Sequencing analysis of a 15·4 kb fragment of yeast chromosome XIV identifies the RPD3, PAS8 and KRE1 loci,and five new open reading frames

The DNA sequence of a 15·4 kb region covering the left arm of chromosome XIV from Saccharomyces cerevisiae was determined. This region contains eight open reading frames (ORFs) which code for proteins of more than 100 amino acids. Three ORFs correspond to the RPD3, PAS8 and KRE1 loci, described previously. Three ORFs show limited homology with known proteins: NO330 with the recessive suppressor of secretory defect SAC1, NO325 with YCR094W identified during chromosome III sequencing; whereas NO315 presents a motif conserved in the dnaJ family. Two ORFs (NO320 and NO325) show no homology to known proteins within the databases screened, but NO320 corresponds to a serine-threonine-rich protein. The sequence has been entered in the EMBL data library under Accession Number Z46259.     

XIV. Yeast sequencing reports. A 43·5 kb segment of yeast chromosome XIV,which contains MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1, predicts an adenosine deaminase gene and 14 new open reading frames

A 43,481 bp fragment from the left arm of chromosome XIV of Saccharomyces cerevisiae was sequenced. A gene for tRNA^phe and 23 non-overlapping open reading frames (ORFs) were identified, seven of which correspond to known yeast genes: MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1. One ORF may correspond to the yet unindentified yeast adenosine deaminase gene. Among the 15 other ORFs, four exhibit known signatures, which include a protein tyrosine phosphatase, a cytoskeleton-associated protein and two ATP-binding proteins, four have similarities with putative proteins of yeast or proteins from other organisms and seven exibit no significant similarity with amino acid sequences described in data banks. One ORF is identical to yeast expressed sequence tags (EST) and therefore corresponds to an expressed gene. Six ORFs present similarities to human dbESTs, thus identifying motifs conserved during evolution. Nine ORFs are putative transmembrane proteins. In addition, one overlapping and three antisense ORFs, which are not likely to be functional, were detected. The sequence has been deposited in the EMBL data bank under Accession Number Z46843.     

X. Yeast sequencing reports. Sequence analysis of a 40·2 kb DNA fragment located near the left telomere of yeast chromosome X

We have sequenced on both strands a 40,257 bp fragment located near the left telomere of chromosome X of Saccharomyces cerevisiae. The sequenced segment contains 21 open reading frames (ORFs) at least 100 amino acids long. Five of the ORFs correspond to known amino acid sequences: two hypothetical proteins in the subtelomeric Y′ repeat region of 65·4 and 12·8 KDa, the cytochrome B pre-mRNA processing CBP1 protein, the mitochondrial nuclease NUC1 and the CRT1 protein. Of the 16 remaining ORFs, eight show highest homologies with the S. cerevisiae hexose transporters family (two ORFs), the yeast α-glucosidase (two ORFs), the yeast PEP1 precursor, the Escherichia coli galactoside O-acetyltransferase, the S. cerevisiae 137·7 KDa protein located in the Y′ region and a protein of unknown function of Schizosaccharomyces pombe. Finally, eight of the ORFs exhibit no significant similarity with any amino acid sequences described in data banks. DNA sequence comparison has revealed the presence of different repeated elements characteristic of yeast chromosome ends. Disruption studies have been performed on two ORFs encoding putative proteins of unknown function. The sequence has been entered in the EMBL Data Library under Accession Number Z34098.     

A 12·8 kb segment,on the right arm of chromosome II from Saccharomyces cerevisiae including part of the DUR1, 2 gene,contains five putative new genes

