Gaillardin C

References (12)

Title : Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization - Louis_2012_G3.(Bethesda)_2_299
Author(s) : Louis VL , Despons L , Friedrich A , Martin T , Durrens P , Casaregola S , Neuveglise C , Fairhead C , Marck C , Cruz JA , Straub ML , Kugler V , Sacerdot C , Uzunov Z , Thierry A , Weiss S , Bleykasten C , De Montigny J , Jacques N , Jung P , Lemaire M , Mallet S , Morel G , Richard GF , Sarkar A , Savel G , Schacherer J , Seret ML , Talla E , Samson G , Jubin C , Poulain J , Vacherie B , Barbe V , Pelletier E , Sherman DJ , Westhof E , Weissenbach J , Baret PV , Wincker P , Gaillardin C , Dujon B , Souciet JL
Ref : G3 (Bethesda) , 2 :299 , 2012
Abstract : Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
ESTHER : Louis_2012_G3.(Bethesda)_2_299
PubMedSearch : Louis_2012_G3.(Bethesda)_2_299
PubMedID: 22384408
Gene_locus related to this paper: picso-g8ycc9 , picso-g8yet0 , picso-g8yb96 , picso-g8ym39 , erecy-g8jrp5 , picso-g8y652

Title : The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications - Falentin_2010_PLoS.ONE_5_E11748
Author(s) : Falentin H , Deutsch SM , Jan G , Loux V , Thierry A , Parayre S , Maillard MB , Dherbecourt J , Cousin FJ , Jardin J , Siguier P , Couloux A , Barbe V , Vacherie B , Wincker P , Gibrat JF , Gaillardin C , Lortal S
Ref : PLoS ONE , 5 :e11748 , 2010
Abstract : BACKGROUND: Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an 11-fold coverage. METHODOLOGY/PRINCIPAL FINDINGS: The circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters. CONCLUSIONS/SIGNIFICANCE: With the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.
ESTHER : Falentin_2010_PLoS.ONE_5_E11748
PubMedSearch : Falentin_2010_PLoS.ONE_5_E11748
PubMedID: 20668525
Gene_locus related to this paper: profr-b3cky9 , profr-b3ckz1 , profr-b3ckz0 , profr-b3cky3

Title : Comparative genomics of protoploid Saccharomycetaceae - Souciet_2009_Genome.Res_19_1696
Author(s) : Souciet JL , Dujon B , Gaillardin C , Johnston M , Baret PV , Cliften P , Sherman DJ , Weissenbach J , Westhof E , Wincker P , Jubin C , Poulain J , Barbe V , Segurens B , Artiguenave F , Anthouard V , Vacherie B , Val ME , Fulton RS , Minx P , Wilson R , Durrens P , Jean G , Marck C , Martin T , Nikolski M , Rolland T , Seret ML , Casaregola S , Despons L , Fairhead C , Fischer G , Lafontaine I , Leh V , Lemaire M , De Montigny J , Neuveglise C , Thierry A , Blanc-Lenfle I , Bleykasten C , Diffels J , Fritsch E , Frangeul L , Goeffon A , Jauniaux N , Kachouri-Lafond R , Payen C , Potier S , Pribylova L , Ozanne C , Richard GF , Sacerdot C , Straub ML , Talla E
Ref : Genome Res , 19 :1696 , 2009
Abstract : Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
ESTHER : Souciet_2009_Genome.Res_19_1696
PubMedSearch : Souciet_2009_Genome.Res_19_1696
PubMedID: 19525356
Gene_locus related to this paper: lactc-c5dci9 , lactc-c5ddi5 , lactc-c5dew5 , lactc-c5dez1 , lactc-c5df11 , lactc-c5dfh7 , lactc-c5dgd1 , lactc-c5dif7 , lactc-c5din7 , lactc-c5dja0 , lactc-c5dm95 , lactc-c5dn06 , lactc-c5dnn9 , lactc-c5e2g8 , lactc-c5e3n5 , lactc-c5e375 , zygrc-c5drr0 , zygrc-c5dvh0 , zygrc-c5dvl2 , zygrc-c5dvx0 , zygrc-c5dvz8 , zygrc-c5dx83 , zygrc-c5dxn5 , zygrc-c5dxq9 , zygrc-c5e0w1 , zygrc-c5e1e4 , zygrc-c5e1h2 , zygro-a0a1q2zt01 , 9sach-a0a0p1kuu1 , lactc-kex1 , zygrc-kex1

