Thomas Miosga

Complete DNA sequence of yeast chromosome II

In the framework of the EU genome‐sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37‐45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT‐rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT‐rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Extracellular K+ and Ba2+ mediate voltage‐dependent inactivation of the outward‐rectifying K+ channel encoded by the yeast gene TOK1

Gating of the yeast K+ channel encoded by the Saccharomyces cerevisiae gene TOK1, unlike other outward‐rectifying K+ channels that have been cloned, is promoted by membrane voltage (inside positive‐going) and repressed by extracellular K+. When expressed in Xenopus laevis oocytes, the TOK1p current rectified strongly outward, its activation shifting in parallel with the K+ equilibrium potential when the external K+ concentration ([K+]o) was increased above 3 mM. Analysis of the TOK1p current indicated that two kinetic components contributed to the conductance and the voltage sensitivity of the conductance. By contrast, the [K+]o sensitivity of the current was accommodated entirely within the slow‐relaxing component; it was diminished near 1 mM [K+]o, and at submillimolar concentrations the voltage dependence of the TOK1p conductance was insensitive to [K+]o. External Rb+, the K+ channel blockers Cs+ and Ba2+ – but not Na+, Ca2+ or Mg2+ – substituted for K+ in control of TOK1p activation, indicating a specificity in cation interaction with the TOK1p gate. These and additional results indicate that external K+ acts as a ligand to inactivate the TOK1p channel, and they implicate a gating process mediated by a single cation binding site within the membrane electric field, but distinct from the permeation pathway.

A rapid and highly efficient method for PCR-based site-directed mutagenesis using only one new primer

We present a rapid, cheap and highly efficient method for site-directed mutagenesis using the polymerase chain reaction (PCR). This method is applicable to every DNA fragment which has to be cloned into the multiple cloning site of any vector, or vector pair, in two different orientations. It requires only two primers, one new and specific mutagenic primer and one of the usual sequencing primers. In the first PCR, a mutagenic DNA fragment is synthesized which is amplified exponentially in the second PCR. In contrast, wild-type sequences are only linearly amplified resulting in an efficiency of mutagenesis of nearly 100%.

CLONING AND CHARACTERIZATION OF THE FIRST TWO GENES OF THE NON-OXIDATIVE PART OF THE SACCHAROMYCES CEREVISIAE PENTOSE-PHOSPHATE PATHWAY

Abstract We have cloned and characterized the two remaining unknown genes of the non-oxidative part of the pentose-phosphate pathway of Saccharomyces cerevisiae encoding the enzymes D-ribulose-5-phosphate 3-epimerase (Rpe1p) and D-ribose-5-phosphate ketol-isomerase (Rki1p). Rpe1p has an unexpected high specific activity of 2148 mU × (mg protein)–1 in crude extracts. Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose. Unexpectedly, haploid rki1 deletion mutants are not viable. Functional expression of RKI1 was demonstrated following an increase of gene dosage in the haploid rki1 deletion mutant, which restored viability and specific D-ribose-5-phosphate ketol-isomerase activity. Both enzymes show high similarity to the deduced protein sequences of various open reading frames, expressed sequence tags or cDNAs from different organisms.

Genetics of pentose-phosphate pathway enzymes in Saccharomyces cerevisiae

Abstract Deletion mutants of transketolase and transaldolase were examined for their growth on xylulose medium. Xylulose can be phosphorylated and degraded via the pentose-phosphate pathway in yeast. Deletion mutants of transaldolase ( TAL1 ) can still grow very slowly with xylulose as the carbon source. In-vitro mutagenesis of TAL1 showed that lysine 144 is essential for the catalytic activity of transaldolase. Two genes code for transketolase in S. cerevisiae . Mutants in the gene TKL2 are unaffected by their growth on xylulose medium, while deletion of TKL1 leads to mutants with only very slow growth when xylulose is used as the carbon source. Double mutants for TKL1 and TKL2 could not use xylulose as the carbon source at all, indicating a complete block of the transketolase reaction. Transformants overexpressing transaldolase, transketolase or both enzymes were constructed by placing their genes on the multicopy vector GS42. The activity of transaldolase or transkatolase, or a combination of both enzymes, could be increased by more than 100 fold compared to the wild-type strain measured in parallel. Growth of the transformants on agar plates with xylulose as the carbon source was not accelerated compared to the wild-type strain.

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.