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C Gaillardin

Publications and source records attributed to C Gaillardin.

At least 73 records · Page 4Linked to original sources

Yarrowia lipolytica TSR1 gene product. A novel endoplasmic reticulum membrane component involved in the signal recognition particle-dependent translocation pathway.

The tsr1-1 mutation has been initially identified as an extragenic suppressor of the scr2.II-13 mutation that alters the 7SL RNA component of the signal recognition particle (SRP) and results in severe defects in protein translocation and SRP stability. We showed previously that the TSR1 gene was essential and that the tsr1-1 mutation allowed complete recovery of scr2.II-13-associated secretory defects. We show here that the tsr1-1 mutation also restores SRP stability in an scr2.II-13 context. The TSR1 gene product (Tsr1p) is stably associated with rapidly sedimenting material and cofractionates with the lumenal protein Kar2p of the endoplasmic reticulum; it behaves in protease protection assays as a transmembrane component. Coimmunoprecipitation experiments revealed a physical interaction with Kar2p and with ribosomal components associated to the 5.8S rRNA as well as with SRP components like Sec65p and 7SL RNA. We propose that Tsr1p is an important component of the endoplasmic reticulum membrane, interacting both with the SRP-ribosome complex in the cytosol and with Kar2p in the lumen of the endoplasmic reticulum.

Biological Transport↗

The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications.

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.

Base Sequence↗

Stationary-phase gene expression in Saccharomyces cerevisiae during wine fermentation.

Genetic engineering of wine yeast strains requires the identification of gene promoters specifically activated under wine processing conditions. In this study, transcriptional activation of specific genes was followed during the time course of wine fermentation by quantifying mRNA levels in a haploid wine strain of Saccharomyces cerevisiae grown on synthetic or natural winery musts. Northern analyses were performed using radioactive probes from 19 genes previously described as being expressed under laboratory growth conditions or on molasses in S. cerevisiae during the stationary phase and/or under nitrogen starvation. Nine genes, including members of the HSP family, showed a transition-phase induction profile. For three of them, mRNA transcripts could be detected until the end of the fermentation. Expression of one of these genes, HSP30, was further studied using a HSP30::lacZ fusion on both multicopy and monocopy expression vectors. The production of beta-galactosidase by recombinant cells was measured during cell growth and fermentation on synthetic and natural winery musts. We showed that the HSP30 promoter can induce high gene expression during late stationary phase and remains active until the end of the wine fermentation process. Similar expression profiles were obtained on five natural winery musts.

Fermentation↗

One-step transformation of the dimorphic yeast Yarrowia lipolytica.

An efficient one-step transformation method for the dimorphic yeast Yarrowia lipolytica is described. Using cells grown overnight on agar plates, the whole process is carried out within 1 h. The transformant clones could be recovered on selective plates as early as 36-48 h after plating. The efficiency was better than 10(5) transformants/micrograms replicative plasmid DNA. Effects of cell density, dithiothreitol, heat shock, poly(ethylene glycol) 4000 concentration and the wetness of selective plates were investigated.

Saccharomycetales↗

Cloning the Yarrowia lipolytica homologue of the Saccharomyces cerevisiae SEC62 gene.

Yarrowia lipolytica SEC62 cDNA was cloned by functional complementation of a thermo-sensitive sec62 Saccharomyces cerevisiae mutant strain. The Y. lipolytica SEC62 promoter region was amplified by the inverse polymerase chain reaction (PCR). The cDNA codes for a 396 amino-acid protein with two potential trans-membrane domains. Y. lipolytica Sec62p behaves as an integral membrane protein as shown by Western blotting. Y. lipolytica SEC62 cDNA is able to complement a S. cerevisiae sec62 null mutant strain confirming functional conservation, although only 53.6% amino-acid similarity is observed between Y. lipolytica and S. cerevisiae Sec62.

Amino Acid Sequence↗

Genomic organization of the yeast Yarrowia lipolytica.

