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Abstract
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 of the 111 genes yielded a “minimal CCM” strain which, despite the elimination of 32% of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes from the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodeling of yeast CCM.
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Kim S, Park HH. Preparation of stable recombinant Osm1 noncovalently bound with flavin adenosine dinucleotide cofactor for structural study. Acta Crystallogr F Struct Biol Commun 2019; 75:159-165. [PMID: 30839289 PMCID: PMC6404855 DOI: 10.1107/s2053230x19000190] [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: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 11/10/2022] Open
Abstract
Osm1, a soluble fumarate reductase from Saccharomyces cerevisiae, is localized in both the mitochondria and the endoplasmic reticulum (ER). OSM1 genetically interacts with ERO1, which encodes an essential ER oxidoreductase for disulfide-bond formation under anaerobic conditions. However, the detailed enzymatic mechanisms involved in this interaction and the cellular roles of Osm1 are not fully understood. In this study, monomeric and stable recombinant Osm1 was successfully prepared for structural study. During purification, it was realized that the majority of recombinant Osm1 expressed in Escherichia coli lacked the flavin adenosine dinucleotide (FAD) cofactor. However, exogenously introduced FAD could be incorporated into recombinant Osm1, generating stable and homogenous holo Osm1. Moreover, after removing a flexible fragment by limited proteolysis, holo Osm1 formed isotropic crystals that retained catalytic activity. X-ray diffraction data were successfully collected from the Osm1 crystals to a resolution of 1.75 Å.
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Affiliation(s)
- Sunghwan Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
- R&D Center, Polus Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
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3
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Schito L, Rey S. Cell-Autonomous Metabolic Reprogramming in Hypoxia. Trends Cell Biol 2017; 28:128-142. [PMID: 29191366 DOI: 10.1016/j.tcb.2017.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022]
Abstract
Molecular oxygen (O2) is a universal electron acceptor that enables ATP synthesis through mitochondrial respiration in all metazoans. Consequently, hypoxia (low O2) has arisen as an organizing principle for cellular evolution, metabolism, and (patho)biology, eliciting a remarkable panoply of metabolic adaptations that trigger transcriptional, translational, post-translational, and epigenetic responses to determine cellular fitness. In this review we summarize current and emerging cell-autonomous molecular mechanisms that induce hypoxic metabolic reprogramming in health and disease.
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Affiliation(s)
- Luana Schito
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada.
| | - Sergio Rey
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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Neal SE, Dabir DV, Wijaya J, Boon C, Koehler CM. Osm1 facilitates the transfer of electrons from Erv1 to fumarate in the redox-regulated import pathway in the mitochondrial intermembrane space. Mol Biol Cell 2017; 28:2773-2785. [PMID: 28814504 PMCID: PMC5638582 DOI: 10.1091/mbc.e16-10-0712] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 11/18/2022] Open
Abstract
Osm1 transfers electrons from fumarate to succinate and functions with Mia40 and Erv1 in the redox-regulated import pathway for proteins that form disulfide bonds in the mitochondrial intermembrane space. Expression of Osm1 and cytochrome c is reciprocally regulated, indicating that the cell has strategies to coordinate expression of terminal electron acceptors. Prokaryotes have aerobic and anaerobic electron acceptors for oxidative folding of periplasmic proteins. The mitochondrial intermembrane space has an analogous pathway with the oxidoreductase Mia40 and sulfhydryl oxidase Erv1, termed the mitochondrial intermembrane space assembly (MIA) pathway. The aerobic electron acceptors include oxygen and cytochrome c, but an acceptor that can function under anaerobic conditions has not been identified. Here we show that the fumarate reductase Osm1, which facilitates electron transfer from fumarate to succinate, fills this gap as a new electron acceptor. In addition to microsomes, Osm1 localizes to the mitochondrial intermembrane space and assembles with Erv1 in a complex. In reconstitution studies with reduced Tim13, Mia40, and Erv1, the addition of Osm1 and fumarate completes the disulfide exchange pathway that results in Tim13 oxidation. From in vitro import assays, mitochondria lacking Osm1 display decreased import of MIA substrates, Cmc1 and Tim10. Comparative reconstitution assays support that the Osm1/fumarate couple accepts electrons with similar efficiency to cytochrome c and that the cell has strategies to coordinate expression of the terminal electron acceptors. Thus Osm1/fumarate is a new electron acceptor couple in the mitochondrial intermembrane space that seems to function in both aerobic and anaerobic conditions.
