Nicaud JM

References (23)

Title : Production of Rhizopus oryzae lipase using optimized Yarrowia lipolytica expression system - Vidal_2023_FEMS.Yeast.Res_23_
Author(s) : Vidal L , Dong Z , Olofsson K , Nordberg Karlsson E , Nicaud JM
Ref : FEMS Yeast Res , 23 : , 2023
Abstract : Yarrowia lipolytica is an alternative yeast for heterologous protein production. Based on auto-cloning vectors, a set of 18 chromogenic cloning vectors was developed, each containing one of the excisable auxotrophic selective markers URA3ex, LYS5ex, and LEU2ex, and one of six different promoters: the constitutive pTEF, the phase dependent hybrid pHp4d, and the erythritol-inducible promoters from pEYK1 and pEYL1 derivatives. These vectors allowed to increase the speed of cloning of the gene of interest. In parallel, an improved new rProt recipient strain JMY8647 was developed by abolishing filamentation and introducing an auxotrophy for lysine (Lys-), providing an additional marker for genetic engineering. Using this cloning strategy, the optimal targeting sequence for Rhizopus oryzae ROL lipase secretion was determined. Among the eight targeting sequences, the SP6 signal sequence resulted in a 23% improvement in the lipase activity compared to that obtained with the wild-type ROL signal sequence. Higher specific lipase activities were obtained using hybrid erythritol-inducible promoters pHU8EYK and pEYL1-5AB, 1.9 and 2.2 times, respectively, when compared with the constitutive pTEF promoter. Two copy strains produce a 3.3 fold increase in lipase activity over the pTEF monocopy strain (266.7 versus 79.7 mU/mg).
ESTHER : Vidal_2023_FEMS.Yeast.Res_23_
PubMedSearch : Vidal_2023_FEMS.Yeast.Res_23_
PubMedID: 37496194

Title : Comprehensive Analysis of a Yeast Lipase Family in the Yarrowia Clade - Meunchan_2015_PLoS.One_10_e0143096
Author(s) : Meunchan M , Michely S , Devillers H , Nicaud JM , Marty A , Neuveglise C
Ref : PLoS ONE , 10 :e0143096 , 2015
Abstract : Lipases are currently the subject of intensive studies due to their large range of industrial applications. The Lip2p lipase from the yeast Yarrowia lipolytica (YlLIP2) was recently shown to be a good candidate for different biotechnological applications. Using a combination of comparative genomics approaches based on sequence similarity, synteny conservation, and phylogeny, we constructed the evolutionary scenario of the lipase family for six species of the Yarrowia clade. RNA-seq based transcriptome analysis revealed the primary role of LIP2 homologues in the assimilation of different substrates. Once identified, these YlLIP2 homologues were expressed in Y. lipolytica. The lipase Lip2a from Candida phangngensis was shown to naturally present better activity and enantioselectivity than YlLip2. Enantioselectivity was further improved by site-directed mutagenesis targeted to the substrate binding site. The mono-substituted variant V232S displayed enantioselectivity greater than 200 and a 2.5 fold increase in velocity. A double-substituted variant 97A-V232F presented reversed enantioselectivity, with a total preference for the R-enantiomer.
ESTHER : Meunchan_2015_PLoS.One_10_e0143096
PubMedSearch : Meunchan_2015_PLoS.One_10_e0143096
PubMedID: 26580812

Title : Draft Genome Sequence of Rhodosporidium toruloides CECT1137, an Oleaginous Yeast of Biotechnological Interest - Morin_2014_Genome.Announc_2_e00641
Author(s) : Morin N , Calcas X , Devillers H , Durrens P , Sherman DJ , Nicaud JM , Neuveglise C
Ref : Genome Announc , 2 : , 2014
Abstract : We report the sequencing of the basidiomycetous yeast Rhodosporidium toruloides CECT1137. The current assembly comprises 62 scaffolds, for a total size of ca. 20.45 Mbp and a G+C content of ca. 61.9%. The genome annotation predicts 8,206 putative protein-coding genes.
ESTHER : Morin_2014_Genome.Announc_2_e00641
PubMedSearch : Morin_2014_Genome.Announc_2_e00641
PubMedID: 25013136
Gene_locus related to this paper: rhot1-m7wd80 , rhot1-m7x154 , rhot1-m7xfd0 , rhot1-m7wh41 , rhot1-m7x3p3 , rhoto-a0a061bfj5

