NORMAL GENOMIC

• Xiang Z, Lyne MH, Wood V, Rajandream MA, Barrell BG, Aves SJ
• DNA sequencing and analysis of a 67.4 kb region from the right arm of Schizosaccharomyces pombe chromosome II reveals 28 open reading frames including the genes his5, pol5, ppa2, rip1, rpb8 and skb1.
• Yeast. 1999; 15: 893-901
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• 67 393 bp of contiguous DNA located between markers cdc18 and cdc14 on the right arm of fission yeast chromosome II has been sequenced as part of the European Union Schizosaccharomyces pombe genome sequencing project. The complete sequence, contained in cosmid clones c15C4 and c21H7, has been determined on both strands. Sequence analysis shows that it contains 28 open reading frames capable of coding for proteins, 16 split by one or more introns, but no tRNA, rRNA or transposon sequences. The gene density is one per 2. 4 kb. Six genes have been previously described (his5, pol5, ppa2, rip1, rpb8 and skb1) and 22 are novel. Of the novel genes, 14 have significant similarity with proteins of known function, three have similarities with proteins of unknown function and five show no extensive similarities with known proteins. Sequence similarities suggest that three of the novel genes encode ATP-dependent RNA helicases, two encode transcription factor components and others encode a G-protein, a dehydrogenase, a Rab escort protein, an Abc1-like protein, a lipase, an ATP-binding transport protein, an amino acid permease, an acid phosphatase and a mannosyltransferase.

• Marini AM, Soussi-Boudekou S, Vissers S, Andre B
• A family of ammonium transporters in Saccharomyces cerevisiae.
• Mol Cell Biol. 1997; 17: 4282-93
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• Ammonium is a nitrogen source supporting growth of yeast cells at an optimal rate. We recently reported the first characterization of an NH4+ transport protein (Mep1p) in Saccharomyces cerevisiae. Here we describe the characterization of two additional NH4+ transporters, Mep2p and Mep3p, both of which are highly similar to Mep1p. The Mep2 protein displays the highest affinity for NH4+ (Km, 1 to 2 microM), followed closely by Mep1p (Km, 5 to 10 microM) and finally by Mep3p, whose affinity is much lower (Km, approximately 1.4 to 2.1 mM). A strain lacking all three MEP genes cannot grow on media containing less than 5 mM NH4+ as the sole nitrogen source, while the presence of individual NH4+ transporters enables growth on these media. Yet, the three Mep proteins are not essential for growth on NH4+ at high concentrations (>20 mM). Feeding experiments further indicate that the Mep transporters are also required to retain NH4+ inside cells during growth on at least some nitrogen sources other than NH4+. The MEP genes are subject to nitrogen control. In the presence of a good nitrogen source, all three MEP genes are repressed. On a poor nitrogen source, MEP2 expression is much higher than MEP1 and MEP3 expression. High-level MEP2 transcription requires at least one of the two GATA family factors Gln3p and Nil1p, which are involved in transcriptional activation of many other nitrogen-regulated genes. In contrast, expression of either MEP1 or MEP3 requires only Gln3p and is unexpectedly down-regulated in a Nil1p-dependent manner. Analysis of databases suggests that families of NH4+ transporters exist in other organisms as well.

• Dietrich FS et al.
• The nucleotide sequence of Saccharomyces cerevisiae chromosome V.
• Nature. 1997; 387: 78-81
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• Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Tyl transposable elements, each of which contains an ORF (included in the count of 271). Of the ORFs, 78 (29%) are new, 81 (30%) have potential homologues in the public databases, and 112 (41%) are previously characterized yeast genes.

• Parle-McDermott AG, Hand NJ, Goulding SE, Wolfe KH
• Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I.
• Yeast. 1996; 12: 999-1004
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• We report a 29,445 bp sequence from the right arm of yeast chromosome XV. It contains the genes MYO2, SNC2, PDR10, SCD5 (also called FTB1), MIP1, VMA4, MRS2, ALA1, KRE5, TEA1, and a homologue of YAL034c. Several discrepancies with previously published sequences were found. PDR10 encodes a protein highly similar to the pleiotropic drug resistance protein Pdr5p. This sequence contig forms part of a region of extended similarity to part of the left arm of chromosome I, which is a relic of an ancient duplicated chromosomal region.

