Additionally, the rate of CBA oxidation decreased in the order Δ8 > Δ8+TSA1 > WT strains both in control and glycerol-adapted (expressing higher TP levels) cells, showing that the CBA competition assay could reliably detect peroxynitrite in real time in live cells, comparing CBA oxidation in strains with reduced and increased TP expression. Finally, there were no signs of compromised TP peroxynitrite reductase activity during experimental runs, even at the highest peroxynitrite levels tested. Altogether, the results show that TP is a major component in the defense of yeast against peroxynitrite insults under basal and increasing stressful conditions.
Collapse
|
13
|
Mark R, Lyu X, Ng KR, Chen WN. Gene Source Screening as a Tool for Naringenin Production in Engineered Saccharomyces cerevisiae. ACS OMEGA 2019; 4:12872-12879. [PMID: 31460414 PMCID: PMC6682025 DOI: 10.1021/acsomega.9b00364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/24/2019] [Indexed: 06/10/2023]
Abstract
Flavonoids are plant secondary metabolites with great potential in the food industry. Metabolic engineering of Saccharomyces cerevisiae is a sustainable production technique. However, the current naringenin production yield is low because of inefficient enzymatic activity. Hence, this study uses gene source screening as a tool to identify the best gene source for enzymes such as 4-coumarate: coenzyme ligase (4CL) and chalcone synthase (CHS). For the first time, the 4CL gene from Medicago truncatula and the CHS gene from Vitis vinifera were expressed in S. cerevisiae, and this combination provided the highest yield of naringenin, which was 28-fold higher as compared to the reference strain. The combinations obtained similar performance in the Y-28 strains, where the highest production was 28.68 mg/L. Our results demonstrated that the selection and combination of enzymes from the correct gene source could greatly improve naringenin production. For the future, this could help commercialize flavonoid production, which would result in natural food preservatives and additives.
Collapse
|
14
|
Baghban R, Farajnia S, Rajabibazl M, Ghasemi Y, Mafi A, Hoseinpoor R, Rahbarnia L, Aria M. Yeast Expression Systems: Overview and Recent Advances. Mol Biotechnol 2019; 61:365-384. [PMID: 30805909 DOI: 10.1007/s12033-019-00164-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Yeasts are outstanding hosts for the production of functional recombinant proteins with industrial or medical applications. Great attention has been emerged on yeast due to the inherent advantages and new developments in this host cell. For the production of each specific product, the most appropriate expression system should be identified and optimized both on the genetic and fermentation levels, considering the features of the host, vector and expression strategies. Currently, several new systems are commercially available; some of them are private and need licensing. The potential for secretory expression of heterologous proteins in yeast proposed this system as a candidate for the production of complex eukaryotic proteins. The common yeast expression hosts used for recombinant proteins' expression include Saccharomyces cerevisiae, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, Arxula adeninivorans, Kluyveromyces lactis, and Schizosaccharomyces pombe. This review is dedicated to discuss on significant characteristics of the most common methylotrophic and non-methylotrophic yeast expression systems with an emphasis on their advantages and new developments.
Collapse
Affiliation(s)
- Roghayyeh Baghban
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran. .,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak, Arabi Ave, Tehran, Iran. .,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - AmirAli Mafi
- Anesthesiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reyhaneh Hoseinpoor
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Aria
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran
| |
Collapse
|
15
|
Palma ML, Garcia-Bates TM, Martins FS, Douradinha B. Genetically engineered probiotic Saccharomyces cerevisiae strains mature human dendritic cells and stimulate Gag-specific memory CD8 + T cells ex vivo. Appl Microbiol Biotechnol 2019; 103:5183-5192. [PMID: 31020381 DOI: 10.1007/s00253-019-09842-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
Recombinant Saccharomyces cerevisiae strains expressing HIV antigens have shown promising pre-clinical results. Probiotic S. cerevisiae strains naturally induce gut immunity; thus, genetically engineered probiotic strains could be used to stimulate immune responses against HIV in the mucosa. Probiotic strains have a higher rate of heterologous protein production, meaning higher antigen's epitope expression levels per yeast cell. We expressed HIV-1 Gag protein in the probiotic yeasts' surface, which was eagerly phagocytosed by and induced type 1 polarization of human monocyte-derived dendritic cells (DCs) from healthy donors in vitro. We further matured DCs derived from HIV-1+ donors with transformed yeasts and incubated them with autologous T cells. Only DCs matured with Gag-expressing probiotic strains were able to efficiently present antigen to CD8+ T cells and induced their clonal expansion. Our results show that genetically engineered probiotic S. cerevisiae strains are a promising vaccination strategy against HIV.