Title : Characterization of the two intracellular lipases of Y. lipolytica encoded by TGL3 and TGL4 genes: New insights into the role of intracellular lipases and lipid body organisation - Dulermo_2013_Biochim.Biophys.Acta_1831_1486
Author(s) : Dulermo T , Treton B , Beopoulos A , Kabran Gnankon AP , Haddouche R , Nicaud JM
Ref : Biochimica & Biophysica Acta , 1831 :1486 , 2013
Abstract : Eukaryotes store lipids in a specialised organelle, the lipid body (LB), mainly as triglycerides (TAGs). Both the rates of synthesis and degradation contribute to the control of the accumulation of TAGs. The synthesis of TAGs in yeasts has been well documented, especially in the model yeast Saccharomyces cerevisiae and in the oleaginous yeast Yarrowia lipolytica. However, descriptions of the processes involved in TAG degradation are more scarce and mostly for S. cerevisiae. Here, we report the characterisation of two Y. lipolytica genes, YlTGL3 and YlTGL4, encoding intracellular lipases involved in TAG degradation. The two proteins are localised in lipid bodies, and YlTgl4 was mainly found at the interface between LBs. Surprisingly, the spatial organisation of YlTgl3 and YlTgl4 depends on the culture medium and on the physiological phase of the cell. Inactivation of one or both genes doubles the lipid accumulation capacity of Y. lipolytica, increasing the cell's capacity to accumulate TAGs. The amino acid sequence of YlTgl4 contains the consensus sequence motif (G/A)XSXG, typical of serine hydrolases, whereas YlTgl3 does not. Single and double mutants are unable to degrade TAGs, and higher expression of YlTgl4 correlates with TAG degradation. Therefore, we propose that YlTgl4 is the main lipase responsible for TAG degradation and that YlTgl3 may act as a positive regulator of YlTgl4 rather than a functional lipase. Thus, contrary to S. cerevisiae, Y. lipolytica possesses two intracellular lipases with distinct roles and with distinct localisations in the LB.
ESTHER : Dulermo_2013_Biochim.Biophys.Acta_1831_1486
PubMedSearch : Dulermo_2013_Biochim.Biophys.Acta_1831_1486
PubMedID: 23856343

Title : The yeast Yarrowia lipolytica as a generic tool for molecular evolution of enzymes - Duquesne_2012_Methods.Mol.Biol_861_301
Author(s) : Duquesne S , Bordes F , Fudalej F , Nicaud JM , Marty A
Ref : Methods Mol Biol , 861 :301 , 2012
Abstract : It has been 20 years since strains of the yeast Yarrowia lipolytica were developed for the expression of recombinant proteins as alternative host to the commonly used yeasts, Pichia pastoris and Saccharomyces cerevisiae. Recently, a new strain, JMY1212, was engineered for protein evolution. With this new strain, a very high reproducibility in protein expression level was demonstrated, thus enabling its use for both rational and directed evolution strategies. Indeed, the coefficient of variation was shown to be of 10.7% for the whole process when all the steps are optimized, i.e. transformation of this strain with the gene of interest, cell growth, and protein production under oleic acid induction, and until activity screening assay. The object of this article is to summarize the fruit of these works and show the interest of Y. lipolytica strain JMY1212 for molecular evolution of enzymes, for both rational and directed evolution strategy. Lipase Lip2 from Y. lipolytica is taken here as an example to describe both strategies of molecular evolution. In these two methods, a first step of PCR creates either one targeted (rational design) or various random mutations (directed evolution), and is followed by the incorporation of the expression cassette in the genome of Y. lipolytica. An easy and direct comparison of variant properties is then allowed thanks to the extracellular and reproducible production of variants.
ESTHER : Duquesne_2012_Methods.Mol.Biol_861_301
PubMedSearch : Duquesne_2012_Methods.Mol.Biol_861_301
PubMedID: 22426726

Title : Isolation of a thermostable variant of Lip2 lipase from Yarrowia lipolytica by directed evolution and deeper insight into the denaturation mechanisms involved - Bordes_2011_J.Biotechnol_156_117
Author(s) : Bordes F , Tarquis L , Nicaud JM , Marty A
Ref : J Biotechnol , 156 :117 , 2011
Abstract : Lip2 lipase from Yarrowia lipolytica is a very promising lipase with many potential applications (e.g. resolution of racemic mixtures, production of fine chemicals). Unfortunately this potential is impeded by a very low thermostability for temperatures higher than 40 degrees C. Error-prone PCR and screening of the library in a high-performance yeast expression system (Y. lipolytica) enabled a thermostable variant to be identified. This variant presents only one mutation, the free cysteine 244 is changed into an alanine. At 60 degrees C, the half-life time of the purified variant was 127-fold increased compared to the WT enzyme (from 1.5 min to 3 h). Saturation mutagenesis experiment at position 244 demonstrated that the presence of a cysteine at this position was responsible for the thermal denaturation. It was demonstrated that WT Lip2 and the thermostable variant are both inactivated through aggregation mechanisms, but that the kinetics and the nature of the aggregation were different. For the WT enzyme, rapid intermolecular disulphide bridge interchanges triggered by the free cysteine 244 mediates aggregation. For the variant C244A, aggregation still occurred but much slower than for the WT lipase and was mainly driven by hydrophobic forces.
ESTHER : Bordes_2011_J.Biotechnol_156_117
PubMedSearch : Bordes_2011_J.Biotechnol_156_117
PubMedID: 21763359

