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2.
Yeast ; 27(11): 941-54, 2010 Nov.
Article in English | MEDLINE | ID: mdl-20602448

ABSTRACT

The transcriptional regulator HAP4, whose expression is induced on respiratory substrates, has been shown to be involved in the balance between fermentation and respiration in Saccharomyces cerevisiae. We have previously identified a HAP4 orthologue in the yeast Hansenula polymorpha, called HpHAP4-A, which, despite its very limited sequence conservation (a 16 amino acid N-terminal motif), is fully functional in S. cerevisiae. Based on the same N-terminal motif, a second gene has now been identified in the same organism. It was shown to contain an additional cis-binding motif of the bZip type. We report on the cloning, heterologous expression and analysis in S. cerevisiae of this novel ScHAP4 orthologue. From these experiments we could conclude that, as with HpHAP4-A, the novel orthologue, designated HpHAP4-B, could functionally replace the S. cerevisiae gene but to a lesser extent. The relationship between the presence of the additional cis-binding motif and the weaker potential as a HAP4 functional homologue is discussed.


Subject(s)
CCAAT-Binding Factor/deficiency , Pichia/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Amino Acid Motifs , Amino Acid Sequence , Genetic Complementation Test , Molecular Sequence Data , Protein Binding , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins
3.
Yeast ; 25(2): 129-40, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18081196

ABSTRACT

To extract functional information on genes and processes from large expression datasets, analysis methods are required that can computationally deal with these amounts of data, are tunable to specific research questions, and construct classifiers that are not overspecific to the dataset at hand. To satisfy these requirements, a stepwise procedure that combines elements from principal component analysis and discriminant analysis, was developed to specifically retrieve genes involved in processes of interest and classify samples based upon those genes. In a global expression dataset of 300 gene knock-outs in Saccharomyces cerevisiae, the procedure successfully classified samples with similar 'cellular component' Gene Ontology annotations of the knock-out gene by expression signatures of limited numbers of genes. The genes discriminating 'mitochondrion' from the other subgroups were evaluated in more detail. The thiamine pathway turned out to be one of the processes involved and was successfully evaluated in a logistic model to predict whether yeast knock-outs were mitochondrial or not. Further, this pathway is biologically related to the mitochondrial system. Hence, this strongly indicates that our approach is effective and efficient in extracting meaningful information from large microarray experiments and assigning functions to yet uncharacterized genes.


Subject(s)
Computational Biology/methods , Gene Expression Profiling , Genes, Mitochondrial/genetics , Genome, Fungal/genetics , Mutation/genetics , Saccharomyces cerevisiae/genetics , Thiamine/biosynthesis , Gene Expression Regulation, Fungal , Genes, Fungal/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
4.
Gene ; 377: 169-76, 2006 Aug 01.
Article in English | MEDLINE | ID: mdl-16777356

ABSTRACT

Mutations in mitochondrial tRNA genes can produce alterations in tRNA structure resulting in defective mitochondrial protein synthesis and hence respiratory defects. Such defects are often at the origin of neurodegenerative diseases in humans and can be easily studied in yeast since respiratory deficient mutants are viable. Several nuclear encoded tRNA interactors have been shown to rescue the mitochondrial defects due to mutations in mitochondrial tRNAs. Among these, we have identified the gene for the mitochondrial protein synthesis elongation factor EF-Tu and the specific mt aminoacyl-tRNA synthetases. We also observed that the respiratory defects and the effect of the TUF1 over-expression were strongly strain dependent. The importance of the nuclear background in which the mitochondrial mutation is expressed was investigated by changing the nuclear context. Finally, we demonstrated, using the RT-PCR method, the existence of significantly variable levels of the TUF1 transcript among strains with functional and dysfunctional mitochondria.


Subject(s)
Mutation , RNA, Fungal/genetics , RNA, Transfer/genetics , RNA/genetics , Saccharomyces cerevisiae/genetics , Amino Acyl-tRNA Synthetases/genetics , Base Sequence , DNA, Fungal/genetics , Genes, Fungal , Peptide Elongation Factor Tu/genetics , Phenotype , RNA, Mitochondrial , Suppression, Genetic , Transcription Factors/genetics , Transcription, Genetic
5.
Curr Genet ; 47(3): 172-81, 2005 Mar.
Article in English | MEDLINE | ID: mdl-15614490