Collapse
Affiliation(s)
- Mariana L Palma
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, 15261, USA
| | - Tatiana M Garcia-Bates
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, 15261, USA
| | - Flaviano S Martins
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Bruno Douradinha
- Unità di Medicina Rigenerativa ed Immunologia, Fondazione Ri.MED c/o IRCCS-ISMETT, Via Ernesto Tricomi 5, 90127, Palermo, Italy.
| |
Collapse
|
16
|
Metabolic engineering of Saccharomyces cerevisiae for efficient production of endocrocin and emodin. Metab Eng 2019; 54:212-221. [PMID: 31028901 DOI: 10.1016/j.ymben.2019.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/16/2019] [Accepted: 04/20/2019] [Indexed: 11/22/2022]
Abstract
The anthraquinones endocrocin and emodin are synthesized by a special class of type I NR-PKSs and a discrete MβL-TE. In this work, we first reconstituted a biosynthetic pathway of endocrocin and emodin in S. cerevisiae by combining enzymes from different sources. We functionally characterized a TE-less NR-PKS (SlACAS) and a MβL-TE (SlTE) from S. lycopersici as well as four orthologous MβL-TEs. SlACAS was coexpressed with different MβL-TEs in S. cerevisiae. SlACAS generated the highest amount of endocrocin when coupled with HyTE, the yield was 115.6% higher than that with the native SlTE. To accumulate more emodin, seven decarboxylases with high homology to HyDC were identified and introduced into the biosynthetic pathway. Among these orthologs, AfDC exhibited the highest catalytic activity and the conversion rate reached 98.6%. A double-point mutant acetyl-CoA carboxylase, ACC1S659A, S1157A, was further introduced to increase the production of malonyl-CoA as a precursor of these anthraquinones. The production of endocrocin (233.6 ± 20.3 mg/L) and emodin (253.2 ± 21.7 mg/L) then dramatically increased. We also optimized the carbon source in the medium and conducted fed-batch fermentation with the engineered strains. The titers of endocrocin and emodin obtained were 661.2 ± 50.5 mg/L and 528.4 ± 62.7 mg/L, respectively, which are higher than previously reported. In this work, by screening a small library of orthologous biosynthetic bricks, an efficient biosynthetic pathway of endocrocin and emodin was first created in S. cerevisiae. This study provides a novel metabolic engineering approach for optimization of the production of desired molecules.
Collapse
|
17
|
Qiao J, Luo Z, Gu Z, Zhang Y, Zhang X, Ma X. Identification of a Novel Specific Cucurbitadienol Synthase Allele in Siraitia grosvenorii Correlates with High Catalytic Efficiency. Molecules 2019; 24:E627. [PMID: 30754652 PMCID: PMC6384864 DOI: 10.3390/molecules24030627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/20/2019] [Accepted: 01/24/2019] [Indexed: 01/17/2023] Open
Abstract
Mogrosides, the main bioactive compounds isolated from the fruits of Siraitia grosvenorii, are a group of cucurbitane-type triterpenoid glycosides that exhibit a wide range of notable biological activities and are commercially available worldwide as natural sweeteners. However, the extraction cost is high due to their relatively low contents in plants. Therefore, molecular breeding needs to be achieved when conventional plant breeding can hardly improve the quality so far. In this study, the levels of 21 active mogrosides and two precursors in 15 S. grosvenorii varieties were determined by HPLC-MS/MS and GC-MS, respectively. The results showed that the variations in mogroside V content may be caused by the accumulation of cucurbitadienol. Furthermore, a total of four wild-type cucurbitadienol synthase protein variants (50R573L, 50C573L, 50R573Q, and 50C573Q) based on two missense mutation single nucleotide polymorphism (SNP) sites were discovered. An in vitro enzyme reaction analysis indicated that 50R573L had the highest activity, with a specific activity of 10.24 nmol min-1 mg-1. In addition, a site-directed mutant, namely, 50K573L, showed a 33% enhancement of catalytic efficiency compared to wild-type 50R573L. Our findings identify a novel cucurbitadienol synthase allele correlates with high catalytic efficiency. These results are valuable for the molecular breeding of luohanguo.
