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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.
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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
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2
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Ramachandra Rao S, Skelton LA, Wu F, Onysk A, Spolnik G, Danikiewicz W, Butler MC, Stacks DA, Surmacz L, Mu X, Swiezewska E, Pittler SJ, Fliesler SJ. Retinal Degeneration Caused by Rod-Specific Dhdds Ablation Occurs without Concomitant Inhibition of Protein N-Glycosylation. iScience 2020; 23:101198. [PMID: 32526701 PMCID: PMC7287266 DOI: 10.1016/j.isci.2020.101198] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/10/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) catalyzes the committed step in dolichol synthesis. Recessive mutations in DHDDS cause retinitis pigmentosa (RP59), resulting in blindness. We hypothesized that rod photoreceptor-specific ablation of Dhdds would cause retinal degeneration due to diminished dolichol-dependent protein N-glycosylation. Dhddsflx/flx mice were crossed with rod-specific Cre recombinase-expressing (Rho-iCre75) mice to generate rod-specific Dhdds knockout mice (Dhddsflx/flx iCre+). In vivo morphological and electrophysiological evaluation of Dhddsflx/flx iCre+ retinas revealed mild retinal dysfunction at postnatal (PN) 4 weeks, compared with age-matched controls; however, rapid photoreceptor degeneration ensued, resulting in almost complete loss of rods and cones by PN 6 weeks. Retina dolichol levels were markedly decreased by PN 4 weeks in Dhddsflx/flx iCre+ mice, relative to controls; despite this, N-glycosylation of retinal proteins, including opsin (the dominant rod-specific glycoprotein), persisted in Dhddsflx/flx iCre+ mice. These findings challenge the conventional mechanistic view of RP59 as a congenital disorder of glycosylation. Deletion of Dhdds in rod cells caused rapid retinal degeneration in mice Retinal dolichol levels markedly decreased before onset of degeneration Protein N-glycosylation was uncompromised despite Dhdds deletion Degeneration also involved gliosis, microglial activation, and phagoptosis
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Affiliation(s)
- Sriganesh Ramachandra Rao
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Lara A Skelton
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Agnieszka Onysk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Spolnik
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 02106, Poland
| | - Witold Danikiewicz
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 02106, Poland
| | - Mark C Butler
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA
| | - Delores A Stacks
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Steven J Pittler
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Steven J Fliesler
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA.
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3
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Guo X, Shen H, Liu Y, Wang Q, Wang X, Peng C, Liu W, Zhao ZK. Enabling Heterologous Synthesis of Lupulones in the Yeast Saccharomyces cerevisiae. Appl Biochem Biotechnol 2019; 188:787-797. [PMID: 30684240 DOI: 10.1007/s12010-019-02957-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/11/2019] [Indexed: 01/26/2023]
Abstract
Lupulones, naturally produced by glandular trichomes of hop (Humulus lupulus), are prenylated phloroglucinol derivatives that contribute the bitter flavor of beer and demonstrate antimicrobial and anticancer activities. It is appealing to develop microbial cell factories such that lupulones may be produced via fermentation technology in lieu of extraction from limited plant resources. In this study, the yeast Saccharomyces cerevisiae transformants harboring a synthetic lupulone pathway that consisted of five genes from hop were constructed. The transformants accumulated several precursors but failed to accumulate lupulones. Overexpression of 3-hydroxy-3-methyl glutaryl co-enzyme A reductase, the key enzyme in precursor formation in the mevalonate pathway, also failed to achieve a detectable level of lupulones. To decrease the consumption of the precursors, the ergosterol biosynthesis pathway was chemically downregulated by a small molecule ketoconazole, leading to successful production of lupulones. Our study demonstrated a combination of molecular biology and chemical biology to regulate the metabolism for heterologous production of lupulones. The strategy may be valuable for future engineering microbial process for other prenylated natural products.
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Affiliation(s)
- Xiaojia Guo
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Shen
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yuxue Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xueying Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chang Peng
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zongbao K Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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4
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Dižová S, Černáková L, Bujdáková H. The impact of farnesol in combination with fluconazole on Candida albicans biofilm: regulation of ERG20, ERG9, and ERG11 genes. Folia Microbiol (Praha) 2017; 63:363-371. [DOI: 10.1007/s12223-017-0574-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 11/28/2017] [Indexed: 11/30/2022]
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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]
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Grabińska KA, Park EJ, Sessa WC. cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases. J Biol Chem 2016; 291:18582-90. [PMID: 27402831 PMCID: PMC5000101 DOI: 10.1074/jbc.r116.739490] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze consecutive condensation reactions of allylic diphosphate acceptor with isopentenyl diphosphate (IPP) in the cis (Z) configuration to generate linear polyprenyl diphosphate. The chain lengths of isoprenoid carbon skeletons vary widely from neryl pyrophosphate (C10) to natural rubber (C>10,000). The homo-dimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS), has been structurally and mechanistically characterized in great detail and serves as a model for understanding the mode of action of eukaryotic cis-PTs. However, recent experiments have revealed that mammals, fungal, and long-chain plant cis-PTs are heteromeric enzymes composed of two distantly related subunits. In this review, the classification, function, and evolution of cis-PTs will be discussed with a special emphasis on the role of the newly described NgBR/Nus1 subunit and its plants' orthologs as essential, structural components of the cis-PTs activity.