ABSTRACT

In Saccharomyces cerevisiae, the HAP transcriptional complex is involved in the fermentation-respiration shift. This complex is composed of four subunits. Three subunits are necessary for DNA-binding, whereas the Hap4p subunit, glucose-repressed, contains the transcriptional activation domain. Hap4p is the key regulator of the complex activity in response to carbon sources in S. cerevisiae. To date, no HAP4 homologue has been identified, except in Kluyveromyces lactis. Examination of these two HAP4 sequences led to the identification of two very short conserved peptides also identified in other yeasts. In the yeast Hansenula polymorpha, two possible HAP4 homologues have been found. Their deduced amino acid sequences are similar to the ScHap4p and KlHap4p proteins only in the N-terminal 16-amino-acid basic motif. Since molecular genetic tools exist and complete genome sequence is known for this yeast, we expressed one of these putative HpHap4 proteins in S. cerevisiae and showed that this protein is able to restore the growth defect of the S. cerevisiae hap4-deleted strain. A set of experiments was performed to confirm the functional homology of this new gene with ScHAP4. The discovery of a Hap4-regulatory protein in H. polymorpha with only the N-terminal conserved domain of the S. cerevisiae protein indicates that this domain may play a crucial role during evolution.


Subject(s)
Gene Expression Regulation, Fungal , Pichia/genetics , Saccharomyces cerevisiae/genetics , CCAAT-Binding Factor , Fermentation/genetics , Oxygen/metabolism , Pichia/metabolism , Protein Structure, Tertiary/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins , Sequence Homology, Amino Acid , Transcription Factors
6.
EMBO Rep ; 4(1): 53-8, 2003 Jan.
Article in English | MEDLINE | ID: mdl-12524521

ABSTRACT

We have taken advantage of the similarity between human and yeast (Saccharomyces cerevisiae) mitochondrial tRNA(Leu)(UUR), and of the possibility of transforming yeast mitochondria, to construct yeast mitochondrial mutations in the gene encoding tRNA(Leu)(UUR) equivalent to the human A3243G, C3256T and T3291C mutations that have been found in patients with the neurodegenerative disease MELAS (for mitochondrial 'myopathy, encephalopathy, lactic acidosis and stroke-like episodes'). The resulting yeast cells (bearing the equivalent mutations A14G, C26T and T69C) were defective for growth on respiratory substrates, exhibited an abnormal mitochondrial morphology, and accumulated mitochondrial DNA deletions at a very high rate, a trait characteristic of severe mitochondrial defects in protein synthesis. This effect was specific at least in the pathogenic mutation T69C, because when we introduced A or G instead of C, the respiratory defect was absent or very mild. All defective phenotypes returned to normal when the mutant cells were transformed by multicopy plasmids carrying the gene encoding the mitochondrial elongation factor EF-Tu. The ability to create and analyse such mutated strains and to select correcting genes should make yeast a good model for the study of tRNAs and their interacting partners and a practical tool for the study of pathological mutations and of tRNA sequence polymorphisms.


Subject(s)
Amino Acid Substitution , MELAS Syndrome/genetics , Mitochondria/physiology , Mutation, Missense , Peptide Elongation Factor Tu/physiology , Point Mutation , RNA, Fungal/genetics , RNA, Transfer, Leu/genetics , Saccharomyces cerevisiae/genetics , Base Sequence , Biolistics , DNA, Mitochondrial/genetics , Gene Expression Regulation, Fungal , Genetic Vectors/genetics , Humans , Molecular Sequence Data , Mutagenesis, Site-Directed , Peptide Elongation Factor Tu/genetics , Phenotype , Protein Biosynthesis , RNA, Fungal/chemistry , RNA, Transfer, Leu/chemistry , Recombinant Fusion Proteins/physiology , Saccharomyces cerevisiae/physiology , Sequence Alignment , Sequence Homology, Nucleic Acid
7.
Comp Funct Genomics ; 4(1): 37-46, 2003.
Article in English | MEDLINE | ID: mdl-18629096

ABSTRACT

We have compared Saccharomyces cerevisiae global gene expression in wild-type and mutants (Deltahap2 and Deltahap4) of the HAP transcriptional complex, which has been shown to be necessary for growth on respiratory substrates. Several hundred ORFs are under positive or negative control of this complex and we analyse here in detail the effect of HAP on mitochondria. We found that most of the genes upregulated in the wild-type strain were involved in organelle functions, but practically none of the downregulated ones. Nuclear genes encoding the different subunits of the respiratory chain complexes figure in the genes more expressed in the wild-type than in the mutants, as expected, but in this group we also found key components of the mitochondrial translation apparatus. This control of mitochondrial translation may be one of the means of coordinating mitochondrial and nuclear gene expression in elaborating the respiratory chain. In addition, HAP controls the nuclear genes involved in several other mitochondrial processes (import, mitochondrial division) that define the metabolic state of the cell, but not mitochondrial DNA replication and transcription. In most cases, a putative CCAAT-binding site is present upstream of the ORF, while in others no such sites are present, suggesting the control to be indirect. The large number of genes regulated by the HAP complex, as well as the fact that HAP also regulates some putative transcriptional activators of unknown function, place this complex at a hierarchically high position in the global transcriptional regulation of the cell.

