Complete DNA sequence of yeast chromosome XI

'Mass-murder' of ORFs from three regions of chromosome XI from Saccharomyces cerevisiae

The complete sequence of the yeast Saccharomyces cerevisiae reveals the presence of many new genes, many of which are without homologs in databases. Characterisation of these genes by novel methods includes systematic deletion followed by phenotypic analysis of mutant strains. We have developed a hierarchical strategy for such a functional analysis of genes, in which the primary phenotypic screening is performed on groups of contiguous genes which are then reinvestigated down to the single gene level. This strategy is applied to the whole chromosome XI as part of EUROFAN (the EUROpean Functional ANalysis) program, and we present here our results on a group of 22 genes from this chromosome. This sample is representative of the results that are emerging for the whole chromosome. Out of the 22 genes deleted, three were shown to be essential, and another three genes confer a mutant growth phenotype to cells when deleted. All phenotypes have been complemented. These figures are in accordance with the previously published fraction of lethal and growth-defective deletions of single genes. We have found no synthetic phenotypes resulting from a combination of deleted genes and have always been able to attribute a mutant phenotype to a single gene.

Sld2, which interacts with Dpb11 in Saccharomyces cerevisiae, is required for chromosomal DNA replication

The DPB11 gene, which genetically interacts with DNA polymerase II (epsilon), one of three replicative DNA polymerases, is required for DNA replication and the S phase checkpoint in Saccharomyces cerevisiae. To identify factors interacting with Dbp11, we have isolated sld (synthetically lethal with dpb11-1) mutations which fall into six complementation groups (sld1 to -6). In this study, we characterized SLD2, encoding an essential 52-kDa protein. High-copy SLD2 suppressed the thermosensitive growth defect caused by dpb11-1. Conversely, high-copy DPB11 suppressed the temperature-sensitive growth defect caused by sld2-6. The interaction between Sld2 and Dpb11 was detected in a two-hybrid assay. This interaction was evident at 25 degreesC but not at 34 degreesC when Sld2-6 or Dpb11-1 replaced its wild-type protein. No interaction between Sld2-6 and Dpb11-1 could be detected even at 25 degreesC. Immunoprecipitation experiments confirmed that Dpb11 physically interacts with Sld2. sld2-6 cells were defective in DNA replication at the restrictive temperature, as were dpb11-1 cells. Further, in dpb11-1 and sld2-6 cells, the bubble-shaped replication intermediates formed in the region of the autonomously replicating sequence reduced quickly after a temperature shift. These results strongly suggest the involvement of the Dpb11-Sld2 complex in a step close to the initiation of DNA replication.

Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes

The heterogeneity within, and similarities between, yeast chromosomes are studied. For the former, we show by the size distribution of domains, coding density, size distribution of open reading frames, spatial power spectra, and deviation from binomial distribution for C + G% in large moving windows that there is a strong deviation of the yeast sequences from random sequences. For the latter, not only do we graphically illustrate the similarity for the above mentioned statistics, but we also carry out a rigorous analysis of variance (ANOVA) test. The hypothesis that all yeast chromosomes are similar cannot be rejected by this test. We examine the two possible explanations of this interchromosomal uniformity: a common origin, such as genome-wide duplication (polyploidization), and a concerted evolutionary process.

Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC

A novel gene encoding a cytosine-5-DNA methyltransferase recognizing the dinucleotide GpC was cloned from Chlorella virus NYs-1 and expressed in both Escherichia coli and Saccharomyces cerevisiae . The gene was sequenced and a predicted polypeptide of 362 amino acids with a molecular weight of 41.903 kDa was identified. The protein contains several amino acid motifs with high similarity to those of other known 5-methylcytosine-forming methyltransferases. In addition, this enzyme, named M. Cvi PI, shares 66% identity and 76% similarity with M. Cvi JI, the only other cytosine-5-DNA methyltransferase cloned from a Chlorella virus. The short, frequently occurring recognition sequence of the new methyltransferase will be very useful for in vivo chromatin structure studies in both yeast and higher organisms.

Asymmetry of coding versus noncoding strand in coding sequences of different genomes

We have used the asymmetry between the coding and noncoding strands in different codon positions of coding sequences of DNA as a parameter to evaluate the coding probability for open reading frames (ORFs). The method enables an approximation of the total number of coding ORFs in the set of analyzed sequences as well as an estimation of the coding probability for the ORFs. The asymmetry observed in the nucleotide composition of codons in coding sequences has been used successfully for analysis of the genomes completed at the time of this analysis.

Computational methods for exon detection

Computer methods for the complete and accurate detection of genes in vertebrate genomic sequences are still a long way to perfection. The intermediate task of identifying the coding moiety of genes (coding exons) is now reasonably well achieved using a combination of methods. After reviewing the intrinsic difficulties in interpreting vertebrate genomic sequences, this article presents the state-of-the-art, with an emphasis on similarity search methods and the resources available through Internet.