Title : The lipases from Yarrowia lipolytica: genetics, production, regulation, biochemical characterization and biotechnological applications - Fickers_2011_Biotechnol.Adv_29_632
Author(s) : Fickers P , Marty A , Nicaud JM
Ref : Biotechnol Adv , 29 :632 , 2011
Abstract : Lipases are serine hydrolases that catalyze in nature the hydrolysis of ester bonds of long chain triacylglycerol into fatty acid and glycerol. However, in favorable thermodynamic conditions, they are also able to catalyze reactions of synthesis such as esterification or amidation. The non-conventional yeast Yarrowia lipolytica possesses 16 paralogs of genes coding for lipase. However, little information on all those paralogs has been yet obtained and only three isoenzymes, namely Lip2p, Lip7p and Lip8p have been partly characterized so far. Microarray data suggest that only a few of them could be expressed and that lipase synthesis seems to be dependent on the fatty acid or oil used as carbon source confirming the high adaptation of Y. lipolytica to hydrophobic substrate utilization. This review focuses on the biochemical characterization of those enzymes with special emphasis on the Lip2p lipase which is the isoenzyme mainly synthesized by Y. lipolytica. Crystallographic data highlight that this latter is a lipase sensu stricto with a lid covering the active site of the enzyme in its closed conformation. Recent findings on enzyme conditioning in dehydrated or liquid formulation, in enzyme immobilization by entrapment in natural polymers from either organic or mineral origins are also discussed together with long-term storage strategies. The development of various biotechnological applications in different fields such as cheese ripening, waste treatment, drug synthesis or human therapeutics is also presented.
ESTHER : Fickers_2011_Biotechnol.Adv_29_632
PubMedSearch : Fickers_2011_Biotechnol.Adv_29_632
PubMedID: 21550394

Title : SOA genes encode proteins controlling lipase expression in response to triacylglycerol utilization in the yeast Yarrowia lipolytica - Desfougeres_2010_FEMS.Yeast.Res_10_93
Author(s) : Desfougeres T , Haddouche R , Fudalej F , Neuveglise C , Nicaud JM
Ref : FEMS Yeast Res , 10 :93 , 2010
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.
ESTHER : Desfougeres_2010_FEMS.Yeast.Res_10_93
PubMedSearch : Desfougeres_2010_FEMS.Yeast.Res_10_93
PubMedID: 19922427

Title : New efficient recombinant expression system to engineer Candida antarctica lipase B - Emond_2010_Appl.Environ.Microbiol_76_2684
Author(s) : Emond S , Montanier C , Nicaud JM , Marty A , Monsan P , Andre I , Remaud-Simeon M
Ref : Applied Environmental Microbiology , 76 :2684 , 2010
Abstract : Here, we report the use of Yarrowia lipolytica as a versatile expression host for developing protein engineering approaches to modify the properties of Candida antarctica lipase B. A reliable screening protocol was defined and validated using a saturation mutagenesis library, yielding mutants displaying higher catalytic efficiencies than the wild-type enzyme.
ESTHER : Emond_2010_Appl.Environ.Microbiol_76_2684
PubMedSearch : Emond_2010_Appl.Environ.Microbiol_76_2684
PubMedID: 20173074

Title : Improvement of Yarrowia lipolytica lipase enantioselectivity by using mutagenesis targeted to the substrate binding site - Bordes_2009_Chembiochem_10_1705
Author(s) : Bordes F , Cambon E , Dossat-Letisse V , Andre I , Croux C , Nicaud JM , Marty A
Ref : Chembiochem , 10 :1705 , 2009
Abstract : Lip2p lipase from Yarrowia lipolytica was shown to be an efficient catalyst for the resolution of 2-bromo-arylacetic acid esters, an important class of chemical intermediates in the pharmaceutical industry. Enantioselectivity of this lipase was improved by site-directed mutagenesis targeted to the substrate binding site. To guide mutagenesis experiments, the three-dimensional model of this lipase was built by homology modelling techniques by using the structures of lipases from Rhizomucor miehei and Thermomyces lanuginosa as templates. On the basis of this structural model, five amino acid residues (T88, V94, D97, V232, V285) that form the hydrophobic substrate binding site of the lipase were selected for site-directed mutagenesis. Position 232 was identified as crucial for the discrimination between enantiomers. Variant V232A displayed an enantioselectivity enhanced by one order of magnitude, whereas variant V232L exhibited a selectivity inversion. To further explore the diversity, position 232 was systematically replaced by the 19 possible amino acids. Screening of this library led to the identification of the V232S variant, which has a tremendously increased E value compared to the parental enzyme for the resolution of 2-bromo-phenylacetic acid ethyl ester (58-fold) and 2-bromo-o-tolylacetic acid ethyl ester (16-fold). In addition to the gain in enantioselectivity, a remarkable increase in velocity was observed (eightfold increase) for both substrates.
ESTHER : Bordes_2009_Chembiochem_10_1705
PubMedSearch : Bordes_2009_Chembiochem_10_1705
PubMedID: 19504508
Gene_locus related to this paper: yarli-lip2

Title : A new recombinant protein expression system for high-throughput screening in the yeast Yarrowia lipolytica - Bordes_2007_J.Microbiol.Methods_70_493
Author(s) : Bordes F , Fudalej F , Dossat V , Nicaud JM , Marty A
Ref : J Microbiol Methods , 70 :493 , 2007
Abstract : Development of a high-throughput eukaryotic screening procedure is important to increase success in obtaining improved enzymes through directed enzyme evolution. This procedure was developed for the yeast Yarrowia lipolytica which becomes the second eukaryotic host for this purpose. The extracellular lipase Lip2 was used as expressed enzyme but this system will be easily adjusted for other enzymes. We adapted and optimized the protocol for protein expression by Y. lipolytica in 96-well microplates. Yeast transformation efficiency and expression cassette insertion were increased by constructing a strain containing a zeta docking platform for targeted integration into the genome. The coefficient of variance of the full process was reduced from 36.3% to 18.9%. The main part of the variability (11.7%) arises from the specific lipase enzyme assay whereas the coefficient of variance concerning transformation, growth and expression steps represents only 7.2%. The rate of clone with no activity was reduced from 5.8% to 0.2%. Both transformation efficiency and variability are then compatible with high-throughput screening in the yeast Y. lipolytica.
ESTHER : Bordes_2007_J.Microbiol.Methods_70_493
PubMedSearch : Bordes_2007_J.Microbiol.Methods_70_493
PubMedID: 17669530