• Escribano V, Eraso P, Portillo F, Mazon MJ
• Sequence analysis of a 14.6 kb DNA fragment of Saccharomyces cerevisiae chromosome VII reveals SEC27, SSM1b, a putative S-adenosylmethionine-dependent enzyme and six new open reading frames.
• Yeast. 1996; 12: 887-92
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• The nucleotide sequence of a fragment from the left arm of Saccharomyces cerevisiae chromosome VII has been determined. Analysis of the 14,607 bp DNA segment reveals nine open reading frames (ORFs) longer than 300 bp. G2827 is the SEC 7 gene, an essential coatomer complex subunit. G2834 encodes SSM1b, a ribosomal protein. The G2838 product shows homology to hypothetical yeast proteins, YIF0 and YE09, of unknown function. The G2830 product shows homology with the cell division protein FtsJ from Escherichia coli, with two hypothetical proteins from yeast, YCF4 and YBR1, and with R74.7, a hypothetical protein from Caenorhabditis elegans. Two of the ORFs are completely internal to longer ones and a third is partially embedded in G2850. The remaining ORFs give no significant homology with proteins in the databases.

• van der Aart QJ, Kleine K, Steensma HY
• Sequence analysis of the 43 kb CRM1-YLM9-PET54-DIE2-SMI1-PHO81-YHB4-PFK1 region from the right arm of Saccharomyces cerevisiae chromosome VII.
• Yeast. 1996; 12: 385-90
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• The nucleotide sequence of a 43 118 bp fragment from chromosome VII of Saccharomyces cerevisiae has been determined and analysed. The fragment originates from the right arm of chromosome VII. It starts approximately 11 kb centromere-proximal to the per54 marker and ends in the middle of the PFK1 gene. The sequence contains a small nuclear RNA gene (SNR7) and 29 open reading frames (ORFs) larger than 100 amino acids. Six of these were completely internal to or partially overlapped other ORFs. Six previously described genes, YLM9/MRPL9, CRM1, DIE2, SMI1, PHO81 and YHB4, were mapped to this region in addition to pet54 and PFK1. Of the remaining 17 ORFs, four showed homology with other S. cerevisiae genes and four, including one of the partially overlapping ORFs, with genes from other organisms. Eight ORFs had no homology with any sequence in the databases.

• Eide LG, Sander C, Prydz H
• Sequencing and analysis of a 35.4 kb region on the right [corrected] arm of chromosome IV from Saccharomyces cerevisiae reveal 23 open reading frames.
• Yeast. 1996; 12: 1085-90
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• The complete DNA sequence of cosmid clone 31A5 containing a 35 452 bp segment from the right [corrected] arm of chromosome IV from Saccharomyces cerevisiae, was determined from an ordered set of subclones in combination with primer walking on the cosmid. The sequence contains 23 open reading frames (ORFs) of more than 100 amino acid residues and the tRNA-Va12a gene. Five ORFs corresponded to the known yeast genes SNQ2, SES1, GCV1, RPL2B and RPS18A. The DNA sequence for RPS18A is interrupted by an intron. One ORF corresponded to a part of the yeast gene HEX2 at the end of the cosmid insert. Four ORFs encoded putative proteins which showed strong homologies to other previously known proteins, three of yeast origin and one of non-yeast origin. Two ORFs were classified as having borderline homologies: one had similarity to two protein families and another to two protein products of unknown function from other species. The remaining 11 ORFs bore no significant similarity to any published protein.

• Haynie DT, Ponting CP
• The N-terminal domains of tensin and auxilin are phosphatase homologues.
• Protein Sci. 1996; 5: 2643-6
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• Tensin, an actin filament capping protein, and auxilin, a component of receptor-mediated endocytosis, are known to have 350 residue regions of significant sequence similarity near their N-termini (Schroder et al., 1995, Eur J Biochem 228:297-304). Here we demonstrate that these regions are homologous, not only to each other, but also to the catalytic domain of a putative protein tyrosine phosphatase (PTP) from Saccharomyces cerevisiae and to other PTPs. We propose that the PTP-like portion of the homology region of tensin and auxilin represents a distinct domain. A detailed sequence comparison indicates that the PTP-like domain in tensin is unlikely to exhibit phosphatase activity, whereas in auxilin it may possess a different phosphatase specificity from tyrosine phosphatases. It is probable that the PTP-like domains in tensin and auxilin mediate binding interactions with phosphorylated polypeptides; they may therefore represent members of a distinct class of phosphopeptide recognition domain.

