Distribution and sequence analysis of a novel Ty3-like element in natural Saccharomyces paradoxus isolates.

Little is known about the transposable elements of species closely related to Saccharomyces cerevisiae. We present a novel transposable element in Saccharomyces paradoxus, a close congener of S. cerevisiae. Sequence analysis of this element, designated Ty3-1p, indicates that it is a homologue of the S. cerevisiae Ty3 element. Ty3-1p shares 82% nucleotide identity with an S. cerevisiae Ty3 element and appears to be structured identically to Ty3, containing two overlapping open reading frames, six retroviral-like domains, a J domain, and flanking sigma-like elements. A sigma element from Ty3-1p is 75% identical to a Ty3 sigma element. There is no evidence of horizontal transfer of Ty3 in Saccharomyces sensu stricto. We assess the distributions of Ty3p and Ty3 element insertions in natural population samples of S. paradoxus and S. cerevisiae. The S. paradoxus population sample exhibits Ty3p insertions present at a variety of sites at low frequency; this suggests that Ty3p elements are active in the sampled population. The S. cerevisiae population sample exhibits a uniform Ty3 hybridization profile in which all element insertions appear to be fixed. We comment on the possible causes of these contrasting observed distributions (GenBank Accession Nos AY198186 and AY198187).

Fingerman EG ，Dombrowski PG ，Francis CA ，Sniegowski PD ... -  《YEAST》

Diversity of the HO gene encoding an endonuclease for mating-type conversion in the bottom fermenting yeast Saccharomyces pastorianus.

Two types of HO gene were cloned, sequenced and characterized from the bottom fermenting yeast Saccharomyces pastorianus. The HO gene present on the 1500 kb chromosome was designated Sc-HO (S. cerevisiae-type HO), because the nucleotide sequence of its promoter region and the open reading frame (ORF) was almost identical to that of the S. cerevisiae laboratory strain HO gene (Lab-HO). The other HO gene, designated Lg-HO (Lager-fermenting-yeast specific HO), showed 64% and 83% homology with the promoter and ORF of the Lab-HO at the nucleotide sequence level, respectively, and was located on the 1100 kb chromosome. Analysis of the 4 kb DNA fragment amplified from S. bayanus type strain indicated that the nucleotide sequence of S. bayanus-HO is almost identical to that of the Lg-HO. The SSB1 gene located downstream of the HO gene in S. cerevisiae was also found in the 3' distal region of the Sc-HO, Lg-HO and S. bayanus HO genes. These results showed that the genetic arrangement around the HO loci both of S. pastorianus and S. bayanus is identical to S. cerevisiae. Southern analysis has revealed that Saccharomyces sensu stricto contain four types of HO genes; S. paradoxus-type HO, the Sc-HO, the Lg-HO and S. uvarum-type HO genes. This HO gene diversity provides useful information for the classification of strains belonging to Saccharomyces sensu stricto. The S. pastorianus Sc-HO, Lg-HO and S. bayanus-HO Accession Nos in the DDBJ Nucleotide Sequence Database are AB027449, AB027450 and AB027451, respectively.

Tamai Y ，Tanaka K ，Umemoto N ，Tomizuka K ，Kaneko Y ... -  《YEAST》

Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex.

The Saccharomyces sensu stricto complex consists of six closely related species and one natural hybrid. Intra- and inter- species variability in repetitive elements can help elucidate the population structure and evolution of these close relatives. The chromosome positions of several telomeric associated sequences (TASs) and LTR-retrotransposons have been determined, using PFGE, in 112 isolates. Most of the repetitive elements studied are found in multiple copies in each strain, although in some subpopulations these elements are present in low copy number or are absent. Hybridization patterns and copy numbers of the repetitive elements correlate with geographic distribution. These patterns may yield interesting clues as to the origins and evolution of some TASs and retrotransposons, e.g. we can infer that Y' originated on the left end of chromosome XIV. There is strong evidence for horizontal transfer of Ty2 between S. cerevisiae and S. mikatae. Ty1 and Ty5 are either lost easily or frequently horizontally transferred. We have also found some gross chromosomal rearrangements in isolates within species and a few new natural hybrids between species, indicating that these processes occur in the wild and are not limited to conditions of human influence. DNA sequences have been deposited with the EMBL/GenBank database under Accession Nos AJ632279-AJ632293.

Liti G ，Peruffo A ，James SA ，Roberts IN ，Louis EJ ... -  《YEAST》

A Saccharomyces servazzii clone homologous to Saccharomyces cerevisiae chromosome III spanning KAR4, ARS 304 and SPB1 lacks the recombination enhancer but contains an unknown ORF.

In order to learn about the evolutionary conservation of the recombination enhancer (RE) that controls donor preference during mating type switching in Saccharomyces cerevisiae, we have cloned a 13 kb region from S. servazzii. We find that the order of four genes surrounding the RE in S. cerevisiae (PRD1, KAR4, SPB1 and PBN1) is preserved in S.servazzii. However, there is an additional ORF in S. servazzii between PRD1 and KAR4 that is not homologous to any gene in S. cerevisiae or to genes in other organisms. Despite a 75-79% amino acid identity for KAR4 and SPB1, respectively, the S. servazzii sequence did not carry a well-conserved RE sequence and these sequences lacked RE function when introduced into S. cerevisiae. The S. servazzii region contains a sequence that supports autonomous DNA replication in S. cerevisiae and may represent a homologue of ARS304. The S. servazziii sequence has Genbank Accession No. BankIt359091 AF307954.

Zhou Z ，Sun K ，Lipstein EA ，Haber JE ... -  《YEAST》

SED1 polymorphism within the genus Saccharomyces.

The SED1 gene is characterised by abundant length and sequence polymorphisms within the species Saccharomyces cerevisiae, due to the expansion and contraction of minisatellite-like sequences located within the ORF. A survey of the SED1 ORFs of 26 yeasts ascribed to the species S. cerevisiae, S. bayanus, S. pastorianus, S. paradoxus, S. cariocanus, S. kudriavzevii and S. mikatae revealed SED1 gene length and sequence variations between the species of the genus. Moreover, results obtained by Neighbour-Joining analysis of a dataset comprising the partial predicted amino acid sequences of SED1 ORFs agreed with the phylogenetic relationships of the seven species. Thus, the SED1 gene may represent a further molecular target for the identification of Saccharomyces isolates.

Marinangeli P ，Clementi F ，Ciani M ，Mannazzu I ... -  《FEMS YEAST RESEARCH》