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Affiliation(s)
- Kariona A Grabińska
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eon Joo Park
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520
| | - William C Sessa
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520
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7
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Enhanced production of β-carotene in recombinant Saccharomyces cerevisiae by inverse metabolic engineering with supplementation of unsaturated fatty acids. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Zhang Q, Huang L, Zhang C, Xie P, Zhang Y, Ding S, Xu F. Synthesis and biological activity of polyprenols. Fitoterapia 2015; 106:184-93. [PMID: 26358482 DOI: 10.1016/j.fitote.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 11/26/2022]
Abstract
The polyprenols and their derivatives are highlighted in this study. These lipid linear polymers of isoprenoid residues are widespread in nature from bacteria to human cells. This review primarily presents the synthesis and biological activities of polyprenyl derivatives. Attention is focused on the synthesis and biological activity of dolichols, polyprenyl ester derivatives and polyprenyl amines. Other polyprenyl derivatives, such as oxides of polyprenols, aromatic polyprenols, polyprenyl bromide and polyprenyl sulphates, are mentioned. It is noted that polyprenyl phosphates and polyprenyl-linked glycosylation have better antibacterial, gene therapy and immunomodulating performance, whereas polyprenyl amines have better for antibacterial and antithrombotic activity. Dolichols, polyprenyl acetic esters, polyprenyl phosphates and polyprenyl-linked glycosylation have pharmacological anti-tumour effects. Finally, the postulated prospect of polyprenols and their derivatives are discussed. Further in vivo studies on the above derivatives are needed. The compatibility of polyprenols and their derivatives with other drugs should be studied, and new preparations of polyprenyl derivatives, such as hydrogel glue and release-controlled drugs, are suggested for future research and development.
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Affiliation(s)
- Qiong Zhang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China; Beijing Forestry University, Beijing 100083, China
| | - Lixin Huang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China.
| | - Caihong Zhang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Pujun Xie
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Yaolei Zhang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Shasha Ding
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Feng Xu
- Beijing Forestry University, Beijing 100083, China
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9
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Piłsyk S, Perlińska-Lenart U, Górka-Nieć W, Graczyk S, Antosiewicz B, Zembek P, Palamarczyk G, Kruszewska JS. Overexpression of erg20 gene encoding farnesyl pyrophosphate synthase has contrasting effects on activity of enzymes of the dolichyl and sterol branches of mevalonate pathway in Trichoderma reesei. Gene 2014; 544:114-22. [PMID: 24793581 DOI: 10.1016/j.gene.2014.04.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 04/28/2014] [Accepted: 04/29/2014] [Indexed: 11/18/2022]
Abstract
The mevalonate pathway is the most diverse metabolic route resulting in the biosynthesis of at least 30,000 isoprenoid compounds, many of which, such as sterols or dolichols, are indispensable for living cells. In the filamentous fungus Trichoderma of major biotechnological interest isoprenoid metabolites are also involved in the biocontrol processes giving the mevalonate pathway an additional significance. On the other hand, little is known about genes coding for enzymes of the mevalonate pathway in Trichoderma. Here, we present cloning and functional analysis of the erg20 gene from Trichoderma reesei coding for farnesyl pyrophosphate (FPP) synthase (EC 2.5.1.10), an enzyme located at the branching point of the mevalonate pathway. Expression of the gene in a thermosensitive erg20-2 mutant of Saccharomyces cerevisiae impaired in the FPP synthase activity suppressed the thermosensitive phenotype. The same gene overexpressed in T. reesei significantly enhanced the FPP synthase activity and also stimulated the activity of cis-prenyltransferase, an enzyme of the dolichyl branch of the mevalonate pathway. Unexpectedly, the activity of squalene synthase from the other, sterol branch, was significantly decreased without, however, affecting ergosterol level.