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Affiliation(s)
- Sonya E Neal
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Deepa V Dabir
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045
| | - Juwina Wijaya
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Cennyana Boon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Carla M Koehler
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 .,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095
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Wang G, Huang M, Nielsen J. Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production. Curr Opin Biotechnol 2017; 48:77-84. [PMID: 28410475 DOI: 10.1016/j.copbio.2017.03.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/19/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023]
Abstract
Production of recombinant proteins by yeast plays a vital role in the biopharmaceutical industry. It is therefore desirable to develop yeast platform strains for over-production of various biopharmaceutical proteins, but this requires fundamental knowledge of the cellular machinery, especially the protein secretory pathway. Integrated analyses of multi-omics datasets can provide comprehensive understanding of cellular function, and can enable systems biology-driven and mathematical model-guided strain engineering. Rational engineering and introduction of trackable genetic modifications using synthetic biology tools, coupled with high-throughput screening are, however, also efficient approaches to relieve bottlenecks hindering high-level protein production. Here we review advances in systems biology and metabolic engineering of yeast for improving recombinant protein production.
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Affiliation(s)
- Guokun Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Mingtao Huang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark.
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6
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Heterologous expression of cellulase genes in natural Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 2016; 100:8241-54. [PMID: 27470141 DOI: 10.1007/s00253-016-7735-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/29/2016] [Accepted: 07/08/2016] [Indexed: 12/17/2022]
Abstract
Enzyme cost is a major impediment to second-generation (2G) cellulosic ethanol production. One strategy to reduce enzyme cost is to engineer enzyme production capacity in a fermentative microorganism to enable consolidated bio-processing (CBP). Ideally, a strain with a high secretory phenotype, high fermentative capacity as well as an innate robustness to bioethanol-specific stressors, including tolerance to products formed during pre-treatment and fermentation of lignocellulosic substrates should be used. Saccharomyces cerevisiae is a robust fermentative yeast but has limitations as a potential CBP host, such as low heterologous protein secretion titers. In this study, we evaluated natural S. cerevisiae isolate strains for superior secretion activity and other industrially relevant characteristics needed during the process of lignocellulosic ethanol production. Individual cellulases namely Saccharomycopsis fibuligera Cel3A (β-glucosidase), Talaromyces emersonii Cel7A (cellobiohydrolase), and Trichoderma reesei Cel5A (endoglucanase) were utilized as reporter proteins. Natural strain YI13 was identified to have a high secretory phenotype, demonstrating a 3.7- and 3.5-fold higher Cel7A and Cel5A activity, respectively, compared to the reference strain S288c. YI13 also demonstrated other industrially relevant characteristics such as growth vigor, high ethanol titer, multi-tolerance to high temperatures (37 and 40 °C), ethanol (10 % w/v), and towards various concentrations of a cocktail of inhibitory compounds commonly found in lignocellulose hydrolysates. This study accentuates the value of natural S. cerevisiae isolate strains to serve as potential robust and highly productive chassis organisms for CBP strain development.