Genetic and biochemical analysis of p23 and ansamycin antibiotics in the function of Hsp90-dependent signaling proteins

The ubiquitous molecular chaperone Hsp90 acts in concert with a cohort of associated proteins to facilitate the functional maturation of a number of cellular signaling proteins, such as steroid hormone receptors and oncogene tyrosine kinases. The Hsp90-associated protein p23 is required for the assembly of functional steroid aporeceptor complexes in cell lysates, and Hsp90-binding ansamycin antibiotics disrupt the activity of Hsp90-dependent signaling proteins in cultured mammalian cells and prevent the association of p23 with Hsp90-receptor heterocomplexes; these observations have led to the hypotheses that p23 is required for the maturation of Hsp90 target proteins and that ansamycin antibiotics abrogate the activity of such proteins by disrupting the interaction of p23 with Hsp90. In this study, I demonstrate that ansamycin antibiotics disrupt the function of Hsp90 target proteins expressed in yeast cells; prevent the assembly of Sba1, a yeast p23-like protein, into steroid receptor-Hsp90 complexes; and result in the assembly of receptor-Hsp90 complexes that are defective for ligand binding. To assess the role of p23 in Hsp90 target protein function, I show that the activity of Hsp90 target proteins is unaffected by deletion of SBA1. Interestingly, steroid receptor activity in cells lacking Sba1 displays increased sensitivity to ansamycin antibiotics, and this phenotype is rescued by the expression of human p23 in yeast cells. These findings indicate that Hsp90-dependent signaling proteins can achieve a functional conformation in vivo in the absence of p23. Furthermore, while the presence of p23 decreases the sensitivity of Hsp90-dependent processes to ansamycin treatment, ansamycin antibiotics disrupt signaling through some mechanism other than altering the Hsp90-p23 interaction.

A 9359 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII includes the FOL2 and YTA7 genes and three unknown open reading frames

In the framework of the EU programme for systematic sequencing of the Saccharomyces cervisiae genome we determined the sequence of a 9359 bp fragment of the right arm of chromosome VII. Five open reading frames (ORFs) of at least 300 nucleotides were found in this region. YGR267c encodes a protein with significant similarity to the enzyme GTP-cyclohydrolase I, that controls the first step in the biosynthetic pathway leading to various pterins and shows a high degree of sequence conservation from bacteria to mammals. We have recently demonstrated (Nardese et al., 1996) that YGR267c corresponds to the FOL2 gene, previously localized in the same chromosomal region by genetic mapping. The protein deduced from YGR270w belongs to the superfamily of putative ATPases associated with diverse cellular activities. It corresponds to the YTA7 gene, a member of a set of yeast genes coding for putative ATPases with high similarity to constituents of the 26S protease. The three ORFs YGR266w, YGR268c and YGR269w encode putative products of unknown function, with neither significant similarity to proteins in databases nor recognizable domains. YGR268c and YGR269w are partially overlapping ORFs: YGR268c seems to correspond to a real gene. whereas YGR269w is probably a fortuitous ORF.

Application of mRNA differential display to investigate gene expression in thermotolerant cells of Saccharomyces cerevisiae

We have described the use of differential display of PCR-amplified reverse transcribed mRNA (DDRT-PCR) to survey changes in gene expression profiles induced by heat shock and carbon catabolite derepression in Saccharomyces cerevisiae. It is well established that either of these states elicits thermotolerant phenotypes. An initial analysis conducted on cells of an inherently thermosensitive strain (Ysen) indicated that approximately 10% of the total number of cDNAs detected were either up or down regulated following heat shock at 37 degrees C (30 min) in comparison to control cells (25 degrees C). In addition, whereas 7% of all PCR products were preferentially expressed during derepressive growth, approximately 2% were found to be common to both heat-shocked and derepressed cells. A repeat analysis, performed on all three cell types of Ysen as well as cells of a relatively thermoresistant strain (Yres) yielded 30 differentially displayed cDNA fragments common to heat-shocked and derepressed cells of both strains. Eighteen of these generated signals on Northern blots, of which three were confirmed as regulated. Five amplicons, including one not detected by Northern analysis and another from the derepressed state, were cloned and sequenced. Three of these exhibited homology to S. cerevisiae genes with well-characterized protein products: HSP 90, HXK1 and STA1. The remaining two applicons showed nucleotide identity to YTIS11, a homolog of the mammalian TIS11 and putative transcriptional activator, and an orphan gene encoding a hypothetical transmembrane protein belonging to the multi-drug resistance translocase family. Our novel application of DDRT-PCR has identified new and known genes that may be further evaluated as factors involved in stress regulation and has demonstrated the potential of the technique to systematically analyse gene expression in yeast.

Systematic gain-of-function genetics in Drosophila

A modular misexpression system was used to carry out systematic gain-of-function genetic screens in Drosophila. The system is based on inducible expression of genes tagged by insertion of a P-element vector carrying a GAL4-regulated promoter oriented to transcribe flanking genomic sequences. To identify genes involved in eye and wing development, the 2300 independent lines were screened for dominant phenotypes. Among many novel genes, the screen identified known genes, including hedgehog and decapentaplegic, implicated in these processes. A genetic interaction screen for suppressors of a cell migration defect in a hypomorphic slow border cells mutant identified known genes with likely roles in tyrosine kinase signaling and control of actin cytoskeleton, among many novel genes. These studies demonstrate the ability of the modular misexpression system to identify developmentally important genes and suggest that it will be generally useful for genetic interaction screens.