Title : Analysis of Yarrowia lipolytica extracellular lipase Lip2p glycosylation - Jolivet_2007_FEMS.Yeast.Res_7_1317
Author(s) : Jolivet P , Bordes F , Fudalej F , Cancino M , Vignaud C , Dossat V , Burghoffer C , Marty A , Chardot T , Nicaud JM
Ref : FEMS Yeast Res , 7 :1317 , 2007
Abstract : Wild-type (WT) Yarrowia lipolytica strain secretes a major extracellular lipase Lip2p which is glycosylated. In silico sequence analysis reveals the presence of two potential N-glycosylation sites (N113IS and N134NT). Strains expressing glycosylation mutant forms were constructed. Esterase activities for the different forms were measured with three substrates: p-nitrophenol butyrate (p-NPB), tributyrin and triolein. Sodium dodecyl sulfate polacrylamide gel electrophoresis analysis of supernatant indicated that the suppression of the two sites of N-glycosylation did not affect secretion. S115V or N134Q mutations led to lipase with similar specific activity compared with WT lipase while a T136V mutation reduced specific activity toward p-NPB and tributyrin. Electrospray ionization MS of the WT entire protein led to an average mass of 36 950 Da, higher than the mass deduced from the amino acid sequence (33 385 Da) and to the observation of at least two different mannose structures: Man(8)GlcNAc(2) and Man(9)GlcNAc(2). LC-tandem MS analysis of the WT Lip2p after trypsin and endoproteinase Asp-N treatments led to high coverage (87%) of protein sequence but the peptides containing N113 and N134 were not identified. We confirmed that the presence of N-glycosylation occurred at both N113 and N134 by MS of digested proteins obtained after enzymatic deglycosylation or from mutant forms.
ESTHER : Jolivet_2007_FEMS.Yeast.Res_7_1317
PubMedSearch : Jolivet_2007_FEMS.Yeast.Res_7_1317
PubMedID: 17784853

Title : Involvement of hexokinase Hxk1 in glucose catabolite repression of LIP2 encoding extracellular lipase in the yeast Yarrowia lipolytica - Fickers_2005_Curr.Microbiol_50_133
Author(s) : Fickers P , Nicaud JM , Destain J , Thonart P
Ref : Curr Microbiol , 50 :133 , 2005
Abstract : The yeast Yarrowia lipolytica produces an extracellular lipase encoded by the LIP2 gene. However, very little is known about the mechanisms controlling its expression, especially on glucose media. In this work, the involvement of hexokinase Hxk1 in the glucose catabolite repression of LIP2 was investigated in a lipase overproducing mutant less sensitive to glucose repression. This mutant has a reduced capacity to phosphorylate hexose compared with the wild-type strain, but no differences could be observed between the HXK1 sequences in the two isolates. This suggested that the reduced phosphorylating activity of the mutant strain probably resulted from a modification in the level of HXK1 expression. However, overexpression of the HXK1 gene in this mutant led to a decrease of both LIP2 induction and extracellular lipase activity, suggesting that the hexokinase is involved in the glucose catabolite repression of LIP2 in Y lipolytica.
ESTHER : Fickers_2005_Curr.Microbiol_50_133
PubMedSearch : Fickers_2005_Curr.Microbiol_50_133
PubMedID: 15883872

Title : Identification and characterisation of LIP7 and LIP8 genes encoding two extracellular triacylglycerol lipases in the yeast Yarrowia lipolytica - Fickers_2005_Fungal.Genet.Biol_42_264
Author(s) : Fickers P , Fudalej F , Le Dall MT , Casaregola S , Gaillardin C , Thonart P , Nicaud JM
Ref : Fungal Genet Biol , 42 :264 , 2005
Abstract : In the lipolytic yeast Yarrowia lipolytica, the LIP2 gene was previously reported to encode an extracellular lipase. The growth of a Deltalip2 strain on triglycerides as sole carbon source suggest an alternative pathway for triglycerides utilisation in this yeast. Here, we describe the isolation and the characterisation of the LIP7 and LIP8 genes which were found to encode a 366 and a 371-amino acid precursor protein, respectively. These proteins which belong to the triacylglycerol hydrolase family (EC presented a high homology with the extracellular lipase CdLIP2 and CdLIP3 from Candida deformans. The physiological function of the lipase isoenzymes was investigated by creating single and multi-disrupted strains. Lip7p and Lip8p were found to correspond to active secreted lipases. The lack of lipase production in a Deltalip2 Deltalip7 Deltalip8 strain suggest that no additional extracellular lipase remains to be discovered in Y. lipolytica. The substrate specificity towards synthetic ester molecules indicates that Lip7p presented a maximum activity centred on caproate (C6) while that of Lip8p is in caprate (C10).
ESTHER : Fickers_2005_Fungal.Genet.Biol_42_264
PubMedSearch : Fickers_2005_Fungal.Genet.Biol_42_264
PubMedID: 15707847
Gene_locus related to this paper: yarli-LIP7 , yarli-LIP8