Collapse
Affiliation(s)
- Jing Qiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Zuliang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Zhe Gu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | | | - Xindan Zhang
- Guilin GFS Monk Fruit Corp., Guilin 541006, China.
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| |
Collapse
|
18
|
High-affinity transport, cyanide-resistant respiration, and ethanol production under aerobiosis underlying efficient high glycerol consumption by Wickerhamomyces anomalus. J Ind Microbiol Biotechnol 2019; 46:709-723. [PMID: 30680472 DOI: 10.1007/s10295-018-02119-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/19/2018] [Indexed: 01/11/2023]
Abstract
Wickerhamomyces anomalus strain LBCM1105 was originally isolated from the wort of cachaça (the Brazilian fermented sugarcane juice-derived Brazilian spirit) and has been shown to grow exceptionally well at high amounts of glycerol. This paramount residue from the biodiesel industry is a promising cheap carbon source for yeast biotechnology. The assessment of the physiological traits underlying the W. anomalus glycerol consumption ability in opposition to Saccharomyces cerevisiae is presented. A new WaStl1 concentrative glycerol-H+ symporter with twice the affinity of S. cerevisiae was identified. As in this yeast, WaSTL1 is repressed by glucose and derepressed/induced by glycerol but much more highly expressed. Moreover, LBCM1105 aerobically growing on glycerol was found to produce ethanol, providing a redox escape to compensate the redox imbalance at the level of cyanide-resistant respiration (CRR) and glycerol 3P shuttle. This work is critical for understanding the utilization of glycerol by non-Saccharomyces yeasts being indispensable to consider their industrial application feeding on biodiesel residue.
Collapse
|
19
|
Qiao J, Luo Z, Cui S, Zhao H, Tang Q, Mo C, Ma X, Ding Z. Modification of isoprene synthesis to enable production of curcurbitadienol synthesis in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2018; 46:147-157. [PMID: 30535727 DOI: 10.1007/s10295-018-2116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/27/2018] [Indexed: 12/23/2022]
Abstract
Cucurbitane-type triterpenoids such as mogrosides and cucurbitacins that are present in the plants of Cucurbitaceae are widely used in Asian traditional medicine. Cucurbitadienol is the skeleton of cucurbitane-type triterpenoids. As an alternative production strategy, we developed baker's yeast Saccharomyces cerevisiae as a microbial host for the eventual transformation of cucurbitadienol. The synthetic pathway of cucurbitadienol was constructed in Saccharomyces cerevisiae by introducing the cucurbitadienol synthase gene from different plants, resulting in 7.80 mg cucurbitadienol from 1 L of fermentation broth. Improving supplies of isoprenoid precursors was then investigated for increasing cucurbitadienol production. Cucurbitadienol production increased to 21.47 mg/L through the overexpression of a global regulatory factor (UPC2) gene of triterpenoid synthase. In addition, knockout of the ERG7 gene increased cucurbitadienol production from 21.47 to 61.80 mg/L. Finally, fed-batch fermentation was performed, and 63.00 mg/L cucurbitadienol was produced. This work is an important step towards the total biosynthesis of valuable cucurbitane-type triterpenoids and demonstrates the potential for developing a sustainable and secure yeast biomanufacturing platform for triterpenoids.