• Naitou M et al.
• Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.
• Yeast. 1996; 12: 77-84
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• Plasmid clone gapB and lambda phage clone 4682, which contain fragments of Saccharomyces cerevisiae chromosome VI, were analysed. A 23 kb sequence was determined and ten open reading frames (ORFs) were revealed. Among them, five ORFs were identical to five yeast genes (SEC4, MSH4, SPB4, DEG1 and NIC96), two were identical to transposable elements (TYA and TYB), one (gapBorfF003) was highly homologous to a yeast expressed sequence tag, and another (4682orfF002) was predicted to be a nuclear protein. Sequence data have been submitted to DDBJ/EMBL/GenBank data library under Accession Number D44604 (clone gapB) and D44600 (clone 4682), respectively.

• Pandolfo D, De Antoni A, Lanfranchi G, Valle G
• The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open reading frames including a novel gene encoding a globin-like domain.
• Yeast. 1996; 12: 1071-6
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• In this paper is described the DNA sequence of cosmid 14-5 from chromosome XIV of Saccharomyces cerevisiae. The sequence is 38 855 bases long and contains 21 open reading frames (ORFs) plus three internal ORFs. Six ORFs correspond to known yeast genes (SLA2, ZWF1, BLH1, KEX2, SIN4 and URE2); two other ORFs had already been sequenced because they are adjacent to known genes; the remaining 12 ORFs are novel genes. Of these, one ORF (NII42) is particularly interesting since it shows a significant similarity to mammalian globin. Another ORF (N1254) displays two zinc finger motifs as well as a DNAJ motif.

• Konopinska A, Szczesniak B, Boguta M
• Nucleotide sequence of the GDS1 gene of Saccharomyces cerevisiae.
• Yeast. 1995; 11: 1513-8
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• We have cloned and sequenced the GDS1 gene located on the right arm of chromosome XV of Saccharomyces cerevisiae. The gene codes for a 522 amino acid serine-rich protein with no obvious homology to proteins in the database. GDS1 gene was isolated as the multicopy suppressor of the glycerol-deficient phenotype caused by the nam9-1 mutation in the yeast nuclear gene encoding the mitochondrial ribosomal protein homologous to S4 proteins from various organisms. Disruption-deletion of the GDS1 open reading frame leads to a partial impairment of growth on medium containing glycerol as the carbon source, indicating mitochondrial function of the gene product.

• Vandenbol M, Durand P, Dion C, Portetelle D, Hilger F
• Sequence of a 17.1 kb DNA fragment from chromosome X of Saccharomyces cerevisiae includes the mitochondrial ribosomal protein L8.
• Yeast. 1995; 11: 57-60
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• We have sequenced a continuous segment of 17,137 bp on chromosome X. Sequence analysis of this stretch revealed 14 open reading frames (ORFs) at least 100 amino acids long. One gene, encoding the mitochondrial 60S ribosomal protein L8, had already been sequenced. Four ORF products show weak homologies with known protein sequences. The nine remaining ORF products have no homologies with sequences in data banks.

• Ouzounis C, Bork P, Casari G, Sander C
• New protein functions in yeast chromosome VIII.
• Protein Sci. 1995; 4: 2424-8
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• The analysis of the 269 open reading frames of yeast chromosome VIII by computational methods has yielded 24 new significant sequence similarities to proteins of known function. The resulting predicted functions include three particularly interesting cases of translation-associated proteins: peptidyl-tRNA hydrolase, a ribosome recycling factor homologue, and a protein similar to cytochrome b translational activator CBS2. The methodological limits of the meaningful transfer of functional information between distant homologues are discussed.

