Analysis of a 23 kb region on the left arm of yeast chromosome IV

We have determined the complete nucleotide sequence of a 23 kb segment from the left arm of chromosome IV, which is carried by the cosmid 1L10. This sequence contains the 3′ coding region of the STE7 and RET1 (COP1) genes, and 13 complete open reading frames longer than 300 bp, of which ten correspond to putative new genes and three (CLB3, MSH5 and RPC53) have been sequenced previously. The sequence from cosmid 1L10 was obtained entirely by a combined subcloning and walking primer strategy.     

Analysis of a 26 kb region on the left arm of yeast chromosome XV

In the framework of the EC programme for sequencing yeast chromosome XV, we have determined the nucleotide sequence of a 26 kb region. Subsequent analysis revealed 13 non-overlapping open reading frames, three of which correspond to known yeast genes. A pair of tRNA genes associated with remnant Ty elements were localized in this region. From structural parameters and/or similarity searches with entries in the current data libraries, a preliminary functional assessment of several of the putative novel gene products can be made. The gene density in this region amounts to one gene in 2 kb. Protein coding regions occupy 61% of the total DNA sequence. Within the intergenic regions, potential regulatory elements can be predicted. The data obtained here may serve as a basis for a more detailed biochemical analysis of the novel genes. The complete nucleotide sequence of the 26 kb segment as depicted in Figure 1 has been deposited at the EBI data library under Accession Number X91067.     

Sequence and analysis of a 33 kb fragment from the right arm of chromosome XV of the yeast Saccharomyces cerevisiae

We have determined the nucleotide sequence of a cosmid (pEOA423) from chromosome XV of Saccharomyces cerevisiae. Analysis of the 33,173 bp sequence reveals the presence of 20 putative open reading frames (ORFs). Five of them correspond to previously known genes (MGM1, STE4, CDC44, STE13, RPB8). The previously published nucleotide sequences are in perfect agreement with our sequence except for STE4 and MGM1. In the latter case, 59 amino acids were truncated from the published protein at its N-terminal end due to a frameshift. The putative translation products of six other ORFs exhibit significant homology with protein sequences in public databases: O50 03 and O50 17 products are homologs of the ANC1 and MIP1 proteins of S. cerevisiae, respectively; O50 05 product is similar to that of a protein of unknown function from Myxococcus xanthus; O50 12 product is probably a new ATP/ADP carrier; O50 13 product shows homology with group II tRNA synthetases; and the O50 16 product exhibits strong similarity with the N-terminal domain of the NifU proteins from several prokaryotes. The remaining nine ORFs show no significant similarity. Among these, two contiguous ORFs (O50 19 and O50 20) are very similar to each other, suggesting an ancient tandem duplication. The 33,173 bp sequence has been submitted to EMBL (Accession Number: X92441).     

Deletion of six open reading frames from the left arm of chromosome IV of Saccharomyces cerevisiae

The construction of six deletion mutants of Saccharomyces cerevisiae and their basic phenotypic characterization are described. Open reading frames YDL148c, YDL109c, YDL021w, YDL019c, YDL018c and YDL015c from the left arm of chromosome IV were deleted using a polymerase chain reaction (PCR)‐based disruption technique, introducing the kanMX4 resistance marker into the respective genes. Gene replacement cassettes (pYORCs) for use in other strain backgrounds were cloned by PCR using DNA templates from haploid or diploid deletion mutants, and inserted into episomal plasmids. Cognate clones of all six ORFs were obtained by gap repair. Deletions were carried out in diploid cells and, after sporulation, yielded four viable spores for clones disrupted in YDL109c, YDL021w, YDL019c and YDL018c. Spores harbouring disruptions in ORFs YDL148c and YDL015c germinated but underwent only a few divisions before ceasing growth, suggesting that the respective genes are essential for vegetative growth on YPD complete media. The other deletion mutants grew like wild‐type at different temperatures and on different carbon sources. A brief computational analysis of the six ORFs studied in this work is presented. Copyright © 1999 John Wiley & Sons, Ltd.     

Nucleotide sequence analysis of a 32,500 bp region of the right arm of Saccharomyces cerevisiae chromosome IV

We have sequenced a region containing 32.5 kb of the right arm of chromosome IV of Saccharomyces cerevisiae. Twenty open reading frames (ORFs) greater than 100 amino acids could be identified in this region. Six ORFs correspond to known yeast genes, including DOA4, UBC5 and UBC3, the gene products of which are involved in ubiquitin metabolism. UBC5 is preceded by the two tRNA genes tRNA-Arg2 and tRNA-Asp. Six genes were discovered with homologies to non-yeast genes or with homologies to other yeast ORFs. One of these could be identified as ribosomal protein gene RPS13. The putative function of eight ORFs remains unclear because comparison to different DNA or protein databases revealed no significant patterns. The sequence from cosmid 2F21 was obtained entirely by a combined subcloning and walking primer strategy, and has been deposited in the EMBL data library under Accession Number X84162.     