A debilitating mutation in transcription factor IIE with differential effects on gene expression in yeast

The influence of transcription factor (TF) IIE on mRNA synthesis in vivo was examined in a temperature-sensitive yeast mutant. A missense mutation in the conserved zinc finger domain severely weakened TFIIE's transcription activity without appreciably affecting its quaternary structure, chromatographic properties, or cellular abundance. The mutation conferred recessive slow-growth and heat-sensitive phenotypes in yeast, but quantitative effects on promoter utilization by RNA polymerase II ranged from strongly negative to somewhat positive. Heat-induced activation of the HSP26, HSP104, and SSA4 genes was attenuated in the mutant, indicating dependence on TFIIE for maximal rates of de novo synthesis. Constitutive HSP expression in mutant cells was elevated, exposing a negative (likely indirect) influence by TFIIE in the absence of heat stress. Our results corroborate and extend recent findings of differential dependence on TFIIE activity for yeast promoters, but reveal an important counterpoint to the notion that dependence is tied to TATA element structure (Sakurai, H., Ohishi, T., and Fukasawa, T. (1997) J. Biol. Chem. 272, 15936-15942). We also provide empirical evidence for conservation of structure-activity relationships in TFIIE's zinc finger domain, and establish a direct link between TFIIE's biochemical activity in reconstituted transcription and its function in cellular mRNA synthesis.

The difficulty of identifying genes in anonymous vertebrate sequences

The identification of genes in newly determined vertebrate genomic sequences can range from a trivial to an impossible task. In a statistical preamble, we show how "insignificant" are the individual features on which gene identification can be rigorously based: promoter signals, splice sites, open reading frames, etc. The practical identification of genes is thus ultimately a tributary of their resemblance to those already present in sequence databases, or incorporated into training sets. The inherent conservatism of the currently popular methods (database similarity search, GRAIL) will greatly limit our capacity for making unexpected biological discoveries from increasingly abundant genomic data. Beyond a very limited subset of trivial cases, the automated interpretation (i.e. without experimental validation) of genomic data, is still a myth. On the other hand, characterizing the 60,000 to 100,000 genes thought to be hidden in the human genome by the mean of individual experiments is not feasible. Thus, it appears that our only hope of turning genome data into genome information must rely on drastic progresses in the way we identify and analyse genes in silico.

Programmed translational frameshifting in a gene required for yeast telomere replication

BACKGROUND

Telomeres are replicated in most eukaryotes by the enzyme telomerase, a specialized reverse transcriptase. A genetic screen in Saccharomyces cerevisiae designed to detect telomerase components previously led to the identification of four EST ('ever shorter telomeres') genes which are required for telomerase function in vivo. This report describes the cloning and characterization of EST3.

RESULTS

We identified a potential site of +1 ribosomal frameshifting in the EST3 coding sequence and demonstrated that translation both upstream and downstream of this site is required for EST3 function. Mutation of EST3 such that it could not frameshift resulted in a strain with the same phenotype as an est3 null mutant, showing that EST3 frameshifting is required for telomere replication. Immunoblot analysis revealed that two proteins were synthesized from EST3: a truncated protein resulting from translation of only the first open reading frame, as well as the full-length 181 amino-acid Est3 protein resulting from translation through the frameshift site. Only the full-length Est3 protein was required for normal EST3 function.

CONCLUSIONS

A programmed translational frameshifting mechanism similar to that used by yeast retrotransposons is employed to produce full-length Est3 protein. This is the first example in yeast of a cellular gene that uses frameshifting to make its protein product, and a potential link is suggested between retrotransposition and the telomerase pathway for telomere maintenance.

Trinucleotide repeats in yeast

The yeast genome exhibits a variety of trinucleotide repeat arrays within protein-coding genes and intergenic regions. In the first situation, repeats are often not random relative to the translational frame, resulting preferably in long stretches of the two acidic amino acids or of their corresponding amine forms. Interestingly, the longest trinucleotide repeats are often found in genes encoding nuclearly located proteins. Repeats tend to be more frequent in long genes, but less frequent among members of gene families compared to unique genes. In the latter case, repeat arrays often differ in length or composition between the gene homologs, indicating their instability.

A sequence-ready physical map of a region of 12q24.1

We developed a sequence-ready map of a part of human chromosome 12q24.1. We utilized a number of sequence-tagged site (STS) markers from 12q24.1 to screen large insert bacterial chromosome libraries and a chromosome 12-specific cosmid library. The clones were assembled into contiguous sets (contigs) by STS-content analysis. Contigs were extended by obtaining end sequences of bacterial clones, generation of additional STSs, rescreening the libraries, and screening the additional clones for the presence of STSs. The resulting contig covers nearly 2 Mb of DNA and provides an average marker resolution of 16 kb. Based on the STS content, we developed fingerprints of a subset of clones. The STS content and fingerprint data allowed us to define a minimal tiling path of clones. These clones are being used to sequence this part of chromosome 12. This contig contains the Ataxin 2 gene, and it covers the interval harboring the gene responsible for Darier disease.

Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII

The nucleotide sequences of five major regions from chromosome VII of Saccharomyces cerevisiae have been determined and analysed. These regions represent 203 kilobases corresponding to approximately one-fifth of the complete yeast chromosome VII. Two fragments originate from the left arm of this chromosome. The first one of about 15.8 kb starts approximately 75 kb from the left telomere and is bordered by the SK18 chromosomal marker. The second fragment covers the 72.6 kb region between the chromosomal markers CYH2 and ALG2. On the right chromosomal arm three regions, a 70.6 kb region between the MSB2 and the KSS1 chromosomal markers and two smaller regions dominated by the KRE11 marker and another one in the vicinity of the SER2 marker were sequenced. We found a total of 114 open reading frames (ORFs), 13 of which were completely overlapping with larger ORFs running in the opposite direction. A total of 44 yeast genes, the physiological functions of which are known, could be precisely mapped on this chromosome. Of the remaining 57 ORFs, 26 shared sequence homologies with known genes, among which were 13 other S. cerevisiae genes and five genes from other organisms. No homology with any sequence in the databases could be found for 31 ORFs. Furthermore, five Ty elements were found, one of which may not be functional due to a frame shift in its Ty1B amino acid sequence. The five chromosomal regions harboured five potential ARS elements and one sigma element together with eight tRNA genes and two snRNAs, one of which is encoded by an intron of a protein-coding gene.

An evolutionarily conserved U5 snRNP-specific protein is a GTP-binding factor closely related to the ribosomal translocase EF-2

The driving forces behind the many RNA conformational changes occurring in the spliceosome are not well understood. Here we characterize an evolutionarily conserved human U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116kD) that is strikingly homologous to the ribosomal elongation factor EF-2 (ribosomal translocase). A 114 kDa protein (Snu114p) homologous to U5-116kD was identified in Saccharomyces cerevisiae and was shown to be essential for yeast cell viability. Genetic depletion of Snu114p results in accumulation of unspliced pre-mRNA, indicating that Snu114p is essential for splicing in vivo. Antibodies specific for U5-116kD inhibit pre-mRNA splicing in a HeLa nuclear extract in vitro. In HeLa cells, U5-116kD is located in the nucleus and colocalizes with snRNP-containing subnuclear structures referred to as speckles. The G domain of U5-116kD/Snu114p contains the consensus sequence elements G1-G5 important for binding and hydrolyzing GTP. Consistent with this, U5-116kD can be cross-linked specifically to GTP by UV irradiation of U5 snRNPs. Moreover, a single amino acid substitution in the G1 sequence motif of Snu114p, expected to abolish GTP-binding activity, is lethal, suggesting that GTP binding and probably GTP hydrolysis is important for the function of U5-116kD/Snu114p. This is to date the first evidence that a G domain-containing protein plays an essential role in the pre-mRNA splicing process.

Sequence analysis of the 33 kb long region between ORC5 and SUI1 from the left arm of chromosome XIV from Saccharomyces cerevisiae

We have determined the nucleotide sequence of a chromosomal region of 33,016 bp located on the left arm of chromosome XIV from budding yeast between the ORC5 and the SUI1 gene. Subsequent sequence analysis revealed the presence of 18 non-overlapping open reading frames (ORFs) including eight previously identified and sequenced genes (ORC5, ATX1, SIP3, NRD1, RAD50, MPA43, RPA49 and SUI1). Three other ORFs (YNL256w, YNL255c and YNL247w) code for putative proteins with significant homology to proteins from other organisms, while 4 ORFs exhibit only weak homology to known proteins. Three ORFs have no homology with sequences in the databases.

DNA sequencing and analysis of 130 kb from yeast chromosome XV

We have determined the nucleotide sequence of 129,524 bases of yeast (Saccharomyces cerevisiae) chromosome XV. Sequence analysis revealed the presence of 59 non-overlapping open reading frames (ORFs) of length > 300 bp, three tRNA genes, four delta elements and one Ty-element. Among the 21 previously known yeast genes (36% of all ORFs in this fragment) were nucleoporin (NUP1), ras protein (RAS1), RNA polymerase III (RPC1) and elongation factor 2 (EF2). Further, 31 ORFs (53% of the total) were found to be homologous to known protein or DNA sequences, or sequence patterns. For seven ORFs (11% of the total) no homology was found. Among the most interesting protein identification in this DNA fragment are an inositol polyphosphatase, the second gene of this type found in yeast (homologous to the human OCRL gene involved in Lowe's syndrome), a new ADP ribosylation factor of the arf6 subfamily, the first protein containing three C2 domains, and an ORF similar to a Bacillus subtilis cell-cycle related protein. For each ORF detailed sequence analysis was carried out, with a full consideration of its biological function and pointing out key regions of interest for further functional analysis.

The STK2 gene, which encodes a putative Ser/Thr protein kinase, is required for high-affinity spermidine transport in Saccharomyces cerevisiae