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Eichhof I, Ernst JF. Oxygen-independent FbFP: Fluorescent sentinel and oxygen sensor component in Saccharomyces cerevisiae and Candida albicans. Fungal Genet Biol 2016; 92:14-25. [PMID: 27126475 DOI: 10.1016/j.fgb.2016.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 02/06/2023]
Abstract
FMN-binding fluorescent proteins (FbFPs) outperform GFP and its derivatives because of their oxygen-independence, small size and rapid maturation. FbFPs have been used successfully as reliable reporters of gene expression in the cytoplasm of pro- and eukaryotes. Here we extend previous findings on the codon-adapted CaFbFP variant, which functions in the apathogenic yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans. In both fungal species, CaFbFP could be targeted to the nucleus and the cell wall by endogenous signals (H2B-/Aga2-fusions) demonstrating its use as a fluorescent beacon in these relevant cellular locations. Transformants of both fungal species producing a CaFbFP-YFP fusion (YFOS) showed variable energy transfer from CaFbFP to YFP (FRET) that depended in its extent on external O2 concentrations. Applications as fluorescent sentinel and oxygen biosensor expand the FbFP toolbox to study oxygen-independent cellular processes under hypoxia.
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Affiliation(s)
- Isabel Eichhof
- Department Biologie, Molekulare Mykologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Joachim F Ernst
- Department Biologie, Molekulare Mykologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany.
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Martínez JL, Petranovic D, Nielsen J. Heme metabolism in stress regulation and protein production: From Cinderella to a key player. Bioengineered 2016; 7:112-5. [PMID: 26731643 DOI: 10.1080/21655979.2015.1126016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Heme biosynthesis is a highly conserved pathway which is present in all kingdoms, from Archaea to higher organisms such as plants and mammals. The heme molecule acts as a prosthetic group for different proteins and enzymes involved in energy metabolism and reactions involved in electron transfer. Based on our recent findings and other recent reports, we here illustrate that heme is more than a co-factor. We also discuss the necessity to gain more insight into the heme biosynthesis pathway regulation, as this interacts closely with overall stress control. Understanding heme biosynthesis and its regulation could impact our ability to develop more efficient yeast cell factories for heterologous protein production.
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Affiliation(s)
- J L Martínez
- a Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , Gothenburg , Sweden.,b Department of Biology and Biological Engineering , Chalmers University of Technology , Göteborg , Sweden
| | - D Petranovic
- a Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , Gothenburg , Sweden.,b Department of Biology and Biological Engineering , Chalmers University of Technology , Göteborg , Sweden
| | - J Nielsen
- a Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , Gothenburg , Sweden.,b Department of Biology and Biological Engineering , Chalmers University of Technology , Göteborg , Sweden.,c Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Hørsholm , Denmark
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Liu L, Zhang Y, Liu Z, Petranovic D, Nielsen J. Improving heterologous protein secretion at aerobic conditions by activating hypoxia-induced genes inSaccharomyces cerevisiae. FEMS Yeast Res 2015. [DOI: 10.1093/femsyr/fov070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Klein T, Niklas J, Heinzle E. Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J Ind Microbiol Biotechnol 2015; 42:453-64. [PMID: 25561318 DOI: 10.1007/s10295-014-1569-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022]
Abstract
Metabolic bottlenecks play an increasing role in yeasts and mammalian cells applied for high-performance production of proteins, particularly of pharmaceutical ones that require complex posttranslational modifications. We review the present status and developments focusing on the rational metabolic engineering of such cells to optimize the supply chain for building blocks and energy. Methods comprise selection of beneficial genetic modifications, rational design of media and feeding strategies. Design of better producer cells based on whole genome-wide metabolic network analysis becomes increasingly possible. High-resolution methods of metabolic flux analysis for the complex networks in these compartmented cells are increasingly available. We discuss phenomena that are common to both types of organisms but also those that are different with respect to the supply chain for the production and secretion of pharmaceutical proteins.
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Affiliation(s)
- Tobias Klein
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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Williams CC, Jan CH, Weissman JS. Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science 2014; 346:748-51. [PMID: 25378625 DOI: 10.1126/science.1257522] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nearly all mitochondrial proteins are nuclear-encoded and are targeted to their mitochondrial destination from the cytosol. Here, we used proximity-specific ribosome profiling to comprehensively measure translation at the mitochondrial surface in yeast. Most inner-membrane proteins were cotranslationally targeted to mitochondria, reminiscent of proteins entering the endoplasmic reticulum (ER). Comparison between mitochondrial and ER localization demonstrated that the vast majority of proteins were targeted to a specific organelle. A prominent exception was the fumarate reductase Osm1, known to reside in mitochondria. We identified a conserved ER isoform of Osm1, which contributes to the oxidative protein-folding capacity of the organelle. This dual localization was enabled by alternative translation initiation sites encoding distinct targeting signals. These findings highlight the exquisite in vivo specificity of organellar targeting mechanisms.