The sequence of a 24 152 bp segment from the left arm of chromosome XIV from Saccharomyces cerevisiae between the BNI1 and the POL2 genes

In the framework of the European Union programme for sequencing the genome of Saccharomyces cerevisiae we have determined the nucleotide sequence of a region of 24 152 bp located on the left arm of chromosome XIV between the BNI1 and the POL2 genes. The sequence was obtained by directed sequence analysis using a mixture of ExoIII and primer walking strategies. Subsequent analysis revealed 13 open reading frames (ORFs) including four small ORFs completely internal to, or partly overlapping with, other ORFs. Five of these ORFs have been described previously (BNI1, APL1, LYP1, PIK1, POL2) and thus 74·8% of the 24 152 bp were already present in the databases prior to this sequencing effort. Interestingly, all 13 identified ORFs are characterized by a low codon adaptation index (0·04–0·22). In addition, this region of chromosome XIV shows an unusually high gene density with about 88% of coding DNA. This amounts to one gene per 2177 bp, which is significantly above the average gene length (about 1500 bp). For eight ORFs considerable homologies to ‘Expressed Sequence Tags’ derived from human cDNAs located in the XREF database could be identified. The complete nucleotide sequence of the 24 152 bp segment has been deposited in the EMBL data library under the Accession Number X92494.     

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 folylpolyglutamate 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 analysis of a 40·7 kb segment from the left arm of yeast chromosome X reveals 14 known genes and 13 new open reading frames including homologues of genes clustered on the right arm of chromosome XI

The complete nucleotide sequence of a 40·7 kb segment about 130 kb from the left end of chromosome X of Saccharomyces cerevisiae was determined from two overlapping cosmids. Computer analysis of that sequence revealed the presence of the previously known genes VPS35, INO1, SnR128, SnR190, MP12, YAK1, RPB4, YUR1, TIF2, MRS3 and URA2, three previously sequenced open reading frames (ORFs) of unknown function 5′ of the INO1, 5′ of the MP12 and 3′ of the URA2 genes and 13 newly identified ORFs. One of the new ORFs is homologous to mammalian glycogenin glycosyltransferases and another has similarities to the human phospholipase D. Some others contain potential transmembrane regions or leucine zipper motifs. The existence of yeast expressed sequence tags for some of the newly identified ORFs indicates that they are transcribed. A cluster of six genes within 10 kb (YUR1, TIF2, two new ORFs, an RSP25 homologue and MRS3) have homologues arranged similarly within 28·5 kb on the right arm of chromosome XI. The sequence has been deposited in the EMBL data library under Accession Number X87371.     

The sequence of a 16691bp segment of Saccharomyces cerevisiae chromosome IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes,and five new open reading frames

As part of the European BIOTECH programme, the nucleotide sequence of a 16691bp fragment from the left arm of chromosome IV of Saccharomyces cerevisiae has been deduced. Analysis of the sequence reveals the presence of 13 open reading frames (ORFs) larger than 100 codons. Five of these were previously identified as genes DUN1, PMT1, PMT5, SRP14 and DPR1. One putative protein, D2371p, contains an ATP-GTP binding site, and shares homology to the ArsA component of an Escherichia coli arsenical pump. No significant homology to any known protein has been found for the other ORFs. D2378p contains a zinc finger domain. The nucleotide sequence has been deposited at EMBL, with Accession Number X95644.     

The complete sequence of a 6794 bp segment located on the right arm of chromosome II of Saccharomyces cerevisiae. Finding of a putative dUTPase in a yeast

The DNA sequence of a 6794 bp fragment located at about 100 kb from the right telomere of chromosome II from Saccharomyces cerevisiae has been determined. Sequence analysis reveals five open reading frames. One is the ARO4 gene encoding the 3-deoxy-D -arabinoheptulosonate 7-phosphate synthase. Another presents strong homology with the S5 ribosomal protein from bacteria. The open reading frame YBR1705 shows significant homology with dUTPase, suggesting for the first time the existence of such an enzyme in S. cerevisiae.     

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 ORFs 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. This sequence has been entered in the EMBL data library under accession number X94357.     