Eukaryotic polyamine transport systems have not yet been characterized at the molecular level. We have used transposon mutagenesis to identify genes controlling polyamine transport in Saccharomyces cerevisiae. A haploid yeast strain was transformed with a genomic minitransposon- and lacZ-tagged library, and positive clones were selected for growth resistance to methylglyoxal bis(guanylhydrazone) (MGBG), a toxic polyamine analog. A 747-bp DNA fragment adjacent to the lacZ fusion gene rescued from one MGBG-resistant clone mapped to chromosome X within the coding region of a putative Ser/Thr protein kinase gene of previously unknown function (YJR059w, or STK2). A 304-amino-acid stretch comprising 11 of the 12 catalytic subdomains of Stk2p is approximately 83% homologous to the putative Pot1p/Kkt8p (Stk1p) protein kinase, a recently described activator of low-affinity spermine uptake in yeast. Saturable spermidine transport in stk2::lacZ mutants had an approximately fivefold-lower affinity and twofold-lower Vmax than in the parental strain. Transformation of stk2::lacZ cells with the STK2 gene cloned into a single-copy expression vector restored spermidine transport to wild-type levels. Single mutants lacking the catalytic kinase subdomains of STK1 exhibited normal parameters for the initial rate of spermidine transport but showed a time-dependent decrease in total polyamine accumulation and a low-level resistance to toxic polyamine analogs. Spermidine transport was repressed by prior incubation with exogenous spermidine. Exogenous polyamine deprivation also derepressed residual spermidine transport in stk2::lacZ mutants, but simultaneous disruption of STK1 and STK2 virtually abolished high-affinity spermidine transport under both repressed and derepressed conditions. On the other hand, putrescine uptake was also deficient in stk2::lacZ mutants but was not repressed by exogenous spermidine. Interestingly, stk2::lacZ mutants showed increased growth resistance to Li+ and Na+, suggesting a regulatory relationship between polyamine and monovalent inorganic cation transport. These results indicate that the putative STK2 Ser/Thr kinase gene is an essential determinant of high-affinity polyamine transport in yeast whereas its close homolog STK1 mostly affects a lower-affinity, low-capacity polyamine transport activity.

Clustering of meiotic double-strand breaks on yeast chromosome III

In the yeast Saccharomyces cerevisiae, meiotic recombination is initiated by transient DNA double-strand breaks (DSBs) that are repaired by interaction of the broken chromosome with its homologue. To identify a large number of DSB sites and gain insight into the control of DSB formation at both the local and the whole chromosomal levels, we have determined at high resolution the distribution of meiotic DSBs along the 340 kb of chromosome III. We have found 76 DSB regions, mostly located in intergenic promoter-containing intervals. The frequency of DSBs varies at least 50-fold from one region to another. The global distribution of DSB regions along chromosome III is nonrandom, defining large (39-105 kb) chromosomal domains, both hot and cold. The distribution of these localized DSBs indicates that they are likely to initiate most crossovers along chromosome III, but some discrepancies remain to be explained.

Complete transcriptional map of yeast chromosome XI in different life conditions

Systematic sequencing of the genome of Saccharomyces cerevisiae has demonstrated the existence of many novel genes, whose functions need to be studied. Entire chromosome sequences also offer the possibility to examine functional properties of the genome at a higher hierarchical level than the genes themselves. We used ordered DNA fragments of chromosome XI to systematically probe yeast DNA and total RNA extracted from MAT a, MAT alpha and diploid cells grown under three different conditions. Taking into account transcript sizes and uniqueness of probes, we attributed 94 transcripts to sequence-predicted open reading frames (ORFs) or tRNA genes; another 83 being tentatively assigned. The remaining 187 ORFs on chromosome XI do not correspond to transcripts detected under our conditions. More than 80% of transcripts are constitutively expressed, others are regulated by medium composition or cell type, the most frequent regulations being determined by carbon source (glycerol/glucose) or rich versus synthetic medium. Moreover, we show that transcript levels and regulation patterns are not statistically different between ORFs of unknown function, which constitute ca. 40% of the total, and previously identified genes (ca. 30%) or their structural homologues.

Sequence and analysis of a 36.2 kb fragment from the right arm of yeast chromosome XV reveals 19 open reading frames including SNF2 (5' end), CPA1, SLY41, a putative transport ATPase, a putative ribosomal protein and an SNF2 homologue

The complete sequence of a 36 196 bp DNA segment located on the right arm of chromosome XV of Saccharomyces cerevisiae has been determined and analysed. The sequence includes the 5' coding region of the SNF2 gene, the CPA1 leader peptide sequence and 17 open reading frames (ORFs) of at least 100 amino acids. Two of these correspond to previously known genes (CPA1, SLY41), whereas 15 correspond to new genes. The putative translation products of three ORFs show significant similarity with known proteins: one is a putative transport ATPase, another appears to be a ribosomal protein, and the third is an Snf2p homologue.

Analysis of the structure of a natural alternating d(TA)n sequence in yeast chromatin

We address here the question of the in vivo structure of a natural alternating d(TA)n sequence found at the 3' region of the Saccharomyces cerevisiae FBP1 gene. This sequence consists of 13 TA pairs interrupted by a TT dinucleotide in the middle of the tract. Previous experiments with cruciform-specific nucleases S1 and Endonuclease VII demonstrated the presence in vitro of a cruciform in this region. We also showed this region to be part of a nuclease hypersensitive site flanked by nucleosomes in yeast chromatin. Here we demonstrate, by means of S1 in vivo footprinting, that in yeast plasmids also adopts in vivo a non B-DNA structure where is not a cruciform. A theoretical analysis of this region that it contains a site susceptible to superhelical stress duplex destabilization. The locations and conditions under which alternative structures form in the wild-type sequence and in deletion mutants agree with these theoretical predictions, suggesting that some kind of denaturation is the alternative structure adopted by the sequence in vivo. This suggests that negative superhelical stress sufficient for local denaturation exists in nucleosomal DNA. We also demonstrate by micrococcal nuclease digestions that the deletion of the alternating d(TA)n sequence modifies the chromatin hypersensitive site but does not affect nucleosome positioning.