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 3.1.1.3) 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 : Evolutionary relationships between the former species Saccharomyces uvarum and the hybrids Saccharomyces bayanus and Saccharomyces pastorianus\; reinstatement of Saccharomyces uvarum (Beijerinck) as a distinct species - Nguyen_2005_FEMS.Yeast.Res_5_471
Author(s) : Nguyen HV , Gaillardin C
Ref : FEMS Yeast Res , 5 :471 , 2005
Abstract : Analysis of the nucleotide sequence of the GDH1 homologues from Saccharomyces bayanus strain CBS 380T and S. pastorianus strains showed that they share an almost identical sequence, SuGDH1*, which is a diverged form of the SuGDH1 from the type strain of the former species S. uvarum, considered as synonym of S. bayanus. SuGDH1* is close to but differs from SuGDH1 by the accumulation of a high number of neutral substitutions designated as Multiple Neutral Mutations Accumulation (MNMA). Further analysis carried out with three other markers, BAP2, HO and MET2 showed that they have also diverged from their S. uvarum counterparts by MNMA. S. bayanus CBS 380T is placed between S. uvarum and S. pastorianus sharing MET2, CDC91 sequences with the former and BAP2, GDH1, HO sequences with the latter. S. bayanus CBS 380T has been proposed to be a S. uvarum/S. cerevisiae hybrid and this proposal is confirmed by the presence in its genome a S. cerevisiae SUC4 gene. Strain S. bayanus CBS 380T, with a composite genome, is genetically isolated from strains of the former S. uvarum species, thus justifying the reinstatement of S. uvarum as a distinct species.
ESTHER : Nguyen_2005_FEMS.Yeast.Res_5_471
PubMedSearch : Nguyen_2005_FEMS.Yeast.Res_5_471
PubMedID: 15691752
Gene_locus related to this paper: yeast-met2

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 : 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 : The genome sequence of Schizosaccharomyces pombe - Wood_2002_Nature_415_871
Author(s) : Wood V , Gwilliam R , Rajandream MA , Lyne M , Lyne R , Stewart A , Sgouros J , Peat N , Hayles J , Baker S , Basham D , Bowman S , Brooks K , Brown D , Brown S , Chillingworth T , Churcher C , Collins M , Connor R , Cronin A , Davis P , Feltwell T , Fraser A , Gentles S , Goble A , Hamlin N , Harris D , Hidalgo J , Hodgson G , Holroyd S , Hornsby T , Howarth S , Huckle EJ , Hunt S , Jagels K , James K , Jones L , Jones M , Leather S , McDonald S , McLean J , Mooney P , Moule S , Mungall K , Murphy L , Niblett D , Odell C , Oliver K , O'Neil S , Pearson D , Quail MA , Rabbinowitsch E , Rutherford K , Rutter S , Saunders D , Seeger K , Sharp S , Skelton J , Simmonds M , Squares R , Squares S , Stevens K , Taylor K , Taylor RG , Tivey A , Walsh S , Warren T , Whitehead S , Woodward J , Volckaert G , Aert R , Robben J , Grymonprez B , Weltjens I , Vanstreels E , Rieger M , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Dusterhoft A , Fritzc C , Holzer E , Moestl D , Hilbert H , Borzym K , Langer I , Beck A , Lehrach H , Reinhardt R , Pohl TM , Eger P , Zimmermann W , Wedler H , Wambutt R , Purnelle B , Goffeau A , Cadieu E , Dreano S , Gloux S , Lelaure V , Mottier S , Galibert F , Aves SJ , Xiang Z , Hunt C , Moore K , Hurst SM , Lucas M , Rochet M , Gaillardin C , Tallada VA , Garzon A , Thode G , Daga RR , Cruzado L , Jimenez J , Sanchez M , del Rey F , Benito J , Dominguez A , Revuelta JL , Moreno S , Armstrong J , Forsburg SL , Cerutti L , Lowe T , McCombie WR , Paulsen I , Potashkin J , Shpakovski GV , Ussery D , Barrell BG , Nurse P
Ref : Nature , 415 :871 , 2002
Abstract : We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.
ESTHER : Wood_2002_Nature_415_871
PubMedSearch : Wood_2002_Nature_415_871
PubMedID: 11859360
Gene_locus related to this paper: schpo-APTH1 , schpo-be46 , schpo-BST1 , schpo-C2E11.08 , schpo-C14C4.15C , schpo-C22H12.03 , schpo-C23C4.16C , schpo-C57A10.08C , schpo-dyr , schpo-este1 , schpo-KEX1 , schpo-PCY1 , schpo-pdat , schpo-PLG7 , schpo-ppme1 , schpo-q9c0y8 , schpo-SPAC4A8.06C , schpo-C22A12.06C , schpo-SPAC977.15 , schpo-SPAPB1A11.02 , schpo-SPBC14C8.15 , schpo-SPBC530.12C , schpo-SPBC1711.12 , schpo-SPBPB2B2.02 , schpo-SPCC5E4.05C , schpo-SPCC417.12 , schpo-SPCC1672.09 , schpo-yb4e , schpo-yblh , schpo-ydw6 , schpo-ye7a , schpo-ye63 , schpo-ye88 , schpo-yeld , schpo-yk68 , schpo-clr3 , schpo-ykv6