Title : Hydrophobic substrate utilisation by the yeast Yarrowia lipolytica, and its potential applications - Fickers_2005_FEMS.Yeast.Res_5_527
Author(s) : Fickers P , Benetti PH , Wache Y , Marty A , Mauersberger S , Smit MS , Nicaud JM
Ref : FEMS Yeast Res , 5 :527 , 2005
Abstract : The alkane-assimilating yeast Yarrowia lipolytica degrades very efficiently hydrophobic substrates such as n-alkanes, fatty acids, fats and oils for which it has specific metabolic pathways. An overview of the oxidative degradation pathways for alkanes and triglycerides in Y. lipolytica is given, with new insights arising from the recent genome sequencing of this yeast. This includes the interaction of hydrophobic substrates with yeast cells, their uptake and transport, the primary alkane oxidation to the corresponding fatty alcohols and then by different enzymes to fatty acids, and the subsequent degradation in peroxisomal beta-oxidation or storage into lipid bodies. Several enzymes involved in hydrophobic substrate utilisation belong to multigene families, such as lipases/esterases (LIP genes), cytochromes P450 (ALK genes) and peroxisomal acyl-CoA oxidases (POX genes). Examples are presented demonstrating that wild-type and genetically engineered strains of Y. lipolytica can be used for alkane and fatty-acid bioconversion, such as aroma production, for production of SCP and SCO, for citric acid production, in bioremediation, in fine chemistry, for steroid biotransformation, and in food industry. These examples demonstrate distinct advantages of Y. lipolytica for their use in bioconversion reactions of biotechnologically interesting hydrophobic substrates.
ESTHER : Fickers_2005_FEMS.Yeast.Res_5_527
PubMedSearch : Fickers_2005_FEMS.Yeast.Res_5_527
PubMedID: 15780653

Title : Selection of new over-producing derivatives for the improvement of extracellular lipase production by the non-conventional yeast Yarrowia lipolytica - Fickers_2005_J.Biotechnol_115_379
Author(s) : Fickers P , Fudalej F , Nicaud JM , Destain J , Thonart P
Ref : J Biotechnol , 115 :379 , 2005
Abstract : The non-conventional yeast Yarrowia lipolytica produces an extracellular lipase encoded by the LIP2 gene. Mutant strains with enhanced productivity were previously obtained either by chemical mutagenesis or genetic engineering. In this work, we used one of these mutants, named LgX64.81 to select new overproducing strains following by amplification of the LIP2 gene. We also developed a process for lipase production in bioreactors and compared lipase production levels in batch and fed-batch cultures. Batch culture led to a lipase production of 26450 U ml(-1) in a media containing olive oil and tryptone as carbon and nitrogen sources. Feeding of a combination of tryptone and olive oil at the end of the exponential growth phase yielded to lipase activity of 158246 U ml(-1) after 80 h of cultivation. In addition this production system developed for the extracellular lipase could also be applied for other heterologous protein production since we have demonstrated that LgX64.81 is an interesting alternative host strain.
ESTHER : Fickers_2005_J.Biotechnol_115_379
PubMedSearch : Fickers_2005_J.Biotechnol_115_379
PubMedID: 15639099