• Van Dyck L, Pascual-Ahuir A, Purnelle B, Goffeau A
• An 8.2 kb DNA segment from chromosome XIV carries the RPD3 and PAS8 genes as well as the Saccharomyces cerevisiae homologue of the thiamine-repressed nmt1 gene and a chromosome III-duplicated gene for a putative aryl-alcohol dehydrogenase.
• Yeast. 1995; 11: 987-91
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• A 8.2 kb DNA segment from the left arm of Saccharomyces cerevisiae chromosome XIV (GenBank/EMBL accession number: X83226) encompasses four open reading frames (ORFs) longer than 100 residues. The ORF N0295 is highly similar to the Aspergillus parasiticus and Schizosaccharomyces pombe nmt1 gene products, which are involved in thiamine biosynthesis and are strongly repressed by thiamine. N0300 is 76% identical to YCR107w, a hypothetical protein of yeast chromosome III, and 55% identical to a ligninolytic aryl-alcohol dehydrogenase from the white-rot fungus Phanerochaete chrysosporium. In addition, this fragment encodes Rpd3, a pleiotropic transcription factor (Vidal and Gaber, 1991), and part of Pas8, a protein essential for the biogenesis of peroxisomes (Voorn-Brouwer et al., 1993).

• Zumstein E, Pearson BM, Kalogeropoulos A, Schweizer M
• 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.
• Yeast. 1995; 11: 975-86
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• 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 sequence 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 beta-transducin repeat signature and in two instances, good similarity to the prokaryotic lipoprotein signal peptide motif.

• Kalogeropoulos A
• Automatic intron detection in nuclear DNA sequences of Saccharomyces cerevisiae.
• Yeast. 1995; 11: 555-65
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• The goal of the present work is the construction of software (EXPLORA) which automatically detects Open Reading Frames (ORF), intron-containing or not, in the nuclear sequences of the yeast Saccharomyces cerevisiae. In order to detect introns within (or preceding) ORFs, one must define precise rules of how an intron is identified. These rules are described here. The software is able to detect correctly an intron-associated ORF in at least 88% of cases. We tested all yeast nuclear entries of the EMBL database with the software, and found, in addition to the known intron-associated ORFs, some others which may include an intron. Finally the software was applied to the DNA sequences of chromosomes III and XI, in which it detected eight new intron-associated ORFs.

• Zumstein E, Griffin H, Schweizer M
• 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.
• Yeast. 1994; 10: 1383-7
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• 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.

• Garcia-Cantalejo J et al.
• The complete sequence of an 18,002 bp segment of Saccharomyces cerevisiae chromosome XI contains the HBS1, MRP-L20 and PRP16 genes, and six new open reading frames.
• Yeast. 1994; 10: 231-45
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• We report the sequence of an 18,002 bp DNA fragment from the right arm of Saccharomyces cerevisiae chromosome XI. This segment contains nine complete open reading frames (ORFs), YKR401 to YKR409, and part of another ORF, YKR400, covering altogether 87.2% of the entire sequence. One of them, YKR400, encodes an NAD-dependent 5,10-methylene-tetrahydrofolate dehydrogenase. YKR404, YKR405 and YKR406 correspond to the previously characterized HBS1, MRP-L20 and PRP16 genes, coding for a translation elongation factor, a mitochondrial ribosomal protein and an ATP-binding protein, respectively. The putative product of YKR407 contains the zinc-binding region signature of neutral zinc metallopeptidases. The five other ORFs do not show significant homology to any known protein.

• Mannhaupt G, Stucka R, Ehnle S, Vetter I, Feldmann H
• Analysis of a 70 kb region on the right arm of yeast chromosome II.
• Yeast. 1994; 10: 1363-81
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• In the framework of the EC programme for sequencing yeast chromosome II, we have determined the nucleotide sequence of a 70 kb region. Subsequent analysis revealed 35 open reading frames, 14 of which correspond to known yeast genes. 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 1.98 kb. Coding regions occupy 75% 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.

• Verhasselt P, Aert R, Voet M, Volckaert G
• Nucleotide sequence analysis of an 8887 bp region of the left arm of yeast chromosome XIV, encompassing the centromere sequence.
• Yeast. 1994; 10: 945-51
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• The nucleotide sequencing of 8887 bp of the left arm of chromosome XIV is described. The sequence includes the centromeric region. Both strands were sequenced with an average redundancy of 5.09 per base pair. The overall G+C content is 37.3% (39.2% for putative coding regions versus 32.5% for non-coding regions). Six open reading frames (ORFs) greater than 100 amino acids were detected, all of which are completely confined to the 8.9 kbp region. Codon frequencies of the six ORFs agree with codon usage in Saccharomyces cerevisiae and all show the characteristics of low-level expressed genes. Comparison of the translated sequences with protein sequences in data bases suggests the presence of two ORFs (N2014 and N2007) encoding ribosomal proteins, the latter of which is the previously sequenced MRP7 gene. Another ORF (N2012) could encode a membrane-associated protein since it contains secretory signal sequence and two presumed transmembrane helices. This protein might be involved in mitochondrial energy transfer. ORF N2016 is immediately adjacent to the centromere, suggesting that it corresponds to the SPO1 gene, which is very tightly linked to the centromere at the left arm side of chromosome XIV (Mortimer et al., 1989).