Title : Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization - Casaregola_2001_Int.J.Syst.Evol.Microbiol_51_1607
Author(s) : Casaregola S , Nguyen HV , Lapathitis G , Kotyk A , Gaillardin C
Ref : Int J Syst Evol Microbiol , 51 :1607 , 2001
Abstract : The lager brewing yeasts, Saccharomyces pastorianus (synonym Saccharomyces carlsbergensis), are allopolyploid, containing parts of two divergent genomes. Saccharomyces cerevisiae contributed to the formation of these hybrids, although the identity of the other species is still unclear. The presence of alleles specific to S. cerevisiae and S. pastorianus was tested for by PCR/RFLP in brewing yeasts of various origins and in members of the Saccharomyces sensu stricto complex. S. cerevisiae-type alleles of two genes, HIS4 and YCL008c, were identified in another brewing yeast, S. pastorianus CBS 1503 (Saccharomyces monacensis), thought to be the source of the other contributor to the lager hybrid. This is consistent with the hybridization of S. cerevisiae subtelomeric sequences X and Y' to the electrophoretic karyotype of this strain. S. pastorianus CBS 1503 (S. monacensis) is therefore probably not an ancestor of S. pastorianus, but a related hybrid. Saccharomyces bayanus, also thought to be one of the contributors to the lager yeast hybrid, is a heterogeneous taxon containing at least two subgroups, one close to the type strain, CBS 380T, the other close to CBS 395 (Saccharomyces uvarum). The partial sequences of several genes (HIS4, MET10, URA3) were shown to be identical or very similar (over 99%) in S. pastorianus CBS 1513 (S. carlsbergensis), S. bayanus CBS 380T and its close derivatives, showing that S. pastorianus and S. bayanus have a common ancestor. A distinction between two subgroups within S. bayanus was made on the basis of sequence analysis: the subgroup represented by S. bayanus CBS 395 (S. uvarum) has 6-8% sequence divergence within the genes HIS4, MET10 and MET2 from S. bayanus CBS 380T, indicating that the two S. bayanus subgroups diverged recently. The detection of specific alleles by PCR/RFLP and hybridization with S. cerevisiae subtelomeric sequences X and Y' to electrophoretic karyotypes of brewing yeasts and related species confirmed our findings and revealed substantial heterogeneity in the genome constitution of Czech brewing yeasts used in production.
ESTHER : Casaregola_2001_Int.J.Syst.Evol.Microbiol_51_1607
PubMedSearch : Casaregola_2001_Int.J.Syst.Evol.Microbiol_51_1607
PubMedID: 11491364
Gene_locus related to this paper: yeast-met2

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 3.1.1.3). 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