DNA sequence analysis of a 23,002 bp DNA fragment of the right arm of Saccharomyces cerevisiae chromosome VII

We report the sequence of a 23,002 bp fragment located on the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of this region revealed 14 complete open reading frames (ORFs) wit more than 300 base pairs. Six of them correspond to previously known genes. G7164 is the QCR9 gene coding for subunit 9 of the cytochrome c reductase; G7168 is UBR1, encoding an ubiquitin protein ligase; G7522 is the TYS1 gene, which encodes for the tyrosyl tRNA synthetase; G7526 is TFG1, the gene coding for the RNA polymerase transcription initiation factor TFIIF (factor G); G7538 is the gene HGH1 which encodes a protein related to the mammalian HMG1 and HMG2 proteins. G7542 is the BUB1 gene which encodes a ser/thr protein kinase involved in spindle assembly during the cell cycle. One of the ORFs, G7553, shares significant homologies with the gene UTR2 from S. cerevisiae. None of the seven remaining ORFs shows similarity to any of the sequences within the public databases. Three ORFs are internal ORFs of the above-described known genes, and two small ORFs are completely contained in larger ORFs on the complementary strand, and therefore probably do not correspond to real genes. This region also contains three genes specifying tRNAs for Leu, Lys and Trp, and several LTR elements.

The DNA sequence of cosmid 14-13b from chromosome XIV of Saccharomyces cerevisiae reveals an unusually high number of overlapping open reading frames

This work is part of the effort for sequencing chromosome XIV of Saccharomyces cerevisiae. Cosmid 14-13b contains a 37.8 kb insert derived from a partial Sau3A digestion of the genome, cloned into the BamHI site of the vector Pou6. The strategy used for sequencing is based on the fragmentation of the whole cosmid by sonication, followed by shotgun sequencing on an Applied Biosystem DNA sequencer. The clones with inserts corresponding to the vector were identified by dot-blot hybridization, without the need of sequencing. The analysis of the DNA sequence reveals 29 open reading frames (ORFs) longer than 300 bases. Nine ORFs are internal to some other ORFs. Similarity searches against DNA and protein data banks show that six ORFs correspond to already known yeast genes (OMP1, PSU1, MLS1, RPC19, DBP2, CYB5) and one ORF matches the sequence of a putative yeast gene (ESBP6).

Analysis of an 11.6 kb region from the right arm of chromosome VII of Saccharomyces cerevisiae between the RAD2 and the MES1 genes reveals the presence of three new genes

Sequence analysis of an 11,628 bp DNA segment from the right arm of Saccharomyces cerevisiae chromosome VII revealed the presence of the 5' end of the RAD2 gene, the MES1 gene and six open reading frames (ORFs) each longer than 300 bp. Four of these ORFs are expressed genes, as indicated by transcript analysis. One of them, YGR261c, which specifies a putative beta-adaptine, corresponds to gene YKS5, which has recently been identified as a suppressor of loss of casein kinase 1 function. The remaining three ORFs are new genes; of these, YGR260w encodes a protein showing similarity to the S. cerevisiae allantoate permease and YGR262c specifies a putative protein kinase.

Complete inventory of the yeast ABC proteins

The complete sequence of the yeast genome predicts the existence of 29 proteins belonging to the ubiquitous ATP-binding cassette (ABC) superfamily. Using binary comparison, phylogenetic classification and detection of conserved amino acid residues, the yeast ABC proteins have been classified in a total of six clusters, including ten subclusters of distinct predicted topology and presumed distinct function. Study of the yeast ABC proteins provides insight into the physiological function and biochemical mechanisms of their human homologues, such as those involved in cystic fibrosis, adrenoleukodystrophy, Zellweger syndrome, multidrug resistance and the antiviral activity of interferons.

Quantification of DNA patchiness using long-range correlation measures

We introduce and develop new techniques to quantify DNA patchiness, and to quantify characteristics of its mosaic structure. These techniques, which involve calculating two functions, alpha(l) and beta(l), measure correlations at length scale l and detect distinct characteristic patch sizes embedded in scale-invariant patch size distributions. Using these new methods, we address a number of issues relating to the mosaic structure of genomic DNA. We find several distinct characteristic patch sizes in certain genomic sequences, and compare, contrast, and quantify the correlation properties of different sequences, including a number of yeast, human, and prokaryotic sequences. We exclude the possibility that the correlation properties and the known mosaic structure of DNA can be explained either by simple Markov processes or by tandem repeats of dinucleotides. We find that the distinct patch sizes in all 16 yeast chromosomes are similar. Furthermore, we test the hypothesis that, for yeast, patchiness is caused by the alternation of coding and noncoding regions, and the hypothesis that in human sequences patchiness is related to repetitive sequences. We find that, by themselves, neither the alternation of coding and noncoding regions, nor repetitive sequences, can fully explain the long-range correlation properties of DNA.