We produced electrophoretic karyotypes of the reference strain E150 and of seven other isolates from different geographical origins to study the genomic organization of the dimorphic yeast Yarrowia lipolytica. These karyotypes differed in the number and size of the chromosomal bands. The karyotype of the reference stain E150 consisted of five bands of between 2.6 and 4.9 Mb in size. This strain contained at least five rDNA clusters, from 190 to 620 kb in size, which were scattered over most of the chromosomes. The assignment of 43 markers, including rRNA genes and three centromeres, to the E150 bands defined five linkage groups. Hybridization to the karyotypes of other isolates with pools of markers of each linkage group showed that linkage groups I, II, IV and V were conserved in the strains tested whereas group III was not and was split between at least two chromosomes in most strains. Use of a meganuclease I-SceI site targeted to one locus of E150 linkage group III showed that two chromosomes actually comigrated in band III of this strain. Our results are compatible with six chromosomes defining the haploid complement of strains of Y. lipolytica and that, despite an unprecedented chromosome length polymorphism, the overall structure of the genome is conserved in different isolates.

Ascomycota↗

Hyperthermostable mutants of Bacillus licheniformis alpha-amylase: thermodynamic studies and structural interpretation.

This paper provides further understanding of the thermodynamic and structural features determining the stability of Bacillus licheniformis alpha-amylase (BLA) at two crucial positions, His133 and Ala209. Results of protein modelling and saturated site-directed mutagenesis at position 133 and 209 have been reported in a previous paper (Declerck et al., 1995, Prot. Engng, 8, 1029-1037). In the first part of the present work, evidence is presented supporting the hypothesis that the stabilizing mutations reduce the rate of initial unfolding of the enzyme during the reversible step of the inactivation reaction and do not modify the irreversible processes undergone subsequently by the unfolded molecules. In the second part, we have examined the three-dimensional structure of BLA which has been determined recently by X-ray analysis (Machius et al., 1995, J. Mol. Biol., 246, 545-559). This analysis showed that our previous predictions made from molecular modelling were partly correct. At position 209, the effect of the stabilizing substitutions can be explained by a groove-filling effect reinforcing the hydrophobic packing between two helices of the central domain, while preserving a well-ordered water structure at the surface. At position 133, the stabilizing substitutions must compensate the loss of the hydrogen bond network in which the original histidine side-chain is involved; this compensation could be achieved through enhanced hydrophobic side-chain interactions within the beta-sheet where residue 133 is located, which correlates with the propensity of the residue to form and maintain a beta-strand conformation of the main chain at this position.

Alanine↗

Physiology and genetics of the dimorphic fungus Yarrowia lipolytica.

The ascomycetous yeast Yarrowia lipolytica (formerly Candida, Endomycopsis, or Saccharomyces lipolytica) is one of the more intensively studied 'non-conventional' yeast species. This yeast is quite different from the well-studied yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe with respect to its phylogenetic evolution, physiology, genetics, and molecular biology. However, Y. lipolytica is not only of interest for fundamental research, but also for biotechnological applications. It secretes several metabolites in large amounts (i.e. organic acids, extracellular proteins) and the tools are available for overproduction and secretion of foreign proteins. This review presents a comprehensive overview on the available data on physiology, cell biology, molecular biology and genetics of Y. lipolytica.

Chromosomes, Fungal↗

Genetic analysis of regulatory mutants affecting synthesis of extracellular proteinases in the yeast Yarrowia lipolytica: identification of a RIM101/pacC homolog.

Depending on the pH of the growth medium, the yeast Yarrowia lipolytica secretes both an acidic proteinase and an alkaline proteinase, the synthesis of which is also controlled by carbon, nitrogen, and sulfur availability, as well as by the presence of extracellular proteins. Recessive mutations at four unlinked loci, named PAL1 to PAL4, were isolated which prevent alkaline proteinase derepression under conditions of carbon and nitrogen limitation at pH 6.8. These mutations markedly affect mating and sporulation. A dominant suppressor of all four PAL mutations was isolated from a wild-type genomic library, which turned out to be a C-terminally truncated form of a 585-residue transcriptional factor of the His2Cys2 zinc finger family, which we propose to call YlRim101p. Another C-terminally truncated version of YlRim101p (419 residues) is encoded by the dominant RPH2 mutation previously isolated as expressing alkaline protease independently of the pH. YlRim101p is homologous to the transcriptional activators Rim101p of Saccharomyces cerevisiae, required for entry into meiosis, and PacC of Aspergillus nidulans and Penicillium chrysogenum, which were recently shown to mediate regulation by ambient pH. YlRim101p appears essential for mating and sporulation and for alkaline proteinase derepression. YlRIM101 expression is autoregulated, maximal at alkaline pH, and strongly impaired by PAL mutations.

Amino Acid Sequence↗

Cloning of SEC61 homologues from Schizosaccharomyces pombe and Yarrowia lipolytica reveals the extent of functional conservation within this core component of the ER translocation machinery.