• Cusick ME
• Purification and identification of two major single-stranded binding proteins of yeast Saccharomyces cerevisiae as ribosomal protein L4 and histone H2B.
• Biochim Biophys Acta. 1994; 1217: 31-40
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• Affinity chromatography on single-stranded DNA cellulose (ssDC) is useful for purification of single-stranded RNA and single-stranded DNA binding proteins. Most of the proteins purified off of this resin have proven to be ribonucleoproteins, with various roles in RNA processing. A homogenate of the yeast Saccharomyces cerevisiae shows perhaps a dozen major protein species, and many more minor protein species, upon elution from ssDC. A major protein species of 30-31 kDa that elutes from ssDC between 0.35 and 0.45 M NaCl was purified to homogeneity. V8 protease was used to fragment this protein, and the peptides so generated were purified by HPLC and sequenced. From the sequence so derived six synthetic oligonucleotides were made. These oligonucleotides were used to pull out the corresponding gene from a yeast genomic library. The entire gene was eventually found on a 4.4 kb BamHI fragment. This entire fragment was sequenced. The sequence showed three open reading frames (ORFs). ORF1 was the p30 gene, for all six V8 peptide fragment sequences were found in it. Published here is the sequence for ORF1. Sequence comparisons of this sequence to the protein sequence databases showed that it is ribosomal protein L4. Another major ssb of yeast, which migrates as a doublet of 15-16 kDa, was also purified. N-terminal peptide sequencing of this protein produced a sequence identical to that for histone H2B.

• Van Dyck L, Jonniaux JL, de Melo Barreiros T, Kleine K, Goffeau A
• Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the ribosomal protein L19 as well as proteins with homologies to components of the hnRNP and snRNP complexes and to the human proliferation-associated p120 antigen.
• Yeast. 1994; 10: 1663-73
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• We report the nucleotide sequence of a 17.4 kb DNA segment from the left arm of Saccharomyces cerevisiae chromosome II. This sequence contains 12 open reading frames (ORFs) longer than 300 bp and a putative autonomously replicating sequence (ARS). The ORF YBL0418 contains the KH motif present in several nucleic acid-binding proteins and shares homologies with the mouse X protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes involved in pre-mRNA processing. YBL0424 is the yeast member of the ribosomal protein L19 (YL14) family. YBL0425 is related to the D1 core polypeptide of the small nuclear ribonucleoprotein (snRNP) particles involved in the splicing of introns. YBL0437 is a putative homologue of the human protein p120, one of the major antigens associated with malignant tumours. Mcm2, a protein important for ARS activity, as well as Aac2, one of the three isoforms of the mitochondrial ATP/ADP carrier, were previously described (Yan et al., 1991; Lawson and Douglas, 1988). Four ORFs show no homology or particular features that could help to assess their functions. The last ORFs are not likely to be expressed for they are localized on the complementary strand of longer ORFs.

• James CM, Gent ME, Indge KJ, Oliver SG
• Sequence analysis of a 10 kb fragment of yeast chromosome XI identifies the SMY1 locus and reveals sequences related to a pre-mRNA splicing factor and vacuolar ATPase subunit C plus a number of unidentified open reading frames.
• Yeast. 1994; 10: 247-55
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• We report the DNA sequence analysis of a region on the left arm of chromosome XI of Saccharomyces cerevisiae extending over 10 kb. The region contains five open reading frames (ORFs) of greater than 100 amino acids which do not show significant overlap with other ORFs. YKL408 contains a sequence with strong similarity to the RNA helicase pre-mRNA splicing factors PRP2, PRP16 and PRP22 (Burgess et al., 1990; Company et al., 1991; Ruby et al., 1991). YKL409 corresponds to the gene SMY1, the sequence of which was previously reported by Lillie and Brown (1992). YKL410 is identical to ATPase subunit C (Beltran et al., 1992) except for an N-terminal extension. YKL406 and YKL407 show no significant identity with any sequences in the databases searched.