The nucleotide sequence of a 39 kb segment of yeast chromosome IV: 12 new open reading frames, nine known genes and one genes for Gly-tRNA

The complete nucleotide sequence of a 39,090 bp segment from the left arm of yeast chromosome IV was determined. Twenty-one open reading frames (ORFs) longer than 100 amino acids and a Gly-tRNA gene were discovered. Nine of the 21 ORFs (D0892, D1022, D1037, D1045, D1057, D1204, D1209, D1214, D1219) correspond to the previously sequenced Saccharomyces cerevisiae genes for the NAD-dependent glutamate dehydrogenase (GDH), the secretory component (SHR3), the GABA transport protein (UGA4), the high mobility group-like protein (NHP2), the hydroxymethylbilane synthase (HEM3), the methylated DNA protein-cysteine S-methyltransferase (MGT1), a putative sugar transport protein, the Shm1 protein (SHM1) and the anti-silencing protein (ASF2). The inferred amino acid sequences of 11 ORFs show significant similarity with known proteins from various organisms, whereas the remaining ORF does not share any similarity with known proteins.

Sequencing of a 40.5 kb fragment located on the left arm of chromosome VII from Saccharomyces cerevisiae

The nucleotide sequence of a 40.5 kb DNA fragment from the left arm of chromosome VII of Saccharomyces cerevisiae was determined and analysed. Twenty-eight open reading frames (ORFs) longer than 300 nucleotides were identified. Eight of the them correspond to the following known yeast genes: EMP24, GCN1, SPO8, COX13, CDC55, RPS26, COX4 and LSR1, also called GTS1. Twelve ORFs are new, among them eight show homology with other genes while four have no homology with any sequence in the databases. Eight additional ORFs are internal to or partially overlapping with other ORFs.

Multidrug-resistant transport proteins in yeast: complete inventory and phylogenetic characterization of yeast open reading frames with the major facilitator superfamily

Screening of the complete genome sequence from the yeast Saccharomyces cerevisiae reveals that 28 open reading frames (ORFs) are homologous to each other and to established bacterial members of the drug-resistant subfamily of the major facilitator superfamily. The phylogenesis of these protein sequences shows that they fall into three major clusters. Cluster I contains 12 ORFs, cluster II contains ten ORFs and cluster III contains six ORFs. Hydropathy analyses indicate that in cluster II and III ORFs, 14 transmembrane spans are predicted whereas only 12 transmembrane spans are predicted in cluster I ORFs. Three ORFs that have known functions as multidrug-resistance pumps in other yeast species such as Schizosaccharomyces pombe (CAR1), Candida albicans (BMRP) or C. maltosa (CYHR), also fall into cluster I. Two S. cerevisiae ORFs of known multidrug-resistance function (ATR1, SGE1) fall into cluster II. Cluster III consists exclusively of ORFs of unknown function but binary sequence comparisons show homology to ORFs from cluster II. Analysis of the multiple alignment for these proteins leads to the identification of characteristic signature sequences for each of the three clusters.

The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes

The Genome Sequence DataBase (GSDB) has completed its conversion to an improved relational database. The new database, GSDB 1.0, is fully operational and publicly available. Data contributions, including both original sequence submissions and community annotation, are being accomplished through the use of a graphical client-server interface tool, the GSDB Annotator, and via GIO (GSDB Input/Output) files. Data retrieval services are being provided through a new Web Query Tool and direct SQL. All methods of data contribution and data retrieval fully support the new data types that have been incorporated into GSDB, including discontiguous sequences, multiple sequence alignments, and community annotation.

Structure, function, and replication of Saccharomyces cerevisiae telomeres

A combination of classical genetic, biochemical, and molecular biological approaches have generated a rather detailed understanding of the structure and function of Saccharomyces telomeres. Yeast telomeres are essential to allow the cell to distinguish intact from broken chromosomes, to protect the end of the chromosome from degradation, and to facilitate the replication of the very end of the chromosome. In addition, yeast telomeres are a specialized site for gene expression in that the transcription of genes placed near them is reversibly repressed. A surprisingly large number of genes have been identified that influence either telomere structure or telomere function (or both), although in many cases the mechanism of action of these genes is poorly understood. This article reviews the recent literature on telomere biology and highlights areas for future research.

The Saccharomyces retrotransposon Ty5 influences the organization of chromosome ends

Retrotransposons are ubiquitous components of eukaryotic genomes suggesting that they have played a significant role in genome organization. In Saccharomyces cerevisiae, eight of 10 endogenous insertions of the Ty5 retrotransposon family are located within 15 kb of chromosome ends, and two are located near the subtelomeric HMR locus. This genomic organization is the consequence of targeted transposition, as 14 of 15 newly transposed Ty5 elements map to telomeric regions on 10 different chromosomes. Nine of these insertions are within 0.8 kb and three are within 1.5 kb of the autonomously replicating consensus sequence in the subtelomeric X repeat. This suggests that the X repeat plays an important role in directing Ty5 integration. Analysis of endogenous insertions from S.cerevisiae and its close relative S.paradoxus revealed that only one of 12 insertions has target site duplications, indicating that recombination occurs between elements. This is further supported by the observation that Ty5 insertions mark boundaries of sequence duplications and rearrangements in these species. These data suggest that transposable elements like Ty5 can shape the organization of chromosome ends through both transposition and recombination.