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Affiliation(s)
- Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Urszula Perlińska-Lenart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Wioletta Górka-Nieć
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Sebastian Graczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Beata Antosiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Patrycja Zembek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Grażyna Palamarczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Joanna S Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
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Koch B, Schmidt C, Daum G. Storage lipids of yeasts: a survey of nonpolar lipid metabolism in Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. FEMS Microbiol Rev 2014; 38:892-915. [PMID: 24597968 DOI: 10.1111/1574-6976.12069] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/21/2014] [Accepted: 02/21/2014] [Indexed: 11/29/2022] Open
Abstract
Biosynthesis and storage of nonpolar lipids, such as triacylglycerols (TG) and steryl esters (SE), have gained much interest during the last decades because defects in these processes are related to severe human diseases. The baker's yeast Saccharomyces cerevisiae has become a valuable tool to study eukaryotic lipid metabolism because this single-cell microorganism harbors many enzymes and pathways with counterparts in mammalian cells. In this article, we will review aspects of TG and SE metabolism and turnover in the yeast that have been known for a long time and combine them with new perceptions of nonpolar lipid research. We will provide a detailed insight into the mechanisms of nonpolar lipid synthesis, storage, mobilization, and degradation in the yeast S. cerevisiae. The central role of lipid droplets (LD) in these processes will be addressed with emphasis on the prevailing view that this compartment is more than only a depot for TG and SE. Dynamic and interactive aspects of LD with other organelles will be discussed. Results obtained with S. cerevisiae will be complemented by recent investigations of nonpolar lipid research with Yarrowia lipolytica and Pichia pastoris. Altogether, this review article provides a comprehensive view of nonpolar lipid research in yeast.
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Affiliation(s)
- Barbara Koch
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
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11
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Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica. Appl Environ Microbiol 2013; 80:1660-9. [PMID: 24375130 DOI: 10.1128/aem.03167-13] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The codon-optimized genes crtB and crtI of Pantoea ananatis were expressed in Yarrowia lipolytica under the control of the TEF1 promoter of Y. lipolytica. Additionally, the rate-limiting genes for isoprenoid biosynthesis in Y. lipolytica, GGS1 and HMG1, were overexpressed to increase the production of lycopene. All of the genes were also expressed in a Y. lipolytica strain with POX1 to POX6 and GUT2 deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene production. Lycopene is located mainly within lipid bodies, and increased lipid body formation leads to an increase in the lycopene storage capacity of Y. lipolytica. Growth-limiting conditions increase the specific lycopene content. Finally, a yield of 16 mg g(-1) (dry cell weight) was reached in fed-batch cultures, which is the highest value reported so far for a eukaryotic host.
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Otero JM, Vongsangnak W, Asadollahi MA, Olivares-Hernandes R, Maury J, Farinelli L, Barlocher L, Østerås M, Schalk M, Clark A, Nielsen J. Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. BMC Genomics 2010; 11:723. [PMID: 21176163 PMCID: PMC3022925 DOI: 10.1186/1471-2164-11-723] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 12/22/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering. RESULTS In this work we performed whole genome high-throughput sequencing and annotation can be used to identify single nucleotide polymorphisms (SNPs) between Saccharomyces cerevisiae strains S288c and CEN.PK113-7D. The yeast strain S288c was the first eukaryote sequenced, serving as the reference genome for the Saccharomyces Genome Database, while CEN.PK113-7D is a preferred laboratory strain for industrial biotechnology research. A total of 13,787 high-quality SNPs were detected between both strains (reference strain: S288c). Considering only metabolic genes (782 of 5,596 annotated genes), a total of 219 metabolism specific SNPs are distributed across 158 metabolic genes, with 85 of the SNPs being nonsynonymous (e.g., encoding amino acid modifications). Amongst metabolic SNPs detected, there was pathway enrichment in the galactose uptake pathway (GAL1, GAL10) and ergosterol biosynthetic pathway (ERG8, ERG9). Physiological characterization confirmed a strong deficiency in galactose uptake and metabolism in S288c compared to CEN.PK113-7D, and similarly, ergosterol content in CEN.PK113-7D was significantly higher in both glucose and galactose supplemented cultivations compared to S288c. Furthermore, DNA microarray profiling of S288c and CEN.PK113-7D in both glucose and galactose batch cultures did not provide a clear hypothesis for major phenotypes observed, suggesting that genotype to phenotype correlations are manifested post-transcriptionally or post-translationally either through protein concentration and/or function. CONCLUSIONS With an intensifying need for microbial cell factories that produce a wide array of target compounds, whole genome high-throughput sequencing and annotation for SNP detection can aid in better reducing and defining the metabolic landscape. This work demonstrates direct correlations between genotype and phenotype that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at http://www.sysbio.se/cenpk.
