DNA sequence analysis of a 35 kb segment from Saccharomyces cerevisiae chromosome VII reveals 19 open reading frames including RAD54, ACE1/CUP2, PMR1, RCK1, AMS1 and CAL1/CDC43.

We present DNA sequence data from a 35,364 bp region on the left arm of chromosome VII of Saccharomyces cerevisiae. This region contains 19 open reading frames (ORFs). ORF G1821 corresponds to the RAD54 gene involved in repair and recombination (Emery et al., 1991). G1810 is identical to the ACE1 gene sequenced by Szczypka and Thiele (1989), required for copper-inducible transcription of the CUP1 gene. The first 693 bp on the minus strand represent part of the 3' non-coding region from the P-type ATPase gene PMR1, previously sequenced by Rudolph et al. (1989), which is identical to the SSC1 gene (Smith et al., 1988). G1845 corresponds to the RCK1 protein kinase gene from S. cerevisiae (Dahlkvist and Sunnerhagen, 1994). G1861 is almost identical to the alpha-mannosidase gene AMS1 reported by Yoshihisa and Anraku (1989) and G1864 has 100% identity with the yeast CAL1 gene (Ohya et al., 1989)/CDC43 gene (Johnson et al., 1990) which is involved in control of cell polarity. This region also contains a gene specifying a Leu-tRNA precursor and a remnant of a tau element. ORF G1880 shows some similarity to the S. cerevisiae SNF2, STH1 and NPS1 genes and to the human ERCC1 gene. A 93 bp region shows similarity to yeast EST sequenced by Burns et al. (1994). None of the remaining ORFs has similarity to any sequence within the databases screened.

Complete DNA sequence of yeast chromosome XI.

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.

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.

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.

A 'hot-spot' for Ty transposition on the left arm of yeast chromosome III.

The small ring derivative of Saccharomyces cerevisiae chromosome III, which was formed by a cross-over between HML on the left arm and HMR on the right arm, contains three Ty elements. The class II element Ty 1-17 lies immediately centromere-distal to LEU2 on the left arm while two class I elements are tandemly arranged distal to PGK on the right arm. We have sequenced the regions of chromosome III surrounding Ty 1-17 and have defined a region where a number of transposition events have occurred. This region is flanked by the 5' ends of two tRNA genes, tRNA3Glu on the centromere distal side and tRNA3Leu immediately in front of LEU2. Close to the tRNA3Glu gene there is a region containing degenerate delta sequences organised in opposite orientations. Immediately distal to Ty 1-17 there are two complete solo delta elements, one inserted into the other. The sequence indicates that these two delta sequences were inserted into chromosome II by separate transposition events. A model is presented to explain how this structure arose and the role of solo delta elements in transposon propagation and maintenance is discussed.

Nucleotide sequence characterization of Ty 1-17, a class II transposon from yeast.

We have determined the nucleotide sequence of a class II yeast transposon (Ty 1-17) which is found just centromere-distal to the LEU2 structural gene on chromosome III of Saccharomyces cerevisiae. The complete element is 5961 bp long and is bounded by two identical, directly repeated, delta sequences of 332 bp each. The sequence organization indicates that Ty 1-17 is a retrotransposon, like the class I elements characterized previously. It contains two long open reading-frames, TyA (439 amino acids) and TyB (1349 amino acids). In this paper, the sequences of the two classes of yeast transposon are compared with one another and with analogous elements, such as retroviral proviruses, cauliflower mosaic virus and copia sequences. Features of the Ty 1-17 sequence which may be important to its mechanism of transposition and its genetic action are discussed.

Variants within the yeast Ty sequence family encode a class of structurally conserved proteins.

The Ty transposable elements of Saccharomyces cerevisiae form a heterogeneous family within which two broad structural classes (I and II) exist. The two classes differ by two large substitutions and many restriction sites. We show that, like class I elements a class II element, Tyl-17, also appears to contain at least two major protein coding regions, designated TYA and TYB, and the organisational relationship of these regions has been conserved. The TYA genes of both classes encode proteins, designated p1 proteins, with an approximate molecular weight of 50 Kd and, despite considerable variation between the TYA regions at the DNA level, the structures of these proteins are remarkably similar. These observations strongly suggest that the p1 proteins of Ty elements are functionally significant and that they have been subject to selection.