Sequence and analysis of a 26.9 kb fragment from chromosome XV of the yeast Saccharomyces cerevisiae

We have determined the nucleotide sequence of a fragment of chromosome XV of Saccharomyces cerevisiae cloned into cosmid pEOA048. The analysis of the 26,857 bp sequence reveals the presence of 19 open reading frames (ORFs), and of one RNA-coding gene (SNR17A). Six ORFs correspond to previously known genes (MKK1/SSP32, YGE1/GRPE/MGE1, KIN4/KIN31/KIN3, RPL37B, DFR1 and HES1, respectively), all others were discovered in this work. Only five of the new ORFs have significant homologs in public databases, the remaining eight correspond to orphans (two of them are questionable). O5248 is a probable folypolyglutamate synthetase, having two structural homologs already sequenced in the yeast genome. O5273 shows homology with a yeast protein required for vanadate resistance. O5268 shows homology with putative oxidoreductases of different organisms. O5257 shows homology with the SAS2 protein and another hypothetical protein from yeast. The last one, O5245, shows homology with a putative protein of Caenorhabditis elegans of unknown function. The present sequence corresponds to coordinates 772,331 to 799,187 of the entire chromosome XV sequence which can be retrieved by anonymous ftp (ftp. mips. embnet. org).

Sequence of a 39,411 bp DNA fragment covering the left end of chromosome VII of Saccharomyces cerevisiae

We have sequenced a DNA fragment of 39,411 bp which includes part of the left telomere of chromosome VII of Saccharomyces cerevisiae. We have identified 19 open reading frames (ORFs); six correspond to known yeast genes (ADH4, FZF1, HKB, RTG2, HFM1 and PDE1), nine have similarity with other genes and four exhibit no significant similarity with any known gene. The average size of these ORFs seems to be related to their location, the eight ORF's nearest the telomere being shorter than the 11 others. These two groups of genes are separated by a region of 4.5 kb devoid of significant ORFs. One ORF, NRF120, is a new member of the seripauperine family, represented once in all sequenced yeast chromosomes, in a subtelomeric location.

Functional analysis of YCL09C: evidence for a role as the regulatory subunit of acetolactate synthase

We have analysed the function of the open reading frame (ORF) YCL09C. The deletion of this ORF from chromosome III does not affect the physiology of the corresponding yeast strain enough to give a distinct phenotype. Nevertheless a computational analysis reveals high homology between this ORF and the enterobacterial genes encoding the regulatory subunit of acetolactate synthase. We have therefore tested the possibility that yc109cp is the regulatory subunit of yeast acetolactate synthase by in vitro enzymatic analysis. The acetolactate synthase was previously shown to be retroinhibited by its final product valine. In Escherichia coli this retro-control is assured by the regulatory subunit. Using a yeast strain carrying a complete deletion of YCL09C, we have observed the loss of such retro-inhibition. These results together with the computational predictions show that YCL09C encodes the regulatory subunit of yeast acetolactate synthase.

New vectors for combinatorial deletions in yeast chromosomes and for gap-repair cloning using 'split-marker' recombination

New tools are needed for speedy and systematic study of the numerous genes revealed by the sequence of the yeast genome. We have developed a novel transformation strategy, based on 'split-marker' recombination, which allows generation of chromosomal deletions and direct gene cloning. For this purpose, pairs of yeast vectors have been constructed which offer a number of advantages for large-scale applications such as one-step cloning of target sequence homologs and combinatorial use. Gene deletions or gap-repair clonings are obtained by cotransformation of yeast by a pair of recombinant plasmids. Gap-repair vectors are based on the URA3 marker. Deletion vectors include the URA3, LYS2 and kanMX selection markers flanked by I-Scel sites, which allow their subsequent elimination from the transformant without the need for counter-selection. The application of the "split-marker' vectors to the analysis of a few open reading frames of chromosome XI is described.

Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon

The complete sequence of a 40247 bp DNA segment located on the left arm of chromosome X of Saccharomyces cerevisiae has been determined and analysed. The sequence encodes the 5' coding region of the URA2 gene and 18 open reading frames of at least 100 amino acids. Ten of these correspond to known genes, whereas eight correspond to new genes. In addition, the sequence contains a tRNA-Ala gene, a tRNA-Asp gene, a Ty4 transposable element and three delta elements.

A modular misexpression screen in Drosophila detecting tissue-specific phenotypes

Genetic screens in Drosophila have lead to the discovery of many genes important for patterning and signal transduction in diverse organisms. Traditionally, the phenotypic effects of loss-of-function mutations are analyzed. As an alternative way to link genes and function, I have developed a versatile misexpression screen in Drosophila, the first such screen in higher eukaryotes. The screen identifies genes that, when over- or misexpressed in a pattern of interest, give a specific phenotype or modulate an existing mutant phenotype. It is based on Gal4 transactivation of a mobile enhancer and promoter that "targets" random endogenous genes for expression. The modular design of the screen allows directed expression in any temporal or spatial pattern. When activated in the developing eye, 4% of target inserts gave dominant phenotypes. One insertion was in the gene encoding Ras GTPase-activating protein; its overexpression phenotype was strongly enhanced by a mutation in Ras1. Thus, biologically relevant phenotypes and genetic interactions are identified using this method. The screen is a powerful new tool for developmental genetics; similar approaches can also be developed for other organisms.