A 12 820 bp fragment from the right arm of chromosome II of Saccharomyces cerevisiae was sequenced and analysed. This fragment contains six non-overlapping long open reading frames (ORFs) designated from the centromere- to the telomere-proximal ends as: YBR1441, 1443, 1444, 1445, 1446 and 1448. YBR1441 encodes a polypeptide of 845 amino acids which shares a long consensus domain with products of S. cerevisiae MCM2, MCM3, CDC46 and Schizosaccharomyces pombe cdc21⁺ genes. These genes are involved in DNA replication. YBR1445 encodes a polypeptide of 404 amino acids which has strong similarity with the S. cerevisiae KRE2/MNT1, YUR1, KTR1 gene products. The KRE2/MNT1 protein is an α-1,2-mannosyltransferase. The product of YBR1444, which encodes a protein of 375 amino acids, presents a lipase signature sequence and a peroxisomal targeting signal. YBR1448, whose sequence extends further on the telomere-proximal end of the fragment, is identical to the 3′ end of the DUR1,2 gene encoding urea amidolyase. The two ORFs, YBR1443 and YBR1446, exhibit no significant similarity with any known gene.     

The Nucleotide Sequence of a 39 kb Segment of Yeast Chromosome IV: 12 New Open Reading Frames,Nine Known Genes and One Gene 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. The nucleotide sequence has been entered in the EMBL data Library under the Accession Number X99000.©1997 John Wiley & Sons, Ltd.     

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.     

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. The sequence has been deposited in the EMBL databank under Accession Numbers: Z75198, Z75199, Z75200, Z75201, Z75202, Z75203, Z75204, Z75205, Z75206, Z75207, Z75209, Z75210, Z75211, Z75212, Z75213, Z75214, Z75215, Z75216. © 1997 John Wiley & Sons, Ltd.     

II. Yeast sequencing reports. Sequence analysis of a 78·6 kb segment of the left end of Saccharomyces cerevisiae chromosome II

We report the sequence analysis of a 78,601 bp DNA segment on the left arm of chromosome II of Saccharomyces cerevisiae. This 78·6 kb segment spans the region from the start of a subtelomeric Y′ element up to the ILS1 gene. It contains 49 open reading frames (ORFs) with more than 100 amino acids length including 14 internal and five overlapping ORFs. The gene density, excluding the internal ORFs, was calculated as one ORF per 2·2 kb. Eight ORFs (PKC1, TyA, TyB, ATP1, ROX3, RPL17a, PET112 and ILS1) correspond to previously characterized genes. ORF YBL0718 was identified as CDC27; YBL0706 as TEL1. Four other ORFs show strong similarities to already known genes. The gene product of YBL0838 is 60% identical to the ribosomal protein RPL32 from rat, mouse and man. YBL0701 encodes a protein with significant similarity to the initiation factor eIF2 associated p67 glycoprotein from rat. Eight ORFs were disrupted and the resulting yeast strains analysed with respect to their phenotype. The sequence has been deposited in the EMBL Nucleotide Sequence Database under the Accession Number X79489.     

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.     

Sequence analysis of the CEN12 region of Saccharomyces cerevisiae on a 43·7 kb fragment of chromosome XII including an open reading frame homologous to the human cystic fibrosis transmembrane conductance regulator protein CFTR

In the framework of the European Union BIOTECH project for systematically sequencing the Saccharomyces cerevisiae genome, we determined the nucleotide sequence of a 43·7 kb DNA fragment spanning the centromeric region of chromosome XII. A novel approach was the distribution of sublibraries prepared by the DNA coordinator (J. Hoheisel, Heidelberg, FRG), using a new hybridization-based DNA mapping method, in order to facilitate ordered sequencing. The sequence contains 22 open reading frames (ORFs) longer than 299 bp, including the published sequences for ATS/DPS1, SCD25, SOF1, DRS1, MMM1, DNM1 and the centromeric region CEN12. Five putative ORF products show similarity to known proteins: the leucine zipper-containing ABC transporter L1313p to the yeast Ycf1p metal resistance protein, to the yeast putative ATP-dependent permease Yhd5p, to the yeast putative proteins Yk83p and Yk84p, to the human cystic fibrosis transmembrane conductance regulator protein (hCFTR) and to the human multidrug resistance-associated protein hMRP1; L1325p to the Drosophila melanogaster Pumilio protein, to the putative yeast regulatory protein Ygl3p and to the yeast protein Mpt5p/Htr1p; L1329p to human lipase A and gastric lipase, to rat lingual lipase and to the putative yeast triglyceride lipase Tgl1p; L1341p to the putative yeast protein Yhg4p; and the leucine zipper-containing L1361p to the two yeast proteins 00953p and Ym8156.08p and to the Arabidopsis thaliana protein HYP1. Eight ORFs show no homology to known sequences in the database, three small ORFs are internal and complementary to larger ones and L1301 is complementary overlapping the ATS/DPS1 gene. Additionally three equally spaced ARS consensus sequences were found. The nucleotide sequence reported here has been submitted to the EMBL data library under the accession number X91488.     