The Sec61 protein is required for protein translocation across the ER membrane in both yeast and mammals and is found in close association with polypeptides during their membrane transit. In Saccharomyces cerevisiae Sec61p is essential for viability and the extent of sequence similarity between the yeast and mammalian proteins (55% sequence identity) suggests that the role of Sec61p in the translocation mechanism is likely to be conserved. In order to further our understanding of the structure and function of Sec61p we have cloned homologues from both Schizosaccharomyces pombe and Yarrowia lipolytica. The S. pombe gene comprises six exons encoding a 479 residue protein which we have immunolocalised to the endoplasmic reticulum. Sequence comparisons reveal that S. pombe Sec61p is 58.6% identical to that of S. cerevisiae. The deduced amino acid sequence of the Y. lipolytica protein shares 68.8% sequence identity with S. cerevisiae Sec61p. Gene disruption studies have shown that the SEC61 is required for viability in both S. pombe and Y. lipolytica demonstrating that the essential nature of this protein is not unique to S. cerevisiae. Moreover, heterologous complementation studies indicate that the Y. lipolytica SEC61 gene can complement a null mutation in S. cerevisiae. Sequence comparisons between the various eukaryotic Sec61p homologues reveal a number of highly conserved domains, including several transmembrane sequences and the majority of cytosolic loops. These comparisons will provide an important framework for the detailed analysis of interactions between Sec61p and other components of the translocation machinery and between Sec61p and translocating polypeptide chains.

Amino Acid Sequence↗

The TSR1 gene of Yarrowia lipolytica is involved in the signal recognition particle-dependent translocation pathway of secretory proteins.

We have isolated suppressors (tsr1 to tsr5) of the thermosensitive growth of the scr2.II-13 mutation, which affects the stability of the signal recognition particle. The growth of these mutants is largely affected in the SCR2 context at 34 degrees C. We have studied the synthesis and secretion of an alkaline extracellular protease (AEP) in both wild-type and tsr1-1(SCR2(+)) thermosensitive mutant strains. Pulse-chase labeling and immunoprecipitation of this protein showed that the level of AEP precursors in the tsr1-1(SCR2(+)) strain is 70% less than in the wild-type strain under conditions where the global protein synthesis is practically unaffected. This defect was observed as early as 10 min after the shift to nonpermissive temperature. In neither strain was there any effect on the kinetics of secretion, and no cytoplasmic accumulation was detected. We have cloned the TSR1 gene by complementing the thermosensitive phenotype of a tsr1-1(SCR2(+)) mutant. Analysis of the TSR1 DNA sequence revealed an open reading frame of 1383 base pairs, encoding a serine-rich protein of 461 amino acids with an amino-terminal signal peptide, and a membrane-spanning domain of 20 amino acids that could act as a stop transfer signal to ensure membrane localization of Tsr1p. Two homologues of the TSR1 gene were identified in Saccharomyces cerevisiae (YHC8) and Hansenula polymorpha (YLU2). Disruption of the TSR1 gene revealed that it is an essential single-copy gene. The TSR1 gene encodes a single mRNA of 1.5 kilobase pairs. The study of the synthesis and secretion of AEP in the complemented tsr1-1(SCR2(+),TSR1(+)) strain revealed that the TSR1 gene ensures complete recovery of the synthesis defect and thus could encode an important component of the endoplasmic reticulum membrane involved in the early steps of the signal recognition particle-dependent translocation pathway.

Amino Acid Sequence↗

Dominant mutations affecting expression of pH-regulated genes in Yarrowia lipolytica.

In the yeast Yarrowia lipolytica the levels of the alkaline extracellular protease (AEP) and acid extracellular protease (AXP) are controlled by the pH of the growth medium. When the pH of growth medium is kept close to 4.0, levels of AXP are high and those of AEP are low, whereas at pH above 6.0 the opposite is true. Mutations which mimic the effects on the protease system of growth at alkaline pH have been identified in two genes, RPH1 and RPH2, in Y. lipolytica. Detailed genetic studies showed that mutations in these two genes are dominant in heterozygous diploids, and that their effects are additive in haploid double mutants. These mutants show that pH regulates AEP expression independently from other metabolic signals. These mutants are not detectably affected in their growth rates, nor in internal pH homeostasis.

Chromosome Mapping↗

Sls1p, an endoplasmic reticulum component, is involved in the protein translocation process in the yeast Yarrowia lipolytica.