Title : Genome evolution in yeasts - Dujon_2004_Nature_430_35
Author(s) : Dujon B , Sherman D , Fischer G , Durrens P , Casaregola S , Lafontaine I , De Montigny J , Marck C , Neuveglise C , Talla E , Goffard N , Frangeul L , Aigle M , Anthouard V , Babour A , Barbe V , Barnay S , Blanchin S , Beckerich JM , Beyne E , Bleykasten C , Boisrame A , Boyer J , Cattolico L , Confanioleri F , de Daruvar A , Despons L , Fabre E , Fairhead C , Ferry-Dumazet H , Groppi A , Hantraye F , Hennequin C , Jauniaux N , Joyet P , Kachouri R , Kerrest A , Koszul R , Lemaire M , Lesur I , Ma L , Muller H , Nicaud JM , Nikolski M , Oztas S , Ozier-Kalogeropoulos O , Pellenz S , Potier S , Richard GF , Straub ML , Suleau A , Swennen D , Tekaia F , Wesolowski-Louvel M , Westhof E , Wirth B , Zeniou-Meyer M , Zivanovic I , Bolotin-Fukuhara M , Thierry A , Bouchier C , Caudron B , Scarpelli C , Gaillardin C , Weissenbach J , Wincker P , Souciet JL
Ref : Nature , 430 :35 , 2004
Abstract : Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
ESTHER : Dujon_2004_Nature_430_35
PubMedSearch : Dujon_2004_Nature_430_35
PubMedID: 15229592
Gene_locus related to this paper: canga-apth1 , canga-ppme1 , canga-q6fik7 , canga-q6fiv5 , canga-q6fiw8 , canga-q6fj11 , canga-q6fjh6 , canga-q6fjl0 , canga-q6fjr8 , canga-q6fkj6 , canga-q6fkm9 , canga-q6fku7 , canga-q6fl14 , canga-q6flb5 , canga-q6fle9 , canga-q6flk8 , canga-q6fly1 , canga-q6fly9 , canga-q6fmz4 , canga-q6fnx4 , canga-q6fp28 , canga-q6fpa8 , canga-q6fpi6 , canga-q6fpv7 , canga-q6fpw6 , canga-q6fqj3 , canga-q6fr97 , canga-q6frt7 , canga-q6ftm9 , canga-q6ftu0 , canga-q6ftv9 , canga-q6ftz9 , canga-q6fuf8 , canga-q6fv41 , canga-q6fvu3 , canga-q6fw36 , canga-q6fw94 , canga-q6fwk6 , canga-q6fwm0 , canga-q6fxc7 , canga-q6fxd7 , debha-apth1 , debha-atg15 , debha-b5rtk1 , debha-b5rub4 , debha-b5rue8 , debha-b5rue9 , debha-bna7 , debha-ppme1 , debha-q6bgx3 , debha-q6bh69 , debha-q6bhb8 , debha-q6bhc1 , debha-q6bhd0 , debha-q6bhj7 , debha-q6bi97 , debha-q6biq7 , debha-q6bj53 , debha-q6bkd8 , debha-q6bks1 , debha-q6bky4 , debha-q6bm63 , debha-q6bmh3 , debha-q6bn89 , debha-q6bnj6 , debha-q6bp08 , debha-q6bpb4 , debha-q6bpc0 , debha-q6bpc6 , debha-q6bq10 , debha-q6bq11 , debha-q6bqd9 , debha-q6bqj6 , debha-q6br33 , debha-q6br93 , debha-q6brg1 , debha-q6brw7 , debha-q6bs23 , debha-q6bsc3 , debha-q6bsl8 , debha-q6bsx6 , debha-q6bta5 , debha-q6bty5 , debha-q6btz0 , debha-q6bu73 , debha-q6buk9 , debha-q6but7 , debha-q6bvc4 , debha-q6bvg4 , debha-q6bvg8 , debha-q6bvp4 , debha-q6bw82 , debha-q6bxr7 , debha-q6bxu9 , debha-q6bym5 , debha-q6byn7 , debha-q6bzj8 , debha-q6bzk2 , debha-q6bzm5 , klula-apth1 , klula-ppme1 , klula-q6cin9 , klula-q6ciu6 , klula-q6cj47 , klula-q6cjc8 , klula-q6cjq9 , klula-q6cjs1 , klula-q6cjv9 , klula-q6ckd7 , klula-q6ckk4 , klula-q6ckx4 , klula-q6cl20 , klula-q6clm1 , klula-q6cly8 , klula-q6clz7 , klula-q6cm48 , klula-q6cm49 , klula-q6cmt5 , klula-q6cn71 , klula-q6cnm1 , klula-q6cr74 , klula-q6cr90 , klula-q6crs0 , klula-q6crv8 , klula-q6crz9 , klula-q6cst8 , klula-q6csv8 , klula-q6ctp8 , klula-q6cu02 , klula-q6cu78 , klula-q6cu79 , klula-q6cuv3 , klula-q6cvd3 , klula-q6cw70 , klula-q6cw92 , klula-q6cwu7 , klula-q6cx84 , klula-q6cxa3 , klula-q6cy41 , yarli-apth1 , yarli-atg15 , yarli-BST1B , yarli-lip2 , yarli-LIP3 , yarli-LIP4 , yarli-LIP5 , yarli-LIP7 , yarli-LIP8 , yarli-lipa1 , yarli-ppme1 , yarli-q6bzp1 , yarli-q6bzv7 , yarli-q6c1f5 , yarli-q6c1f7 , yarli-q6c1r3 , yarli-q6c2z2 , yarli-q6c3h1 , yarli-q6c3i6 , yarli-q6c3l1 , yarli-q6c3u6 , yarli-q6c4h8 , yarli-q6c5j1 , yarli-q6c5m4 , yarli-q6c6m4 , yarli-q6c6p7 , yarli-q6c6v2 , yarli-q6c7h3 , yarli-q6c7i7 , yarli-q6c7j5 , yarli-q6c7y6 , yarli-q6c8m4 , yarli-q6c8q4 , yarli-q6c8u4 , yarli-q6c8y2 , yarli-q6c9r0 , yarli-q6c9r1 , yarli-q6c9u0 , yarli-q6c9v4 , yarli-q6c209 , yarli-q6c225 , yarli-q6c493 , yarli-q6c598 , yarli-q6c687 , yarli-q6c822 , yarli-q6cau6 , yarli-q6cax2 , yarli-q6caz1 , yarli-q6cb63 , yarli-q6cba7 , yarli-q6cbb1 , yarli-q6cbe6 , yarli-q6cby1 , yarli-q6ccr0 , yarli-q6cdg1 , yarli-q6cdi6 , yarli-q6cdv9 , yarli-q6ce37 , yarli-q6ceg0 , yarli-q6cep3 , yarli-q6cey5 , yarli-q6cf60 , yarli-q6cfp3 , yarli-q6cfx2 , yarli-q6cg13 , yarli-q6cg27 , yarli-q6cgj3 , yarli-q6chb8 , yarli-q6ci59 , yarli-q6c748 , canga-q6fpj0 , klula-q6cp11 , yarli-q6c4p0 , debha-q6btp5 , debha-kex1