• Miosga T, Zimmermann FK
• Sequence and function analysis of a 2.73 kb fragment of Saccharomyces cerevisiae chromosome II.
• Yeast. 1993; 9: 1273-7
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• The nucleotide sequence of a fragment of 2728 base pairs of Saccharomyces cerevisiae chromosome II has been determined. The sequence contains two open reading frames, one of them being incomplete. Deletion mutants of YBR11.21 are viable. YBR11.20 is identical to the recessive omnipotent suppressor SUP45 (SUP1).

• Tanaka S, Isono K
• Correlation between observed transcripts and sequenced ORFs of chromosome III of Saccharomyces cerevisiae.
• Nucleic Acids Res. 1993; 21: 1149-53
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• Most of the 155 transcripts of the genes on chromosome III of S.cerevisiae that were identified by a series of Northern hybridization experiments (Yoshikawa, A. and Isono, K., Yeast 6, 383-401, 1990) have been correlated with the open reading frames (ORFs) deduced from the nucleotide sequence data for this chromosome (Oliver, S.G. et al., Nature 357, 38-46, 1992). This was performed by comparing the experimentally constructed physical map and the one produced from the nucleotide sequence data, and then the sizes and positions of observed transcripts and those of sequenced ORFs. The data thus provide information for possible products of the sequenced ORFs (genes) of chromosome III of S.cerevisiae as well as their likely levels of expression in vegetatively growing cells.

• Sapolsky RJ, Brendel V, Karlin S
• A comparative analysis of distinctive features of yeast protein sequences.
• Yeast. 1993; 9: 1287-98
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• The recently published sequence of yeast chromosome III (YCIII) provides the longest continuous stretch of a eukaryotic DNA molecule sequenced to date (315 kb). The sequence contains 116 distinct AUG-initiated open reading frames of at least 200 codons in length, more than 50 of which had not been described previously nor bear significant similarity to known proteins. We have analysed the YCIII known and putative protein sequences with respect to significant statistical features which might reflect on structural and functional characteristics. The YCIII proteins have striking similarities and differences in their sequence attribute distributions compared to the corresponding distributions for all available yeast sequences and other protein collections. Nine examples of YCIII proteins with distinctive sequence features are discussed in detail.

• Doignon F, Biteau N, Crouzet M, Aigle M
• The complete sequence of a 19,482 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae.
• Yeast. 1993; 9: 189-99
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• 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.

• Purnelle B, Tettelin H, Van Dyck L, Skala J, Goffeau A
• The sequence of a 17.5 kb DNA fragment on the left arm of yeast chromosome XI identifies the protein kinase gene ELM1, the DNA primase gene PRI2, a new gene encoding a putative histone and seven new open reading frames.
• Yeast. 1993; 9: 1379-84
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• A 17.5 kb DNA fragment of chromosome XI, located between the genetic loci mif2 and mak11 was sequenced and analysed. Ten open reading frames were identified. Two of them are the previously sequenced genes ELM1 and PRI2, two (YKL253 and YKL256) show homologies to proteins from other organisms and one (YKL262) to yeast and mouse histone.

• Baur A, Schaaff-Gerstenschlager I, Boles E, Miosga T, Rose M, Zimmermann FK
• Sequence of a 4.8 kb fragment of Saccharomyces cerevisiae chromosome II including three essential open reading frames.
• Yeast. 1993; 9: 289-93
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• The nucleotide sequence of a fragment of 4867 base pairs of Saccharomyces cerevisiae chromosome II has been determined. The sequence contains three complete open reading frames. In addition to the already known gene RPB5, coding for a subunit shared by all three DNA directed RNA polymerases, two new open reading frames could be identified. YBR12.03 codes for a protein of 183 amino acids with homology to one of the proteins of the Bacillus subtilis riboflavin biosynthesis operon (RibG). Deletion mutants of YBR12.03 can germinate but stop growing after five to seven cell divisions on YPD. Supplementation with high concentrations of riboflavin does promote growth. YBR12.05 codes for a protein of 386 amino acids with homology to STI1, a stress-inducible protein of S. cerevisiae. Deletion mutants of YBR12.05 are not viable.