Collapse
Affiliation(s)
- Jing Qiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Zuliang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Shengrong Cui
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Huan Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qi Tang
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resources and Initiative and Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Changming Mo
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Zimian Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|
20
|
Identification of Key Amino Acid Residues Determining Product Specificity of 2,3-Oxidosqualene Cyclase in Siraitia grosvenorii. Catalysts 2018. [DOI: 10.3390/catal8120577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sterols and triterpenes are structurally diverse bioactive molecules generated through cyclization of linear 2,3-oxidosqualene. Based on carbocationic intermediates generated during the initial substrate preorganization step, oxidosqualene cyclases (OSCs) are roughly segregated into a dammarenyl cation group that predominantly catalyzes triterpenoid precursor products and a protosteryl cation group which mostly generates sterol precursor products. The mechanism of conversion between two scaffolds is not well understood. Previously, we have characterized a promiscuous OSC from Siraitia grosvenorii (SgCS) that synthesizes a novel cucurbitane-type triterpene cucurbitadienol as its main product. By integration of homology modeling, molecular docking and site-directed mutagenesis, we discover that five key amino acid residues (Asp486, Cys487, Cys565, Tyr535, and His260) may be responsible for interconversions between chair–boat–chair and chair–chair–chair conformations. The discovery of euphol, dihydrolanosterol, dihydroxyeuphol and tirucallenol unlocks a new path to triterpene diversity in nature. Our findings also reveal mechanistic insights into the cyclization of oxidosqualene into cucurbitane-type and lanostane-type skeletons, and provide a new strategy to identify key residues determining OSC specificity.
Collapse
|
21
|
Vogl T, Kickenweiz T, Pitzer J, Sturmberger L, Weninger A, Biggs BW, Köhler EM, Baumschlager A, Fischer JE, Hyden P, Wagner M, Baumann M, Borth N, Geier M, Ajikumar PK, Glieder A. Engineered bidirectional promoters enable rapid multi-gene co-expression optimization. Nat Commun 2018; 9:3589. [PMID: 30181586 DOI: 10.1038/s41467-018-0591-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/25/2018] [Indexed: 05/22/2023] Open
Abstract
Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature's use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications.
Collapse
Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Thomas Kickenweiz
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Julia Pitzer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | - Lukas Sturmberger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | - Astrid Weninger
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Bradley W Biggs
- Manus Biosynthesis, 1030 Massachusetts Avenue, Suite 300, Cambridge, MA, 02138, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Eva-Maria Köhler
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Armin Baumschlager
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Jasmin Elgin Fischer
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Patrick Hyden
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Marlies Wagner
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martina Geier
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | | | - Anton Glieder
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| |
Collapse
|
22
|
Engineered bidirectional promoters enable rapid multi-gene co-expression optimization. Nat Commun 2018; 9:3589. [PMID: 30181586 PMCID: PMC6123417 DOI: 10.1038/s41467-018-05915-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/25/2018] [Indexed: 01/24/2023] Open
Abstract
Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature’s use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications. Classic monodirectional promoters are of limited use for multiple gene co-expression. Here the authors generate a library of 168 bidirectional promoters for the yeast K. phaffii (syn. P. pastoris) with diverse expression profiles to optimize metabolic pathway design.
Collapse
|
23
|
Paramasivan K, Mutturi S. Regeneration of NADPH Coupled with HMG-CoA Reductase Activity Increases Squalene Synthesis in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8162-8170. [PMID: 28845666 DOI: 10.1021/acs.jafc.7b02945] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although overexpression of the tHMG1 gene is a well-known strategy for terpene synthesis in Saccharomyces cerevisiae, the optimal level for tHMG1p has not been established. In the present study, it was observed that two copies of the tHMG1 gene on a dual gene expression cassette improved squalene synthesis in laboratory strain by 16.8-fold in comparison to single-copy expression. It was also observed that tHMG1p is limited by its cofactor (NADPH), as the overexpression of NADPH regenerating genes', viz., ZWF1 and POS5 (full length and without mitochondrial presequence), has led to its increased enzyme activity. Further, it was demonstrated that overexpression of full-length POS5 has improved squalene synthesis in cytosol. Finally, when tHMG1 and full-length POS5 were co-overexpressed there was a net 27.5-fold increase in squalene when compared to control strain. These results suggest novel strategies to increase squalene accumulation in S. cerevisiae.