XIV. Yeast sequencing reports. The sequence of a 44 420 bp fragment located on the left arm of chromosome XIV from Saccharomyces cerevisiae

We have determined the complete nucleotide sequence of a 44 420 bp DNA fragment from chromosome XIV of Saccharomyces cerevisiae. The sequence data revealed 23 open reading frames (ORFs) larger than 300 bp, covering 73·5% of the sequence. The ORFs N2418, N2441, N2474 and N2480 correspond to previously sequenced S. cerevisiae genes coding respectively for the mitochondrial import protein Mas5, the nucleolar protein Nop2, the outer mitochondrial membrane porin Por1, the cytochrome c oxidase polypeptide VA precursor CoxA and the yeast protein tyrosine phosphatase Msg5. Translation products of three other ORFs N2406, N2411 and N2430 exhibit similarity to previously known S. cerevisiae proteins: the ribosomal protein YL9A, the protein Nca3 involved in the mitochondrial expression of subunits 6 and 8 of the ATP synthase and actin; in addition N2505 presents strong similarity to an ORF of chromosome IX. The predicted protein products of ORFs N2417 and N2403 present similarities with domains from proteins of other organisms: the Candida maltosa cycloheximide-resistance protein, the human interleukin enhancer-binding factor (ILF-2). The 12 remaining ORFs show no significant similarity to known proteins. In addition, we have detected a DNA region very similar to the yeast transposon Ty 1–15 of which insertion has disrupted a tRNA^Asp gene. The sequence has been deposited in the GenBank database with the Accession Number U12141.     

The Sequence of a 36·7 kb Segment on the Left Arm of Chromosome IV from Saccharomyces cerevisiae Reveals 20 Non-overlapping Open Reading Frames (ORFs) Including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 New ORFs

A 36 688 bp fragment from the left arm of chromosome IV of Saccharomyces cerevisiae was sequenced. Sequence analysis identified 20 complete non-overlapping open reading frames (ORFs) of at least 100 amino acids. Nine of these correspond to previously identified and sequenced genes: SIT4/PPH1, FAD1, NAM1/MTF2, RNA11, SIR2/MAR1, NAT1/AAA1, PRP9, ACT2 and MPS1/RPK1. Three ORFs show homology to previously sequenced genes. One ORF exhibits a hypothetical yabO/yceC/yfiI family signature and one has the ATP-dependent helicase signature of the DEAD and DEAH box families. Six ORFs show no appreciable homology to any proteins in the database. One of these is identical to yeast expressed sequence tags and therefore corresponds to an expressed gene. In addition, two partial ORFs and 11 ORFs that are totally internal and are not likely to be functional were detected. The sequence has been submitted to the EMBL data library under Accession Number Z71781. © 1997 by John Wiley & Sons, Ltd.     

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.     

XIV. Yeast sequencing reports. Twelve open reading frames revealed in the 23·6 kb segment flanking the centromere on the Saccharomyces cerevisiae chromosome XIV right arm

The nucleotide sequence of 23·6 kb of the right arm of chromosome XIV is described, starting from the centromeric region. Both strands were sequenced with an average redundancy of 4·87 per base pair. The overall G+C content is 38·8% (42·5% for putative coding regions versus 29·4% for non-coding regions). Twelve open reading frames (ORFs) greater than 100 amino acids were detected. Codon frequencies of the twelve ORFs agree with codon usage in Saccharomyces cerevisiae and all show the characteristics of low level expressed genes. Five ORFs (N2019, N2029, N2031, N2048 and N2050) are encoded by previously sequenced genes (the mitochondrial citrate synthase gene, FUN34, RPC34, PRP2 and URK1, respectively). ORF N2052 shows the characteristics of a transmembrane protein. Other elements in this region are a tRNA^Pro gene, a tRNA^Asn gene, a τ₃₄ and a truncated δ₃₄ element. Nucleotide sequence comparison results in relocation of the SIS1 gene to the left arm of the chromosome as confirmed by colinearity analysis. The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession number X77395.     