8.
Gene ; 286(1): 43-51, 2002 Mar 06.
Article in English | MEDLINE | ID: mdl-11943459

ABSTRACT

We have previously characterized a Saccharomyces cerevisiae mutant which contains a mutation in the essential rpn11/mpr1 gene coding for the proteasomal regulatory subunit Rpn11. The mpr1-1 mutation shows the phenotypic characteristics generally associated with proteasomal mutations, such as cell cycle defects and accumulation of polyubiquitinated proteins. However, for the first time, mitochondrial defects have also been found to be a consequence of a mutation in a proteasomal gene (Mol. Biol. Cell 9 (1998) 2917-2931). Since the mutant strain is thermosensitive both on glucose and on glycerol, we searched for revertants in order to shed light on the Rpn11/Mpr1 functions. Spontaneous revertants able to grow on glucose but not on glycerol at 36 degrees C were isolated, and, only from them, revertants able to grow at 36 degrees C on glycerol were selected. Revertants of the two classes were found to be extragenic. The detailed characterization of these extragenic suppressors demonstrates that the phenotypes related to cell cycle defects can be dissociated from those concerned with mitochondrial organization.


Subject(s)
Cell Cycle Proteins/genetics , Cysteine Endopeptidases/genetics , Endopeptidases , Mitochondria/genetics , Multienzyme Complexes/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Amino Acid Sequence , Cell Cycle/genetics , Microscopy, Confocal , Molecular Sequence Data , Mutation , Proteasome Endopeptidase Complex , Sequence Homology, Amino Acid , Suppression, Genetic/genetics
9.
Yeast ; 18(6): 563-75, 2001 Apr.
Article in English | MEDLINE | ID: mdl-11284012

ABSTRACT

The yeast genome has been shown to contain a significant number of gene families with more than three members. In order to study these families it is often necessary to generate strains carrying deletions of all members of the family, which can require a wide range of auxotrophic markers. To facilitate such studies, we have generated yeast strains containing deletions of a selection of nutritional marker genes (ade2, ade4, ade8, met3 and met14). We have also cloned the corresponding cognate genes, allowing their use in PCR-based gene disruptions. Two new pRS family Saccharomyces cerevisiae-Escherichia coli shuttle vectors containing ADE8 (one low-copy, pRS4110, and one high-copy, pRS4210) have been produced for use in conjunction with the new strains. A system for easier synthetic lethal screening using one of these new markers is also presented. The ADE8 and HIS3 genes have been cloned together on a high-copy vector (pRS4213), providing a plasmid for red-white colour screening in the ade2 Delta 0 ade8 Delta 0 strains we have generated. In contrast to some conventional systems, this plasmid allows for screening using gene libraries constructed in URA3 plasmids.


Subject(s)
Genetic Vectors/genetics , Plasmids/genetics , Saccharomyces cerevisiae/genetics , Base Sequence , Cloning, Molecular , DNA Primers , Gene Deletion , Genes, Fungal/physiology , Genetic Markers/genetics , Genome, Fungal , Molecular Sequence Data , Plasmids/chemistry , Polymerase Chain Reaction , Sequence Analysis, DNA
10.
Yeast ; 18(3): 219-27, 2001 Feb.
Article in English | MEDLINE | ID: mdl-11180455

ABSTRACT

We report the identification and characterization of a new mutation (ts9) in the Saccharomyces cerevisiae mitochondrial genome, which was first genetically mapped in the tRNAgly region and further identified by means of sequencing as consisting of a G to A transition at position 30 in the tRNA. The mutation causes an almost complete disappearance of mature tRNAgly, while a second mitochondrial mutation with a compensatory C to T change restores it in normal quantities; this points to the importance of the strong bond between bases 30 and 40 of the anticodon stem in the stabilization of the tRNA. In addition to resulting in a clear-cut heat-sensitive phenotype, the ts9 mutation creates a new EcoRV restriction site. Both properties were used as markers to monitor the successful (re) introduction of the mutated allele into a wild-type mitochondrial genome through biolistic transformation. The mutant frequency in the progeny as well as the correct integration of the mutated allele at its proper site demonstrate the feasibility of this method for creating and investigating specific mitochondrial tRNA mutations. The method will provide important applications for the use of yeast as a model system of human mitochondrial pathologies.