Title : Carbon and nitrogen sources modulate lipase production in the yeast Yarrowia lipolytica - Fickers_2004_J.Appl.Microbiol_96_742
Author(s) : Fickers P , Nicaud JM , Gaillardin C , Destain J , Thonart P
Ref : J Appl Microbiol , 96 :742 , 2004
Abstract : AIMS: To analyse the influence of nitrogen and carbon sources on extracellular lipase production by Yarrowia lipolytica-overproducing mutant in order to optimize its production in large-scale bioreactors. METHODS AND
RESULTS: The level of lipase production and LIP2 induction, measured using an LIP2-LacZ reporter gene, were compared for different carbon and nitrogen sources and for different concentrations. The localization of the enzyme during growth was also determined by Western blotting analysis using a six-histidine-tagged lipase. SIGNIFICANCE AND IMPACT OF THE STUDY: Tryptone N1 and oleic acid are the most suitable nitrogen and carbon sources for the production of the extracellular lipase by the Y. lipolytica mutant. Higher levels of lipase production were obtained as the tryptone concentration increased in the culture medium. Such a positive correlation was not observed with oleic acid media where the highest lipolytic productivities were obtained in the presence of low concentration. We also demonstrate that in the presence of oleic acid, lipase is cell-bound during the growth phase before being released in the media.
CONCLUSIONS: This work provides a better understanding of the mechanism controlling LIP2 expression and, thus, extracellular lipase production in the yeast Y. lipolytica.
ESTHER : Fickers_2004_J.Appl.Microbiol_96_742
PubMedSearch : Fickers_2004_J.Appl.Microbiol_96_742
PubMedID: 15012812

Title : Identification of a triacylglycerol lipase gene family in Candida deformans: molecular cloning and functional expression - Bigey_2003_Yeast_20_233
Author(s) : Bigey F , Tuery K , Bougard D , Nicaud JM , Moulin G
Ref : Yeast , 20 :233 , 2003
Abstract : The yeast Candida deformans CBS 2071 produces an extracellular lipase which was shown to catalyse the production of various esters by the esterification of free fatty acids, even in the presence of a large molar excess of water. To clone the gene encoding this extracellular lipase, Saccharomyces cerevisiae was transformed with C. deformans genomic libraries and screened for lipolytic activity on a medium containing rapeseed oil emulsion and rhodamine B. Three members of a lipase gene family (CdLIP1, CdLIP2 and CdLIP3) were cloned and characterized. Each deduced lipase sequence has a Gly-His-Ser-Leu-Gly-(Gly/Ala)-Ala conserved motif, eight cysteine residues and encodes an N-terminal signal sequence. MALDI-TOF mass spectrometry analysis of a proteolytic digest of the lipase produced was used to obtain experimental evidence that the CdLIP1 gene encoded the extracellular lipase. Recombinant expression studies confirmed that the cloned genes encoded functional lipases. The three lipases are very similar to lipases from the related species Yarrowia lipolytica. Significant homologies were also found with several yeast and fungal lipases. As C. deformans CBS 2071 was previously considered to be synonymous with Y. lipolytica, the strains were compared for the extent of nucleotide divergence in the variable regions (D1/D2) at the 5'-end of the large-subunit (26S) ribosomal DNA (rDNA) gene. This rDNA region has diverged sufficiently to suggest that C. deformans is a separate species. The nucleotide sequences of the CdLIP1, CdLIP2 and CdLIP3 genes will appear in the EMBL nucleotide sequence database under Accession Nos AJ428393, AJ428394 and AJ428395, respectively.
ESTHER : Bigey_2003_Yeast_20_233
PubMedSearch : Bigey_2003_Yeast_20_233
PubMedID: 12557276

Title : Overproduction of lipase by Yarrowia lipolytica mutants - Fickers_2003_Appl.Microbiol.Biotechnol_63_136
Author(s) : Fickers P , Nicaud JM , Destain J , Thonart P
Ref : Applied Microbiology & Biotechnology , 63 :136 , 2003
Abstract : Non-genetically modified mutants with increased capacities of extracellular lipase production were obtained from Yarrowia lipolytica strain CBS6303 by chemical mutagenesis. Of the 400 mutants isolated, LgX64.81 had the highest potential for the development of an industrial lipase production process. This mutant exhibits lipase production uncoupled from catabolite repression by glucose, and a 10-fold increased productivity upon addition of oleic acid. Using a LIP2- LacZ reporter gene, we demonstrate that the mutant phenotype originates from a trans-acting mutation. The glucose uptake capacity of LgX64.81 is reduced 2.5-fold compared to the wild-type-strain, and it exhibits high lipase production on glucose medium. A trans-acting mutation in a gene involved in glucose transport could thus explain this mutant phenotype.
ESTHER : Fickers_2003_Appl.Microbiol.Biotechnol_63_136
PubMedSearch : Fickers_2003_Appl.Microbiol.Biotechnol_63_136
PubMedID: 12768246