XV. Yeast sequencing reports. A 29·425 kb segment on the left arm of yeast chromosome XV contains more than twice as many unknown as known open reading frames

The nucleotide sequence of a 29·425 kb fragment localized on the left arm of chromosome XV from Saccharomyces cerevisiae has been determined. The sequence contains 13 open reading frames (ORFs) of which four encode the known genes ADH1, COQ3, MSH2 and RCF4. Predictions are made concerning the functions of the unknown ORFs. Some of the ORFs contain sequences similar to expressed sequences tags (EST) found in the database made available by TIGR. In particular, the highly expressed ADH1 gene is represented in this database by no less than 20 EST sequences. Two ARS sequences and a putative functional GCN4 motif have also been detected. One ORF (O0953) containing nine putative transmembrane segments is similar to a hypothetical membrane protein of Arabidopsis thaliana. Characteristic features of the other ORFs include ATP/GTP binding sites, a fungal Zn(2)-Cys(6) binuclear centre, an endoplasmic reticulum targeting sequence, a β-transducin repeat signature and in two instances, good similarity to the prokaryotic lipoprotein signal peptide motif. The sequence has been deposited in the EMBL data library under Accession Number X83121.     

The Sequence of a 54·7 kb Fragment of Yeast Chromosome XV Reveals the Presence of Two tRNAs and 24 New Open Reading Frames

A 54 719 bp fragment from the right arm of Saccharomyces cerevisiae chromosome XV has been sequenced from the inserts of two cosmids (pEOA213 and pEOA217). The computer analysis of this sequence has revealed the presence of eight known genes (CKA2, CYC1, ALG8, TCM1, TMP1, UFE1, RTS2 and ASE1) and four open reading frames (ORFs) with strong homologies with known yeast genes (MLP1, SIS2 and HBS1 and the allantoin permease). The characteristics of the other ORFs and of the corresponding proteins do not allow postulation of a precise function. Several have features reminiscent of cytoskeleton or motor elements (keratin-like, myosin-like) and several others have characteristics of proteins which interact with DNA (extremely basic, b-Zip structure and/or acidic domains). Two tRNAs (tRNA^Lys and tRNA^Pro) have also been identified on this fragment. Many of these ORFs present similarities with ORFs located on chromosome XI, indicating some information reshuffling between the two chromosomal fragments. The sequence has been deposited in the EMBL library data bank under Accession Number Z70678. © 1997 John Wiley & Sons, Ltd.     

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).     

Sequence Analysis of a 33·2 kb Segment from the Left Arm of Yeast Chromosome XV Reveals Eight Known Genes and Ten New Open Reading Frames Including Homologues of ABC Transporters,Inositol Phosphatases and Human Expressed Sequence Tags

The complete nucleotide sequence of a 33 221 bp segment, contained in cosmid pEOA1044, derived from the left arm of chromosome XV of Saccharomyces cerevisiae, appears in public databases between coordinates 177013 and 210234 (http://speedy.mips.biochem.mpg.de/). Computer analysis of that sequence revealed the presence of the previously known genes IRA2, DEC1, NUF2, HST1, RTG1, RIB2 and HAL2, one previously partially sequenced open reading frame (ORF) of unknown function (SCORFAC) and ten newly identified ORFs. One of the new ORFs is similar to the Drosophila melanogaster white gene and other transmembrane ABC transporters, another one has similarities to inositol phosphatases and others are similar to ORFs of unknown function from various organisms, including human Expressed Sequence Tags (ESTs). Potential transmembrane regions, ATP/GTP-binding and WD motifs have also been identified. The existence of yeast ESTs for two of the newly identified ORFs indicates that they are transcribed. © 1997 John Wiley & Sons, Ltd.