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Affiliation(s)
| | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA. These authors contributed equally to this work.
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Abu-Jamous B, Fa R, Roberts DJ, Nandi AK. Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis. BMC Bioinformatics 2014; 15:322. [PMID: 25267386 PMCID: PMC4262117 DOI: 10.1186/1471-2105-15-322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scale and complexity of genomic data lend themselves to analysis using sophisticated mathematical techniques to yield information that can generate new hypotheses and so guide further experimental investigations. An ensemble clustering method has the ability to perform consensus clustering over the same set of genes from different microarray datasets by combining results from different clustering methods into a single consensus result. RESULTS In this paper we have performed comprehensive analysis of forty yeast microarray datasets. One recently described Bi-CoPaM method can analyse expressions of the same set of genes from various microarray datasets while using different clustering methods, and then combine these results into a single consensus result whose clusters' tightness is tunable from tight, specific clusters to wide, overlapping clusters. This has been adopted in a novel way over genome-wide data from forty yeast microarray datasets to discover two clusters of genes that are consistently co-expressed over all of these datasets from different biological contexts and various experimental conditions. Most strikingly, average expression profiles of those clusters are consistently negatively correlated in all of the forty datasets while neither profile leads or lags the other. CONCLUSIONS The first cluster is enriched with ribosomal biogenesis genes. The biological processes of most of the genes in the second cluster are either unknown or apparently unrelated although they show high connectivity in protein-protein and genetic interaction networks. Therefore, it is possible that this mostly uncharacterised cluster and the ribosomal biogenesis cluster are transcriptionally oppositely regulated by some common machinery. Moreover, we anticipate that the genes included in this previously unknown cluster participate in generic, in contrast to specific, stress response processes. These novel findings illuminate coordinated gene expression in yeast and suggest several hypotheses for future experimental functional work. Additionally, we have demonstrated the usefulness of the Bi-CoPaM-based approach, which may be helpful for the analysis of other groups of (microarray) datasets from other species and systems for the exploration of global genetic co-expression.
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Affiliation(s)
- Basel Abu-Jamous
- />Department of Electronic and Computer Engineering, Brunel University, Uxbridge, Middlesex, UB8 3PH UK
| | - Rui Fa
- />Department of Electronic and Computer Engineering, Brunel University, Uxbridge, Middlesex, UB8 3PH UK
| | - David J Roberts
- />National Health Service Blood and Transplant, Oxford, UK
- />Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Asoke K Nandi
- />Department of Electronic and Computer Engineering, Brunel University, Uxbridge, Middlesex, UB8 3PH UK
- />Department of Mathematical Information Technology, University of Jyväskylä, Jyväskylä, Finland
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Martínez JL, Liu L, Petranovic D, Nielsen J. Engineering the oxygen sensing regulation results in an enhanced recombinant human hemoglobin production bySaccharomyces cerevisiae. Biotechnol Bioeng 2014; 112:181-8. [DOI: 10.1002/bit.25347] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022]
Affiliation(s)
- José L. Martínez
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
| | - Lifang Liu
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
| | - Dina Petranovic
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
- Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Fremtidsvej 3 DK-2970 Hørsholm Denmark
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Overcoming the metabolic burden of protein secretion in Schizosaccharomyces pombe – A quantitative approach using 13C-based metabolic flux analysis. Metab Eng 2014; 21:34-45. [DOI: 10.1016/j.ymben.2013.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/27/2013] [Accepted: 11/11/2013] [Indexed: 01/20/2023]
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