Collapse
Affiliation(s)
- Kalaivani Paramasivan
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute , Mysore, India
- Academy of Scientific and Innovative Research , Mysore, New Delhi, India
| | - Sarma Mutturi
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute , Mysore, India
- Academy of Scientific and Innovative Research , Mysore, New Delhi, India
| |
Collapse
|
24
|
Öztürk S, Ergün BG, Çalık P. Double promoter expression systems for recombinant protein production by industrial microorganisms. Appl Microbiol Biotechnol 2017; 101:7459-7475. [DOI: 10.1007/s00253-017-8487-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 01/19/2023]
|
25
|
Hochrein L, Machens F, Gremmels J, Schulz K, Messerschmidt K, Mueller-Roeber B. AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies. Nucleic Acids Res 2017; 45:e80. [PMID: 28130422 PMCID: PMC5449548 DOI: 10.1093/nar/gkx034] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/13/2017] [Indexed: 11/20/2022] Open
Abstract
The assembly of large DNA constructs coding for entire pathways poses a major challenge in the field of synthetic biology. Here, we present AssemblX, a novel, user-friendly and highly efficient multi-gene assembly strategy. The software-assisted AssemblX process allows even unexperienced users to rapidly design, build and test DNA constructs with currently up to 25 functional units, from 75 or more subunits. At the gene level, AssemblX uses scar-free, overlap-based and sequence-independent methods, allowing the unrestricted design of transcriptional units without laborious parts domestication. The assembly into multi-gene modules is enabled via a standardized, highly efficient, polymerase chain reaction-free and virtually sequence-independent scheme, which relies on rare cutting restriction enzymes and optimized adapter sequences. Selection and marker switching strategies render the whole process reliable, rapid and very effective. The assembly product can be easily transferred to any desired expression host, making AssemblX useful for researchers from various fields.
Collapse
Affiliation(s)
- Lena Hochrein
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Fabian Machens
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Juergen Gremmels
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Karina Schulz
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Katrin Messerschmidt
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.,University of Potsdam, Department of Molecular Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| |
Collapse
|
26
|
Lyu X, Ng KR, Lee JL, Mark R, Chen WN. Enhancement of Naringenin Biosynthesis from Tyrosine by Metabolic Engineering of Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6638-6646. [PMID: 28707470 DOI: 10.1021/acs.jafc.7b02507] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Flavonoids are an important class of plant polyphenols that possess a variety of health benefits. In this work, S. cerevisiae was metabolically engineered to produce the flavonoid naringenin, using tyrosine as the precursor. Our strategy to improve naringenin production comprised three modules. In module 1, we employed a modified GAL system to overexpress the genes of the naringenin biosynthesis pathway and investigated their synergistic action. In module 2, we simultaneously up-regulated acetyl-CoA production and down-regulated fatty acid biosynthesis in order to increase the precursor supply, malonyl-CoA. In module 3, we engineered the tyrosine biosynthetic pathway to eliminate the feedback inhibition of tyrosine and also down-regulated competing pathways. It was found that modules 1 and 3 played important roles in improving naringenin production. We succeeded in producing up to ∼90 mg/L of naringenin in our final strain, which is a 20-fold increase as compared to the parental strain.