Subject(s)
Bacterial Proteins , RNA, Fungal/genetics , RNA, Transfer, Gly/genetics , RNA/genetics , Saccharomyces cerevisiae/genetics , Base Sequence , Biolistics , Blotting, Northern , Blotting, Southern , DNA, Mitochondrial/chemistry , DNA, Mitochondrial/genetics , DNA, Mitochondrial/physiology , Deoxyribonucleases, Type II Site-Specific/chemistry , Genome, Fungal , Hot Temperature , Humans , Mitochondria/genetics , Molecular Sequence Data , Neurodegenerative Diseases/genetics , Peptide Elongation Factor Tu , Point Mutation/physiology , RNA/chemistry , RNA, Mitochondrial , RNA, Transfer, Gly/chemistry , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/growth & development , Sequence Analysis, DNA , Transformation, Genetic
11.
Enzyme Microb Technol ; 26(9-10): 771-780, 2000 Jun 01.
Article in English | MEDLINE | ID: mdl-10862884

ABSTRACT

In the recent past, through advances in development of genetic tools, the budding yeast Kluyveromyces lactis has become a model system for studies on molecular physiology of so-called "Nonconventional Yeasts." The regulation of primary carbon metabolism in K. lactis differs markedly from Saccharomyces cerevisiae and reflects the dominance of respiration over fermentation typical for the majority of yeasts. The absence of aerobic ethanol formation in this class of yeasts represents a major advantage for the "cell factory" concept and large-scale production of heterologous proteins in K. lactis cells is being applied successfully. First insight into the molecular basis for the different regulatory strategies is beginning to emerge from comparative studies on S. cerevisiae and K. lactis. The absence of glucose repression of respiration, a high capacity of respiratory enzymes and a tight regulation of glucose uptake in K. lactis are key factors determining physiological differences to S. cerevisiae. A striking discrepancy exists between the conservation of regulatory factors and the lack of evidence for their functional significance in K. lactis. On the other hand, structurally conserved factors were identified in K. lactis in a new regulatory context. It seems that different physiological responses result from modified interactions of similar molecular modules.

12.
Mol Microbiol ; 36(4): 830-45, 2000 May.
Article in English | MEDLINE | ID: mdl-10844671

ABSTRACT

Yeast genes regulated by the transcriptional activator Yap1p were screened by two independent methods: (i) use of a LacZ-fused gene library and (ii) high-density membrane hybridization. Changes in transcriptome profile were examined in the presence and in the absence of Yap1p, as well as under normal and H2O2-mediated stress conditions. Both approaches gave coherent results, leading to the identification of many genes that appear to be directly or indirectly regulated by Yap1p. Promoter sequence analysis of target genes revealed that this regulatory effect is not always dependent upon the presence of a Yap1p binding site. The results show that the regulatory role of Yap1p is not restricted to the activation of stress response but that this factor can act as a positive or a negative regulator, both under normal and oxidative stress conditions. Among the targets, a few genes participating in growth control cascades were detected. In particular, the RPI1 gene, a repressor of the ras-cAMP pathway, was found to be downregulated by Yap1p during the early phase of growth, but upregulated in the stationary phase or after oxidative stress.


Subject(s)
DNA-Binding Proteins/physiology , Fungal Proteins/physiology , Gene Expression Regulation, Fungal , Genes, Fungal , Hydrogen Peroxide/pharmacology , Oxidative Stress , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Transcription Factors/physiology , Aerobiosis , Cell Division , Gene Expression Regulation, Fungal/drug effects , Genes, Fungal/drug effects , Glutathione/biosynthesis , Lac Operon , Nucleic Acid Hybridization , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae/growth & development
13.
FEBS Lett ; 487(1): 3-12, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152876

ABSTRACT

The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the 'yeast-specific' genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated 'Génolevures'.


Subject(s)
Ascomycota/genetics , Evolution, Molecular , Genome, Fungal , Phylogeny , Ascomycota/physiology , Genomics/methods , Molecular Sequence Data , RNA, Ribosomal , Sequence Analysis, DNA
14.
FEBS Lett ; 487(1): 17-30, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152878

ABSTRACT

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.


Subject(s)
Ascomycota/genetics , Genomics/methods , Sequence Alignment/methods , Sequence Analysis, DNA/methods , Amino Acid Sequence , Electronic Data Processing/methods , Gene Library , Genetic Code , Genome, Fungal , Molecular Sequence Data , Reproducibility of Results , Sequence Homology, Amino Acid
15.
FEBS Lett ; 487(1): 31-6, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152879

ABSTRACT

Since its completion more than 4 years ago, the sequence of Saccharomyces cerevisiae has been extensively used and studied. The original sequence has received a few corrections, and the identification of genes has been completed, thanks in particular to transcriptome analyses and to specialized studies on introns, tRNA genes, transposons or multigene families. In order to undertake the extensive comparative sequence analysis of this program, we have entirely revisited the S. cerevisiae sequence using the same criteria for all 16 chromosomes and taking into account publicly available annotations for genes and elements that cannot be predicted. Comparison with the other yeast species of this program indicates the existence of 50 novel genes in segments previously considered as 'intergenic' and suggests extensions for 26 of the previously annotated genes.