XV. Yeast sequencing reports. Sequence of a 10·27 kb segment on the left arm of chromosome XV from Saccharomyces cerevisiae includes part of the IRA2 gene and a putative new gene

A 10 270 bp fragment from the left arm of chromosome XV of Saccharomyces cerevisiae was sequenced and analysed. The sequence reveals the presence of two open reading frames (ORFs), one of them is the larger part of the previously sequenced gene IRA2 (YOL0951). The other ORF, YOL0950, has a length of 1245 nucleotides and exhibits no significant homology with any known gene, although there is some similarity of its upstream region to the corresponding region of the Schizosaccharomyces pombe cdr1/nim1 gene which is involved in the control of mitotic cell size. The sequence has been deposited in the EMBL data library under Accession Number X75449.     

The complete sequence of a 19,482 bp segment located on the right arm of Chromosome II from Saccharomyces cerevisiae

We report here the sequence of a 19,482 bp DNA segment of chromosome II of Saccharomyces cerevisiae. The fragment contains 16 open reading frames (ORFs) covering 74% of the sequence. Four predicted products present homology with known proteins. The ORF YBR1732 exhibits a strong homology to serine hydroxymethyl transferase; the best score is 53·1% identity in 458 amino acids overlap with the serine hydroxymethyl transferase from rabbit liver. YBR1724, which shows homology with riboflavin synthase of Bacillus subtilis, is probably the RIB5 gene implied in riboflavine synthesis and mapped in this region. YBR1733 is homologous to rab protein and YBR1728 is presumably a GTPase activating protein.     

IV. Yeast sequencing reports. Sequence of the PHO2-POL3 (CDC2) region of chromosome IV of Saccharomyces cerevisiae

The nucleotide sequence of a 5 kb EcoRI-NcoI fragment of chromosome IV, contiguous to gene POL3 (CDC2), has been determined. It contains three open reading frames: QRI1, QRI2 and QRI7. Two of them are essential genes. QRI7 is homologous to the Escherichia coli orf_x gene. Accession number to EMBL/Genbank Data Library is X79380.     

Analysis of the DNA sequence of a 15,500 bp fragment near the left telomere of chromosome XV from Saccharomyces cerevisiae reveals a putative sugar transporter,a carboxypeptidase homologue and two new open reading frames

We report the sequence of a 15·5 kb DNA segment located near the left telomere of chromosome XV of Saccharomyces cerevisiae. The sequence contains nine open reading frames (ORFs) longer than 300 bp. Three of them are internal to other ones. One corresponds to the gene LGT3 that encodes a putative sugar transporter. Three adjacent ORFs were separated by two stop codons in frame. These ORFs presented homology with the gene CPS1 that encodes carboxypeptidase S. The stop codons were not found in the same sequence derived from another yeast strain. Two other ORFs without significant homology in databases were also found. One of them, O0420, is very rich in serine and threonine and presents a series of repeated or similar amino acid stretches along the sequence. The nucleotide sequence has been deposited in the EMBL data library under Accession Number X89715.     

Analysis of a 32·8 kb segment of yeast chromosome IV reveals 21 open reading frames,including TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and a tRNA for arginine

We report the nucleotide sequence of a 32·8 kb DNA segment from the right arm of Saccharomyces cerevisiae chromosome IV. The sequence contains 20 open reading frames (ORFs) longer than 300 bp as well as the 240 bp gene coding for the essential SSS1 secretory protein. Nine ORFs previously totally or partially sequenced (TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and D4478) are presented, as well as the transmembrane protein D4405, the leucine zipper containing D4495 and a new tRNA for arginine. D4456 and D4461 are separated by a single in-frame stop codon only. The other five ORFs show no particular features or significant homology. The sequence is recorded in EMBL database under Accession Number X82086.     

The sequence of a 9.3 kb segment located on the left arm of the yeast chromosome XI reveals five open reading frames including the CCE1 gene and putative products related to MYO2 and to the ribosomal protein L10.

We report here the sequence of a 9.3 kb DNA segment of chromosome XI of Saccharomyces cerevisiae, located between the MAK11 locus and the centromere. This sequence contains four long open reading frames (ORFs), YKL160, YKL162, YKL164, YKL165 and part of another ORF, YKL166, covering altogether 90% of the entire sequence. One of these ORFs, YKL164, corresponds to CCE1. Translation products of two other ORFs, YKL160 and YKL165, exhibit homology with previously known S. cerevisiae proteins: the ribosomal protein L10, and the MYO2 gene product, respectively.