The probability that complex enzyme kinetic curves can be caused by activators of inhibitors.

Numerous chemical compounds are known that alter the rate of conversion of substrates into products in enzyme-catalysed reactions by interacting with the enzyme rather than substrates. Where this takes place in such a way that the effect is reversible on removing the compound, say by dialysis, and where the compound is unchanged chemically by the enzyme system, we refer to such a compound as a modifier. So protons, inorganic salts, activators, inhibitors or even specific allosteric effectors would all be modifiers, and any chemically reasonable kinetic scheme that is proposed to account for such effects is referred to as modifier mechanism. Three versions of a modifier mechanism of enzyme action are studied. The implicit representation is 2:2 in [S] (with alpha(0)=0) and 2:2 in [M] (with alpha(0) not equal0), and this is a short-hand scheme for the minimum chemical formulation, the explicit one, involving discrete ES and EP species, which is 2:2 in [S] (with alpha(0)=0) and 3:3 in [M] (with alpha(0) not equal0). If m extra steps are allowed between interconversion of ES and EP species, the degree of the rate equation remains 2:2 in [S] (with alpha(0)=0), but increases to degree (m+3):(m+3) in modifier (with alpha(0) not equal0). It is proved that this increase in degree is genuine and that highly complex v([M]) (i.e. v-versus-[M]) curves can occur. Computation of the probabilities of the five possible double-reciprocal plots in 1/v versus 1/[S] show that all of these formulations of the modifier mechanism give similar probabilities, and these are characteristic for the mechanism and quite distinct from the intrinsic curve-shape probabilities. It is also established that the probabilities of alternative complex v([M]) plots are similar for the various formulations, and again the probabilities of the allowed complex curves for the mechanism are quite distinct from the instrinsic probabilities of the ten possible v([M]) curves for a 2:2 function (with alpha(0) not equal0). The computer studies reported lead to several conclusions about the probability of modifiers leading to inhibition or activation or causing changes in v([S]) curve shapes, and suggest that differentiation between model mechanisms may be facilitated by knowledge of the intrinsic curve-shape probabilities for the appropriate degree rational function and the characteristic way that this is altered by specific mechanisms. It is shown that, although in some instances new curve-shape complexities are possible when schemes are considered that allow for interconversion of ES and EP species, these are highly improbable and, for theoretical purposes, schemes formulated with node compression provide good approximations to the more complicated explicit schemes. By node compression we refer to the procedure whereby enzyme kinetic schemes are simplified by replacing sequences of steps such as ESright harpoon over left harpoonX(1)right harpoon over left harpoonX(2)right harpoon over left harpoon...right harpoon over left harpoonEP... by a single step... ES/EP... that does not formally recognize the existence of the intermediate species. We show that the modifier mechanism studied is one where this process alters the form of the rate equation.

Application of topological methods in enzyme kinetics.

A criticism [Cornish-Bowden (1976) Biochem. J. 159, 167] of an algebraic method for deriving steady-state rate equations [Indge & Childs (1976) Biochem. J. 155, 567-570] is theoretically founded.

A new method for deriving steady-state rate equations suitable for manual or computer use.

A schematic method for the derivation of steady-state enzyme rate equations by using the Wang algebra is described. The method is simple, easy to learn and offers a substantial decrease in analytical effort over previously published algorithms. Being essentially an algebraic procedure the method can be readily computerized. Computer programs in BASIC and ALGOL languages have been deposited as Supplementary Publication SUP 50065 (19 pages) at the British Library (Lending Division), Boston Spa, Wetherby, W. Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1976). 153, 5.

Interctions between potassium ions and glycine transport in the yeast Saccharomyces carlsbergensis.

A study has been made of the effects of both varying the pH and extracellular [K(+)] on the initial rate of uptake of glycine (v) by a strain of Saccharomyces carlsbergensis that concentrated the amino acid, with respect to the extracellular phase, by up to 1400 times. When no other substrate than glycine was provided and [glycine] was relatively small (