Collapse
Affiliation(s)
- Xiaomei Lyu
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University , 62 Nanyang Drive, Singapore 637459, Singapore
| | - Kuan Rei Ng
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University , 62 Nanyang Drive, Singapore 637459, Singapore
| | - Jie Lin Lee
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University , 62 Nanyang Drive, Singapore 637459, Singapore
| | - Rita Mark
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University , 62 Nanyang Drive, Singapore 637459, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University , 62 Nanyang Drive, Singapore 637459, Singapore
| |
Collapse
|
27
|
Paramasivan K, Mutturi S. Progress in terpene synthesis strategies through engineering of Saccharomyces cerevisiae. Crit Rev Biotechnol 2017; 37:974-989. [DOI: 10.1080/07388551.2017.1299679] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Sarma Mutturi
- CSIR-Central Food Technological Research Institute, Mysore, India
| |
Collapse
|
28
|
Gnügge R, Rudolf F. Saccharomyces cerevisiaeShuttle vectors. Yeast 2017; 34:205-221. [DOI: 10.1002/yea.3228] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 01/25/2023] Open
Affiliation(s)
- Robert Gnügge
- D-BSSE; ETH Zurich and Swiss Institute of Bioinformatics; Zurich Switzerland
- Life Science Zurich PhD Program on Molecular and Translational Biomedicine; Zurich Switzerland
- Competence Centre for Personalized Medicine; Zurich Switzerland
| | - Fabian Rudolf
- D-BSSE; ETH Zurich and Swiss Institute of Bioinformatics; Zurich Switzerland
| |
Collapse
|
29
|
Peng B, Plan MR, Chrysanthopoulos P, Hodson MP, Nielsen LK, Vickers CE. A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metab Eng 2017; 39:209-219. [DOI: 10.1016/j.ymben.2016.12.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/17/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
|
30
|
Zhang GC, Kong II, Wei N, Peng D, Turner TL, Sung BH, Sohn JH, Jin YS. Optimization of an acetate reduction pathway for producing cellulosic ethanol by engineered yeast. Biotechnol Bioeng 2016; 113:2587-2596. [DOI: 10.1002/bit.26021] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Guo-Chang Zhang
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - In Iok Kong
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences; University of Notre Dame; South Bend Indiana
| | - Dairong Peng
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Timothy L. Turner
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center; Korea Research Institute of Bioscience and Biotechnology; Daejeon Korea
| | - Jung-Hoon Sohn
- Bioenergy and Biochemical Research Center; Korea Research Institute of Bioscience and Biotechnology; Daejeon Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois
| |
Collapse
|
31
|
Yeast Expression Systems for Industrial Biotechnology. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
32
|
Li L, Yang T, Hu C, Ju X, Hu C, Tang B. Transformation of the yeast Trichosporonoides oedocephalis. Antonie van Leeuwenhoek 2015; 109:305-9. [PMID: 26671413 DOI: 10.1007/s10482-015-0633-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
The osmotolerant yeast, Trichosporonoides oedocephalis, is an excellent producer of erythritol, which has wide industrial applications. In this study, we developed an efficient transformation method for T. oedocephalis. To evaluate the T. oedocephalis transformation, we constructed a DNA fragment (loxP-Kan-loxP/Cre system) that was targeted to the mitogen-activated protein kinase HOG1 gene. Transformants were selected on plates containing G418 and response surface methodology was employed to obtain optimum transformation conditions. Optimal transformation could be achieved at an incubation time of 40 min, when the concentration of zymolyase-100T was 30 µg/mL, and when 100 mM CaCl2 was added to the mixture. The predicted optimal transformation efficiency was 133 transformants per µg of DNA. This novel method will facilitate studies in synthetic biology and metabolic engineering of T. oedocephalis.