Signal recognition particle-dependent targeting of secretory proteins to the endoplasmic reticulum membrane is predominant in the yeast Yarrowia lipolytica. A conditional lethal mutant of the SCR2-encoded 7S RNA provided the first in vivo evidence for involvement of this particle in cotranslational translocation (He, F., Beckerich, J. M., and Gaillardin, C. M. (1992) J. Biol. Chem. 267, 1932-1937). In order to identify partners of 7S RNA or signal recognition particle in their function, we selected synthetic lethal mutations with the 7S RNA mutation (sls). The SLS1 gene, cloned by complementation of the sls1 mutant growth defect, encodes a 426-amino acid polypeptide containing a NH2-terminal signal peptide and a COOH-terminal endoplasmic reticulum (ER) retention motif. The SLS1 gene product behaves as a lumenal protein of the ER. Sls1p was sedimented with membrane-rich organelles and was resistant to protease degradation without prior membrane solubilization. Immunofluorescence microscopy showed a typical endoplasmic reticulum perinuclear staining. Co-immunoprecipitation revealed that Sls1p resides close to the major translocation apparatus component, Sec61p. Deletion of the SLS1 gene led to a temperature-sensitive growth phenotype. Synthesis of several secretory proteins was shown to be specifically reduced in delta sls1 cells. We propose that Sls1p acts in the preprotein translocation process, interacting directly with translocating polypeptides to facilitate their transfer and/or help their folding in the ER.

Amino Acid Sequence↗

Sequencing of a 9.2 kb telomeric fragment from the right arm of Saccharomyces cerevisiae chromosome XIV.

We report the complete sequence of a 9.2 kb fragment next to and including the right telomere of Saccharomyces cerevisiae chromosome XIV. Four open reading frames (ORFs) longer than 100 amino acids were observed in the sequenced segment. One ORF (378 codons) does not show any significant homology with proteins in the databases and corresponds to a putative new gene. Two ORFs are almost identical to the known YCR007/YKL219 and PAU1-like hypothetical protein families already identified on several S. cerevisiae chromosomes. These ORFs, whose function is unknown, are generally associated with sub-telomeric regions of chromosomes. The fourth one shows significant identities with bacterial mannitol dehydrogenases. It could be a yeast gene implicated in the metabolism of mannitol (or a related substrate). The sequence has been deposited in the EMBL data library under Accession Number X86790.

Amino Acid Sequence↗

Sticky-end polymerase chain reaction method for systematic gene disruption in Saccharomyces cerevisiae.

We describe a new procedure for the generation of plasmids containing a large promoter and terminator region of a gene of interest, useful for gene disruption. In a two-step polymerase chain reaction (PCR), a fragment, corresponding to the terminator and promoter regions separated by a 16 bp sequence containing a rare restriction site (e.g. AscI), is synthesized (T-P fragment). This PCR fragment is cloned in vectors presenting a rare blunt-end cloning site and a yeast marker for selection in Saccharomyces cerevisiae (TRP1, HIS3 and KanMX). The final plasmids are used directly for gene disruption after linearization by the enzyme (e.g. AscI) specific for the rare restriction site. This approach was used to disrupt three open reading frames identified during the sequencing of COS14-1 from chromosome XIV of S. cerevisiae.

Aldose-Ketose Isomerases↗

Cloning and sequencing of the LYS1 gene encoding homocitrate synthase in the yeast Yarrowia lipolytica.

The alpha-aminoadipate pathway for the biosynthesis of lysine is present only in fungi and euglena. The first step in the pathway is the condensation of acetyl-CoA and alpha-ketoglutarate into homocitrate, and this step is carried out by the enzyme homocitrate synthase (EC 4.1.3.21). In spite of extensive genetic analysis, no mutation affecting this step has been isolated until now in model organisms such as Saccharomyces cerevisiae or Neurospora crassa, although identification of mutations affecting the structural gene (LYS1) for homocitrate synthase was reported in the yeast Yarrowia lipolytica several years ago. Here we used these mutants for the cloning and sequencing of the Yarrowia LYS1 gene. The LYS1 gene encodes a predicted 446 amino acid polypeptide, with a molecular mass of 48442 Da. The Lys1p sequence displays two regions, one near the N-terminal section and the other in the central region, that contain conserved signatures found in prokaryotic homocitrate synthases (nifV genes of Azotobacter vinelandii and Klebsiella pneumoniae), as well as in all alpha-isopropyl malate synthases so far described. A putative mitochondrial targeting signal of 41-45 amino acids is predicted at the N-terminus. The Lys1p sequence shows 84% identity at the amino acid level with the putative product of open reading frame D1298 of S. cerevisiae. Northern blot hybridizations revealed a LYS1 transcript of approximately 1.7 kb in Y. lipolytica. Deletion of the LYS1 gene resulted in a Lys- phenotype. Our results indicate that we cloned the structural gene for homocitrate synthase in Y. lipolytica, and that the enzyme is encoded by a single gene in this yeast.

