Yarrowia lipolytica vesicle-mediated protein transport pathways

<p>Abstract</p> <p>Background</p> <p>Protein secretion is a universal cellular process involving vesicles which bud and fuse between organelles to bring proteins to their final destination. Vesicle budding is mediated by protein coats; vesicle targeting and fusion depend on Rab GTPase, tethering factors and SNARE complexes. The Génolevures II sequencing project made available entire genome sequences of four hemiascomycetous yeasts, <it>Yarrowia lipolytica</it>, <it>Debaryomyces hansenii</it>, <it>Kluyveromyces lactis </it>and <it>Candida glabrata</it>. <it>Y. lipolytica </it>is a dimorphic yeast and has good capacities to secrete proteins. The translocation of nascent protein through the endoplasmic reticulum membrane was well studied in <it>Y. lipolytica </it>and is largely co-translational as in the mammalian protein secretion pathway.</p> <p>Results</p> <p>We identified <it>S. cerevisiae </it>proteins involved in vesicular secretion and these protein sequences were used for the BLAST searches against Génolevures protein database (<it>Y. lipolytica</it>, <it>C. glabrata</it>, <it>K. lactis </it>and <it>D. hansenii</it>). These proteins are well conserved between these yeasts and <it>Saccharomyces cerevisiae</it>. We note several specificities of <it>Y. lipolytica </it>which may be related to its good protein secretion capacities and to its dimorphic aspect. An expansion of the <it>Y. lipolytica </it>Rab protein family was observed with autoBLAST and the Rab2- and Rab4-related members were identified with BLAST against NCBI protein database. An expansion of this family is also found in filamentous fungi and may reflect the greater complexity of the <it>Y. lipolytica </it>secretion pathway. The Rab4p-related protein may play a role in membrane recycling as <it>rab4 </it>deleted strain shows a modification of colony morphology, dimorphic transition and permeability. Similarly, we find three copies of the gene (<it>SSO</it>) encoding the plasma membrane SNARE protein. Quantification of the percentages of proteins with the greatest homology between <it>S. cerevisiae, Y. lipolytica </it>and animal homologues involved in vesicular transport shows that 40% of <it>Y. lipolytica </it>proteins are closer to animal ones, whereas they are only 13% in the case of <it>S. cerevisiae</it>.</p> <p>Conclusion</p> <p>These results provide further support for the idea, previously noted about the endoplasmic reticulum translocation pathway, that <it>Y. lipolytica </it>is more representative of vesicular secretion of animals and other fungi than is <it>S. cerevisiae</it>.</p

Yarrowia lipolytica: a model organism for protein secretion studies

This paper reviews the advantages of the yeast Yarrowia lipolytica as a tool in the study of protein secretion. Work has been focused on the early steps leading the polypeptide, from the cytoplasmic ribosomes where it is synthesized, to the lumen of the endoplasmic reticulum. Using a thermosensitive allele of the 7SL RNA, the first in vivo evidence for a co-translational translocation was shown. Genetic screens allowed the identification of several new components of the translocation apparatus: Sls1p, an ER lumenal component involved in both translocation and lumenal transit; Tsr1p, involved in SRP-ribosome targeting; Tsr3p. Major translocation partners were also identified by reverse genetics (Sec61p, Sec62p, Kar2p, Srp54p, Sec65p)

TRANSLOCATION ET REPLIEMENT DES PROTEINES DANS LE LUMEN DU RETICULUM ENDOPLASMIQUE CHEZ LA LEVURE

ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Contrôle qualité des glycoprotéines chez la levure Yarrowia lipolytica

PARIS-AgroParisTech Centre Paris (751052302) / SudocSudocFranceF

Resilience in a cheese ecosystem

Resilience in a cheese ecosystem. 14. Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 201

Ecosystème fromager : de l'étude du métabolisme du soufre chez Kluyveromyces lactis et Yarrowia lipolytica à l'interaction entre Kluyveromyces lactis et Brevibacterium aurantiacum

en français : Le métabolisme du soufre, qui occupe une place centrale au sein de la cellule, est aussi important lors de la fabrication des fromages à pâte molle à croûte lavée. L'écosystème fromager assimile les acides aminés soufrés et peut ainsi produire des composés soufrés volatils (CSVs) indispensables à la flaveur de ces produits. Nous avons étudié le métabolisme du soufre chez deux micro-organismes d'affinage, les levures hémiascomycètes Kluyveromyces lactis et Yarrowia lipolytica. L'analyse in silico du phylum des hémiascomycètes nous a donné pour la première fois une vision évolutive de ce métabolisme. Nous avons relevé des différences fondamentales au niveau de la synthèse de la cystéine mais aussi au niveau des enzymes impliquées dans la production de CSVs. Cette analyse constitue une base solide pour l'étude du métabolisme du soufre. Nous avons combiné plusieurs approches exploratoires (transcriptome, métabolome, dosage des CSVs) afin d'avoir une vision globale de ce métabolisme chez K. lactis et Y.lipolytica. Les différences observées se situent notamment au niveau des voies de synthèse de la cystéine et de la taurine. La production de CSVs semble liée à la surexpression de transaminases spécifiques à chaque espèce combinée à l'accumulation de méthionine intracellulaire. L'affinage du fromage dépendant de tout un écosystème, nous avons également étudié l'interaction entre deux micro-organismes d'affinage, K. lactis et Brevibacterium aurantiacum via une approche transcriptomique, en comparant l'expression d'une co-culture à celle des cultures pures. Nous avons observé de profondes modifications métaboliques touchant notamment le métabolisme du carbone et celui de la biotine.en anglais : Sulphur metabolism, which has a central role in the cell, is also important during the manufacturing of smear ripened cheeses. The cheese ecosystem degrades sulphur aminoacids, producing volatile sulphur compounds (VSCs) indispensable for the flavour of these products. We studied sulphur metabolism in two cheese-ripening microorganisms, the hemiascomycetous yeasts Kluyveromyces lactis and Yarrowia lipolytica. The in silico analysis of the phylum of hemiascomycetes gave us for the first time an evolutionary vision of this metabolism. We found fundamental differences at the level of cysteine synthesis, but also at the level of the enzymes involved in the production of VSCs. This analysis constitutes a solid basis for the study of sulphur metabolism. Thus, we combined several exploratory approaches (transcriptome, metabolome, VSCs measurement) to have a global vision of this metabolism in K. lactis and Y. lipolytica. Major differences are observed in particular at the level of cysteine and taurine biosynthesis pathways. VSCs production seems to be connected to the surexpression of species-specific transaminases combined with the accumulation of intracellular methionine. Cheese ripening being dependent on a whole ecosystem, we also studied the interaction between two cheese-ripening microorganisms, K. lactis and Brevibacterium aurantiacum, by a transcriptomic approach comparing the genes expression of a co-culture to that of the pure cultures. We observed profound metabolic modifications especially with respect to carbon and biotin metabolisms.PARIS-AgroParisTech Centre Paris (751052302) / SudocSudocFranceF

Combining kinetic modeling and transcriptomic analysis to study the resilience 2014 on a model of microbial ecosystem

Combining kinetic modeling and transcriptomic analysis to study the resilience 2014 on a model of microbial ecosystem. ECCB'14 : European Conference on Computational Biolog