Collapse
Affiliation(s)
- Liangzhi Li
- School of Chemistry and Bioengineering, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China. .,Key Laboratory of New Energy and Low-carbon Technology of Suzhou City, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Tianyi Yang
- School of Chemistry and Bioengineering, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| | - Chao Hu
- School of Chemistry and Bioengineering, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.,School of Materials, University of Manchester, Manchester, M13 9PL, UK
| | - Xin Ju
- School of Chemistry and Bioengineering, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| | - Cuiying Hu
- School of Chemistry and Bioengineering, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| | - Bingyu Tang
- School of Chemistry and Bioengineering, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| |
Collapse
|
33
|
Stovicek V, Borja GM, Forster J, Borodina I. EasyClone 2.0: expanded toolkit of integrative vectors for stable gene expression in industrial Saccharomyces cerevisiae strains. J Ind Microbiol Biotechnol 2015; 42:1519-31. [PMID: 26376869 PMCID: PMC4607720 DOI: 10.1007/s10295-015-1684-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/02/2015] [Indexed: 12/29/2022]
Abstract
Saccharomyces cerevisiae is one of the key cell factories for production of chemicals and active pharmaceuticals. For large-scale fermentations, particularly in biorefinery applications, it is desirable to use stress-tolerant industrial strains. However, such strains are less amenable for metabolic engineering than the standard laboratory strains. To enable easy delivery and overexpression of genes in a wide range of industrial S. cerevisiae strains, we constructed a set of integrative vectors with long homology arms and dominant selection markers. The vectors integrate into previously validated chromosomal locations via double cross-over and result in homogenous stable expression of the integrated genes, as shown for several unrelated industrial strains. Cre-mediated marker rescue is possible for removing markers positioned on different chromosomes. To demonstrate the applicability of the presented vector set for metabolic engineering of industrial yeast, we constructed xylose-utilizing strains overexpressing xylose isomerase, xylose transporter and five genes of the pentose phosphate pathway.
Collapse
Affiliation(s)
- Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark
| | - Gheorghe M Borja
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark
| | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark.
| |
Collapse
|
34
|
Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins. Proc Natl Acad Sci U S A 2015; 112:10685-90. [PMID: 26261310 DOI: 10.1073/pnas.1505315112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aerobic respiration is a fundamental energy-generating process; however, there is cost associated with living in an oxygen-rich environment, because partially reduced oxygen species can damage cellular components. Organisms evolved enzymes that alleviate this damage and protect the intracellular milieu, most notably thiol peroxidases, which are abundant and conserved enzymes that mediate hydrogen peroxide signaling and act as the first line of defense against oxidants in nearly all living organisms. Deletion of all eight thiol peroxidase genes in yeast (∆8 strain) is not lethal, but results in slow growth and a high mutation rate. Here we characterized mechanisms that allow yeast cells to survive under conditions of thiol peroxidase deficiency. Two independent ∆8 strains increased mitochondrial content, altered mitochondrial distribution, and became dependent on respiration for growth but they were not hypersensitive to H2O2. In addition, both strains independently acquired a second copy of chromosome XI and increased expression of genes encoded by it. Survival of ∆8 cells was dependent on mitochondrial cytochrome-c peroxidase (CCP1) and UTH1, present on chromosome XI. Coexpression of these genes in ∆8 cells led to the elimination of the extra copy of chromosome XI and improved cell growth, whereas deletion of either gene was lethal. Thus, thiol peroxidase deficiency requires dosage compensation of CCP1 and UTH1 via chromosome XI aneuploidy, wherein these proteins support hydroperoxide removal with the reducing equivalents generated by the electron transport chain. To our knowledge, this is the first evidence of adaptive aneuploidy counteracting oxidative stress.