Amino Acid Sequence↗

Transformations of membrane-bound organelles in sec 14 mutants of the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica.

BACKGROUND: In early descriptions of ultrastructural alterations of secretory (sec) mutants of the yeast Saccharomyces cerevisiae, two mutants, sec7 and sec14, were shown to produce cell structures, the so-called Berkeley bodies thought at first to correspond to Golgi structures. In sec7 mutants grown at restrictive temperature, secretion granules soon dis-appeared, whereas networks of Golgi tubules increased in size and transformed into stacks of seven to eight flattened elements. At these time intervals, structures resembling Berkeley bodies appeared to be extensions of the endoplasmic reticulum (Rambourg et al., 1993). It is the purpose of the present study to examine by electron microscopy S. cerevisiae sec14 mutants and to compare the modifications along their secretory pathway with those occurring in a homologous mutant of Yarrowia lipolytica. METHODS: S. cerevisiae sec 14 mutant cells coming from exponentially growing cultures were examined either at 24 degrees C or after shifting at 37 degrees C for 0, 2, 5, 10, 15, 20, 30, 45, 60, 90, and 120 min. Y. lipolytica mutant cells were first cultured in YNB in 5000 medium and then transferred for 0, 6, 8, 12, 20, and 24 hr, in a phosphate-buffered YPD medium, which allows wild cells to differentiate from yeast to mycelian form. In both cases, cells were fixed in 2% glutaraldehyde, treated for 15 min in 1% sodium metaperiodate, post-fixed in reduced osmium, and embedded in Epon. To visualize the three-dimensional configuration of cell organelles, stereopairs were prepared from section stained with lead citrate and tilted at +/- 15 degrees from the 0 degree position of the goniometric stage of the electron microscope. RESULTS: In S. cerevisiae mutant cells shifted for 2 min at the restrictive temperature, faintly stained networks of thin anastomosed tubules were located at close proximity and often continuous with faintly stained ER cisternae. More intensely stained tubular networks with nodular dilations having the size of secretion granules were dispersed throughout the cytoplasm. Later on, the faintly stained ER elements and related tubular networks decreased in number, whereas the intensely stained nodular tubular networks increased in frequency. The incidence of secretion granules also increased and were distributed at random throughout the cytoplasm. Widemeshed, intensely stained fenestrated spheres were often encountered and increased in number, in parallel to the increase in the number of nodular tubular networks. At late time intervals, the fenestrated spheres decreased in number as they seemingly transformed into spherical bodies identical to vacuoles. In contrast to what occurred in S. cerevisiae sec14 mutant, the main ultrastructural modification observed in Y. lipolytica transferred to the YPD medium was the formation of deep plasma membrane invaginations. CONCLUSIONS: It appears that two functionally homologous PI/PC transfer proteins (Sec14psc and Sec14pyl) control distinct physiological processes in the two sec14 mutants examined. Such differences are perhaps related to the regulatory role of these proteins in different target organelles, i.e., the Golgi apparatus in S. cerevisiae or the plasma membrane in Y. lipolytica.

Carrier Proteins↗

Efficient selection of hygromycin-B-resistant Yarrowia lipolytica transformants.

The yeast Yarrowia lipolytica was shown to be sensitive to the aminoglycoside antibiotic hygromycin B. Spontaneous resistants appeared at a frequency of (2-5) x 10(-7) in media containing 100 mg/l drug. In order to develop a new selective marker for the transformation of this yeast, we constructed new plasmids expressing the Escherichia coli hygromycin-resistance gene (hph) under the control of the promoter and terminator sequences of the strongly expressed XPR2 gene of Y. lipolytica. Direct selection of hygromycin-B-resistant transformants on complete medium was very efficient and resulted in transformation frequencies comparable to those observed with conventional auxotrophic markers. This new marker can be used for integrating single copies of plasmid and for gene disruption and provides a convenient tag for genetic studies.

Anti-Bacterial Agents↗