Title : Characterization of an extracellular lipase encoded by LIP2 in yarrowia lipolytica - Pignede_2000_J.Bacteriol_182_2802
Author(s) : Pignede G , Wang H , Fudalej F , Gaillardin C , Seman M , Nicaud JM
Ref : Journal of Bacteriology , 182 :2802 , 2000
Abstract : We isolated the LIP2 gene from the lipolytic yeast Yarrowia lipolytica. It was found to encode a 334-amino-acid precursor protein. The secreted lipase is a 301-amino-acid glycosylated polypeptide which is a member of the triacylglycerol hydrolase family (EC The Lip2p precursor protein is processed by the KEX2-like endoprotease encoded by XPR6. Deletion of the XPR6 gene resulted in the secretion of an active but less stable proenzyme. Thus, the pro region does not inhibit lipase secretion and activity. However, it does play an essential role in the production of a stable enzyme. Processing was found to be correct in LIP2(A) (multiple LIP2 copy integrant)-overexpressing strains, which secreted 100 times more activity than the wild type, demonstrating that XPR6 maturation was not limiting. No extracellular lipase activity was detected with the lip2 knockout (KO) strain, strongly suggesting that extracellular lipase activity results from expression of the LIP2 gene. Nevertheless, the lip2 KO strain is still able to grow on triglycerides, suggesting an alternative pathway for triglyceride utilization in Y. lipolytica..
ESTHER : Pignede_2000_J.Bacteriol_182_2802
PubMedSearch : Pignede_2000_J.Bacteriol_182_2802
PubMedID: 10781549
Gene_locus related to this paper: aspnc-a5abh9 , yarli-lip2

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications - Philippsen_1997_Nature_387_93
Author(s) : Philippsen P , Kleine K , Pohlmann R , Dusterhoft A , Hamberg K , Hegemann JH , Obermaier B , Urrestarazu LA , Aert R , Albermann K , Altmann R , Andre B , Baladron V , Ballesta JP , Becam AM , Beinhauer J , Boskovic J , Buitrago MJ , Bussereau F , Coster F , Crouzet M , D'Angelo M , Dal Pero F , De Antoni A , del Rey F , Doignon F , Domdey H , Dubois E , Fiedler T , Fleig U , Floeth M , Fritz C , Gaillardin C , Garcia-Cantalejo JM , Glansdorff NN , Goffeau A , Gueldener U , Herbert C , Heumann K , Heuss-Neitzel D , Hilbert H , Hinni K , Iraqui Houssaini I , Jacquet M , Jimenez A , Jonniaux JL , Karpfinger L , Lanfranchi G , Lepingle A , Levesque H , Lyck R , Maftahi M , Mallet L , Maurer KC , Messenguy F , Mewes HW , Mosti D , Nasr F , Nicaud JM , Niedenthal RK , Pandolfo D , Pierard A , Piravandi E , Planta RJ , Pohl TM , Purnelle B , Rebischung C , Remacha M , Revuelta JL , Rinke M , Saiz JE , Sartorello F , Scherens B , Sen-Gupta M , Soler-Mira A , Urbanus JH , Valle G , van Dyck L , Verhasselt P , Vierendeels F , Vissers S , Voet M , Volckaert G , Wach A , Wambutt R , Wedler H , Zollner A , Hani J
Ref : Nature , 387 :93 , 1997
Abstract : In 1992 we started assembling an ordered library of cosmid clones from chromosome XIV of the yeast Saccharomyces cerevisiae. At that time, only 49 genes were known to be located on this chromosome and we estimated that 80% to 90% of its genes were yet to be discovered. In 1993, a team of 20 European laboratories began the systematic sequence analysis of chromosome XIV. The completed and intensively checked final sequence of 784,328 base pairs was released in April, 1996. Substantial parts had been published before or had previously been made available on request. The sequence contained 419 known or presumptive protein-coding genes, including two pseudogenes and three retrotransposons, 14 tRNA genes, and three small nuclear RNA genes. For 116 (30%) protein-coding sequences, one or more structural homologues were identified elsewhere in the yeast genome. Half of them belong to duplicated groups of 6-14 loosely linked genes, in most cases with conserved gene order and orientation (relaxed interchromosomal synteny). We have considered the possible evolutionary origins of this unexpected feature of yeast genome organization.
ESTHER : Philippsen_1997_Nature_387_93
PubMedSearch : Philippsen_1997_Nature_387_93
PubMedID: 9169873
Gene_locus related to this paper: yeast-SCYNR064C , yeast-hda1

Title : Sequencing analysis of a 24.7 kb fragment of yeast chromosome XIV identifies six known genes, a new member of the hexose transporter family and ten new open reading frames - Maftahi_1995_Yeast_11_1077
Author(s) : Maftahi M , Nicaud JM , Levesque H , Gaillardin C
Ref : Yeast , 11 :1077 , 1995
Abstract : The DNA sequence of a 24.7 kb region covering the left arm of chromosome XIV from Saccharomyces cerevisiae was determined. This region contains 17 open reading frames (ORFs) which code for proteins of more than 100 amino acids. Five ORFs correspond to the KRE1, ATP11, DAL82, RFA2 and MCK1 loci, described previously. Two ORFs present high similarity to known proteins: NO345 with the hexose transporter family, and NO351 with the yeast chorismate mutase/prephenate dehydratase enzyme encoded by PHA2. Six ORFs show limited similarity with known proteins or some specific features: NO339 presents 11 potential transmembrane domains. NO343, which is internal to NO345, presents a putative signal sequence and a potential transmembrane domain. NO348 shows similarity with YCW2, TUP1 and SEC13. NO364 reveals a signature for a pyridoxal-phosphate attachment site. Finally, NO384 and NO388 present a biased amino acid composition, being rich in Asn or Glu/Lys/Arg, respectively. Four other ORFs (NO342, NO376, NO381 and NO397) show no similarity to proteins within the databases screened.
ESTHER : Maftahi_1995_Yeast_11_1077
PubMedSearch : Maftahi_1995_Yeast_11_1077
PubMedID: 7502583
Gene_locus related to this paper: yeast-yn60