Collapse
|
35
|
Peng B, Williams TC, Henry M, Nielsen LK, Vickers CE. Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microb Cell Fact 2015; 14:91. [PMID: 26112740 PMCID: PMC4480987 DOI: 10.1186/s12934-015-0278-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background Predictable control of gene expression is necessary for the rational design and optimization of cell factories. In the yeast Saccharomyces cerevisiae, the promoter is one of the most important tools available for controlling gene expression. However, the complex expression patterns of yeast promoters have not been fully characterised and compared on different carbon sources (glucose, sucrose, galactose and ethanol) and across the diauxic shift in glucose batch cultivation. These conditions are of importance to yeast cell factory design because they are commonly used and encountered in industrial processes. Here, the activities of a series of “constitutive” and inducible promoters were characterised in single cells throughout the fermentation using green fluorescent protein (GFP) as a reporter. Results The “constitutive” promoters, including glycolytic promoters, transcription elongation factor promoters and ribosomal promoters, differed in their response patterns to different carbon sources; however, in glucose batch cultivation, expression driven by these promoters decreased sharply as glucose was depleted and cells moved towards the diauxic shift. Promoters induced at low-glucose levels (PHXT7, PSSA1 and PADH2) varied in induction strength on non-glucose carbon sources (sucrose, galactose and ethanol); in contrast to the “constitutive” promoters, GFP expression increased as glucose decreased and cells moved towards the diauxic shift. While lower than several “constitutive” promoters during the exponential phase, expression from the SSA1 promoter was higher in the post-diauxic phase than the commonly-used TEF1 promoter. The galactose-inducible GAL1 promoter provided the highest GFP expression on galactose, and the copper-inducible CUP1 promoter provided the highest induced GFP expression following the diauxic shift. Conclusions The data provides a foundation for predictable and optimised control of gene expression levels on different carbon sources and throughout batch fermentation, including during and after the diauxic shift. This information can be applied for designing expression approaches to improve yields, rates and titres in yeast cell factories. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0278-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Thomas C Williams
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Matthew Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| |
Collapse
|
36
|
Ignea C, Ioannou E, Georgantea P, Loupassaki S, Trikka FA, Kanellis AK, Makris AM, Roussis V, Kampranis SC. Reconstructing the chemical diversity of labdane-type diterpene biosynthesis in yeast. Metab Eng 2015; 28:91-103. [DOI: 10.1016/j.ymben.2014.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/09/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023]
|
37
|
Production of Industrially Relevant Isoprenoid Compounds in Engineered Microbes. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
38
|
Protocols for the Production and Analysis of Isoprenoids in Bacteria and Yeast. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
39
|
Thiol peroxidase deficiency leads to increased mutational load and decreased fitness in Saccharomyces cerevisiae. Genetics 2014; 198:905-17. [PMID: 25173844 DOI: 10.1534/genetics.114.169243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiol peroxidases are critical enzymes in the redox control of cellular processes that function by reducing low levels of hydroperoxides and regulating redox signaling. These proteins were also shown to regulate genome stability, but how their dysfunction affects the actual mutations in the genome is not known. Saccharomyces cerevisiae has eight thiol peroxidases of glutathione peroxidase and peroxiredoxin families, and the mutant lacking all these genes (∆8) is viable. In this study, we employed two independent ∆8 isolates to analyze the genome-wide mutation spectrum that results from deficiency in these enzymes. Deletion of these genes was accompanied by a dramatic increase in point mutations, many of which clustered in close proximity and scattered throughout the genome, suggesting strong mutational bias. We further subjected multiple lines of wild-type and ∆8 cells to long-term mutation accumulation, followed by genome sequencing and phenotypic characterization. ∆8 lines showed a significant increase in nonrecurrent point mutations and indels. The original ∆8 cells exhibited reduced growth rate and decreased life span, which were further reduced in all ∆8 mutation accumulation lines. Although the mutation spectrum of the two independent isolates was different, similar patterns of gene expression were observed, suggesting the direct contribution of thiol peroxidases to the observed phenotypes. Expression of a single thiol peroxidase could partially restore the growth phenotype of ∆8 cells. This study shows how deficiency in nonessential, yet critical and conserved oxidoreductase function, leads to increased mutational load and decreased fitness.
Collapse
|
40
|
Vickers CE, Bongers M, Liu Q, Delatte T, Bouwmeester H. Metabolic engineering of volatile isoprenoids in plants and microbes. PLANT, CELL & ENVIRONMENT 2014; 37:1753-75. [PMID: 24588680 DOI: 10.1111/pce.12316] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 05/09/2023]
Abstract
The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids.
Collapse
Affiliation(s)
- Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | | | | | | | | |
Collapse
|