Subject(s)
Genome, Fungal , Saccharomyces cerevisiae/genetics , Ascomycota/genetics , Chromosomes, Fungal , DNA, Intergenic , Genes, Fungal , Multigene Family , Open Reading Frames , RNA, Transfer/genetics , Sequence Alignment/methods
16.
FEBS Lett ; 487(1): 66-70, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152886

ABSTRACT

Random sequencing of the Kluyveromyces lactis genome allowed the identification of 2235-2601 open reading frames (ORFs) homologous to S. cerevisiae ORFs, 51 ORFs which were homologous to genes from other species, 64 tRNAs, the complete rDNA repeat, and a few Ty1- and Ty2-like sequences. In addition, the complete sequence of plasmid pKD1 and a large coverage of the mitochondrial genome were obtained. The global distribution into general functional categories found in Saccharomyces cerevisiae and as defined by MIPS is well conserved in K. lactis. However, detailed examination of certain subcategories revealed a small excess of genes involved in amino acid metabolism in K. lactis. The sequences are deposited at EMBL under the accession numbers AL424881-AL430960.


Subject(s)
Genome, Fungal , Kluyveromyces/genetics , Ascomycota/genetics , Centromere/genetics , Chromosomes, Fungal , DNA Transposable Elements , DNA, Mitochondrial , DNA, Ribosomal , Fungal Proteins/genetics , Gene Dosage , Gene Order , Molecular Sequence Data , Open Reading Frames , Plasmids/genetics , RNA, Transfer/genetics , Saccharomyces cerevisiae/genetics , Sequence Homology, Amino Acid
17.
FEBS Lett ; 487(1): 101-12, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152893

ABSTRACT

We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events.


Subject(s)
Ascomycota/genetics , Chromosome Mapping/methods , Chromosomes, Fungal , Gene Order , Genomics/methods , Computational Biology/methods , Gene Deletion , Gene Duplication , Saccharomyces cerevisiae/genetics
18.
FEBS Lett ; 487(1): 113-21, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152894

ABSTRACT

Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from 'maverick' genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the 'maverick' genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear 'Ascomycetes-specific'. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the 'Ascomycetes-specific' genes tend to diverge more rapidly in evolution than that of other genes. Half of the 'Ascomycetes-specific' genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them.


Subject(s)
Ascomycota/genetics , Genes, Fungal , Base Sequence , Conserved Sequence , Evolution, Molecular , Genetic Variation , Saccharomyces cerevisiae/genetics , Species Specificity
19.
FEBS Lett ; 487(1): 122-33, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152895

ABSTRACT

We have evaluated the degree of gene redundancy in the nuclear genomes of 13 hemiascomycetous yeast species. Saccharomyces cerevisiae singletons and gene families appear generally conserved in these species as singletons and families of similar size, respectively. Variations of the number of homologues with respect to that expected affect from 7 to less than 24% of each genome. Since S. cerevisiae homologues represent the majority of the genes identified in the genomes studied, the overall degree of gene redundancy seems conserved across all species. This is best explained by a dynamic equilibrium resulting from numerous events of gene duplication and deletion rather than by a massive duplication event occurring in some lineages and not in others.


Subject(s)
Ascomycota/genetics , Evolution, Molecular , Genes, Fungal , Base Sequence , Conserved Sequence , Genetic Variation , Genome, Fungal , Models, Genetic , Multigene Family , Saccharomyces cerevisiae/genetics , Telomere/genetics
20.
FEBS Lett ; 487(1): 134-49, 2000 Dec 22.
Article in English | MEDLINE | ID: mdl-11152896

ABSTRACT

We explored the biological diversity of hemiascomycetous yeasts using a set of 22000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well-known species-specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete-specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species-specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.


Subject(s)
Ascomycota/genetics , Fungal Proteins/classification , Fungal Proteins/metabolism , Genes, Fungal , Fungal Proteins/genetics , Gene Amplification , Genetic Variation , Genomics/methods , Phylogeny , Saccharomyces cerevisiae , Sequence Homology, Nucleic Acid , Software , Species Specificity , Yeasts/genetics
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