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Affiliation(s)
- José Manuel Otero
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
- Vaccine & Biologics Process Development, Vaccine Research & Development, Merck Research Labs, West Point, PA, USA
| | - Wanwipa Vongsangnak
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Mohammad A Asadollahi
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
- Biotechnology Group, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441, Iran
| | - Roberto Olivares-Hernandes
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
| | - Jérôme Maury
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
- Fluxome Sciencies A/S, Research & Development, DK-3660 Stenlose, Denmark
| | | | | | | | - Michel Schalk
- Firmenich SA, Corporate Research & Development Division, Geneva, Switzerland
| | - Anthony Clark
- Firmenich SA, Corporate Research & Development Division, Geneva, Switzerland
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
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Paradise EM, Kirby J, Chan R, Keasling JD. Redirection of flux through the FPP branch-point inSaccharomyces cerevisiaeby down-regulating squalene synthase. Biotechnol Bioeng 2008; 100:371-8. [DOI: 10.1002/bit.21766] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Cole SL, Vassar R. Isoprenoids and Alzheimer's disease: a complex relationship. Neurobiol Dis 2006; 22:209-22. [PMID: 16406223 DOI: 10.1016/j.nbd.2005.11.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Revised: 11/04/2005] [Accepted: 11/13/2005] [Indexed: 11/22/2022] Open
Abstract
Cholesterol metabolism has been linked to Alzheimer's disease (AD) neuropathology, which is characterized by amyloid plaques, neurofibrillary tangles and neuroinflammation. Indeed, the use of statins, which inhibit cholesterol and isoprenoid biosynthesis, as potential AD therapeutics is under investigation. Whether statins offer benefit for AD will be determined by the outcome of large, placebo-controlled, randomized clinical trials. However, their use as pharmacological tools has delineated novel roles for isoprenoids in AD. Protein isoprenylation regulates multiple cellular and molecular events and here we review the complex roles of isoprenoids in AD-relevant processes and carefully evaluate isoprenoid pathways as potential AD therapeutic targets.
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Affiliation(s)
- S L Cole
- Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, IL 60611, USA.
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Maury J, Asadollahi MA, Møller K, Clark A, Nielsen J. Microbial Isoprenoid Production: An Example of Green Chemistry through Metabolic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 100:19-51. [PMID: 16270655 DOI: 10.1007/b136410] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Saving energy, cost efficiency, producing less waste, improving the biodegradability of products, potential for producing novel and complex molecules with improved properties, and reducing the dependency on fossil fuels as raw materials are the main advantages of using biotechnological processes to produce chemicals. Such processes are often referred to as green chemistry or white biotechnology. Metabolic engineering, which permits the rational design of cell factories using directed genetic modifications, is an indispensable strategy for expanding green chemistry. In this chapter, the benefits of using metabolic engineering approaches for the development of green chemistry are illustrated by the recent advances in microbial production of isoprenoids, a diverse and important group of natural compounds with numerous existing and potential commercial applications. Accumulated knowledge on the metabolic pathways leading to the synthesis of the principal precursors of isoprenoids is reviewed, and recent investigations into isoprenoid production using engineered cell factories are described.
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Affiliation(s)
- Jérôme Maury
- Center for Microbial Biotechnology, BioCentrum-DTU, Building 223, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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GrabiÅska K, Palamarczyk G. Dolichol biosynthesis in the yeastSaccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase. FEMS Yeast Res 2002. [DOI: 10.1111/j.1567-1364.2002.tb00093.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Plochocka D, Karst F, Swiezewska E, Szkopińska A. The role of ERG20 gene (encoding yeast farnesyl diphosphate synthase) mutation in long dolichol formation. Molecular modeling of FPP synthase. Biochimie 2000; 82:733-8. [PMID: 11018290 DOI: 10.1016/s0300-9084(00)01155-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The yeast Saccharomyces cerevisiae strain LB332 bearing a mutation in the ERG20 gene encoding farnesyl diphosphate synthase (FPPS) synthesizes significantly longer dolichols than the wild type strain FL100 (14-31 and 14-19 isoprene units, respectively). The measurement of the short chain prenyl alcohols excreted into the medium shows that increased amounts of geraniol, dimethylallyl and isopentenyl alcohols but not farnesol are synthesized by the mutant strain. The wild type FPPS synthesizes farnesyl diphosphate (FPP) as the only product. The K197E substitution, as opposed to F112A/F113S in avian FPPS, does not change product specificity. Consequently, the possibility that mutated yeast FPPS synthesizes longer polyprenols is unlikely. This is supported by additional evidence such as in vitro analysis of the mutated FPPS products and molecular modeling. We suggest that formation of longer dolichols in vivo is the result of a change in the isopentenyl diphosphate/farnesyl diphosphate ratio caused by the erg20 mutation which in turn affects the activity of cis-prenyltransferase.
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Affiliation(s)
- D Plochocka
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106, Warsaw, Poland
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