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Johansson SA, Dulermo T, Jann C, Smith JD, Pryszlak A, Pignede G, Schraivogel D, Colavizza D, Desfougères T, Rave C, Farwick A, Merten CA, Roy KR, Wei W, Steinmetz LM. Large scale microfluidic CRISPR screening for increased amylase secretion in yeast. Lab Chip 2023; 23:3704-3715. [PMID: 37483015 PMCID: PMC7614956 DOI: 10.1039/d3lc00111c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Key to our ability to increase recombinant protein production through secretion is a better understanding of the pathways that interact to translate, process and export mature proteins to the surrounding environment, including the supporting cellular machinery that supplies necessary energy and building blocks. By combining droplet microfluidic screening with large-scale CRISPR libraries that perturb the expression of the majority of coding and non-coding genes in S. cerevisiae, we identified 345 genes for which an increase or decrease in gene expression resulted in increased secretion of α-amylase. Our results show that modulating the expression of genes involved in the trafficking of vesicles, endosome to Golgi transport, the phagophore assembly site, the cell cycle and energy supply improve α-amylase secretion. Besides protein-coding genes, we also find multiple long non-coding RNAs enriched in the vicinity of genes associated with endosomal, Golgi and vacuolar processes. We validated our results by overexpressing or deleting selected genes, which resulted in significant improvements in α-amylase secretion. The advantages, in terms of precision and speed, inherent to CRISPR based perturbations, enables iterative testing of new strains for increased protein secretion.
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Affiliation(s)
- S Andreas Johansson
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Thierry Dulermo
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Cosimo Jann
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Justin D Smith
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Anna Pryszlak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Georges Pignede
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Didier Colavizza
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Thomas Desfougères
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Christophe Rave
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Alexander Farwick
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Christoph A Merten
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Kevin R Roy
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Wu Wei
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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Lefevre M, Racedo SM, Denayrolles M, Ripert G, Desfougères T, Lobach AR, Simon R, Pélerin F, Jüsten P, Urdaci MC. Safety assessment of Bacillus subtilis CU1 for use as a probiotic in humans. Regul Toxicol Pharmacol 2017; 83:54-65. [DOI: 10.1016/j.yrtph.2016.11.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 11/25/2022]
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Desfougères T, Haddouche R, Fudalej F, Neuvéglise C, Nicaud JM. SOA genes encode proteins controlling lipase expression in response to triacylglycerol utilization in the yeast Yarrowia lipolytica. FEMS Yeast Res 2009; 10:93-103. [PMID: 19922427 DOI: 10.1111/j.1567-1364.2009.00590.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The oleaginous yeast Yarrowia lipolytica efficiently metabolizes hydrophobic substrates such as alkanes, fatty acids or triacylglycerol. This yeast has been identified in oil-polluted water and in lipid-rich food. The enzymes involved in lipid breakdown, for use as a carbon source, are known, but the molecular mechanisms controlling the expression of the genes encoding these enzymes are still poorly understood. The study of mRNAs obtained from cells grown on oleic acid identified a new group of genes called SOA genes (specific for oleic acid). SOA1 and SOA2 are two small genes coding for proteins with no known homologs. Single- and double-disrupted strains were constructed. Wild-type and mutant strains were grown on dextrose, oleic acid and triacylglycerols. The double mutant presents a clear phenotype consisting of a growth defect on tributyrin and triolein, but not on dextrose or oleic acid media. Lipase activity was 50-fold lower in this mutant than in the wild-type strain. The impact of SOA deletion on the expression of the main extracellular lipase gene (LIP2) was monitored using a LIP2-beta-galactosidase promoter fusion protein. These data suggest that Soa proteins are components of a molecular mechanism controlling lipase gene expression in response to extracellular triacylglycerol.
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Affiliation(s)
- Thomas Desfougères
- INRA, UMR1238, CNRS, UMR2585, AgroParisTech, Laboratoire de Microbiologie et Génétique Moléculaire, Thiverval-Grignon, France
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Desfougères T, Ferreira T, Bergès T, Régnacq M. SFH2 regulates fatty acid synthase activity in the yeast Saccharomyces cerevisiae and is critical to prevent saturated fatty acid accumulation in response to haem and oleic acid depletion. Biochem J 2007; 409:299-309. [PMID: 17803462 DOI: 10.1042/bj20071028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The yeast Saccharomyces cerevisiae is a facultative anaerobic organism. Under anaerobiosis, sustained growth relies on the presence of exogenously supplied unsaturated fatty acids and ergosterol that yeast is unable to synthesize in the absence of oxygen or upon haem depletion. In the absence of exogenous supplementation with unsaturated fatty acid, a net accumulation of SFA (saturated fatty acid) is observed that induces significant modification of phospholipid profile [Ferreira, Régnacq, Alimardani, Moreau-Vauzelle and Bergès (2004) Biochem. J. 378, 899–908]. In the present paper, we focus on the role of SFH2/CSR1, a hypoxic gene related to SEC14 and its involvement in lipid metabolism upon haem depletion in the absence of oleic acid supplementation. We observed that inactivation of SFH2 results in enhanced accumulation of SFA and phospholipid metabolism alterations. It results in premature growth arrest and leads to an exacerbated sensitivity to exogenous SFA. This phenotype is suppressed in the presence of exogenous oleic acid, or by a controlled expression of FAS1, one of the two genes encoding FAS. We present several lines of evidence to suggest that Sfh2p and oleic acid regulate SFA synthase in yeast at different levels: whereas oleic acid acts on FAS2 at the transcriptional level, we show that Sfh2p inhibits fatty acid synthase activity in response to haem depletion.
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Affiliation(s)
- Thomas Desfougères
- Laboratoire de Génétique de la Levure CNRS-UMR6161, Université de Poitiers, 40 avenue du Recteur Pineau, 86022 Poitiers cedex, France
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