Size threshold for Saccharomyces cerevisiae chromosomes: generation of telocentric chromosomes from an unstable minichromosome.

A 9-kilobase pair CEN4 linear minichromosome constructed in vitro transformed Saccharomyces cerevisiae with high frequency but duplicated or segregated inefficiently in most cells. Stable transformants were only produced by events which fundamentally altered the structure of the minichromosome: elimination of telomeres, alteration of the centromere, or an increase of fivefold or greater in its size. Half of the stable transformants arose via homologous recombination between an intact chromosome IV and the CEN4 minichromosome. This event generated a new chromosome from each arm of chromosome IV. The other "arm" of each new chromosome was identical to one "arm" of the unstable minichromosome. Unlike natural yeast chromosomes, these new chromosomes were telocentric: their centromeres were either 3.9 or 5.4 kilobases from one end of the chromosome. The mitotic stability of the telocentric chromosome derived from the right arm of chromosome IV was determined by a visual assay and found to be comparable to that of natural yeast chromosomes. Both new chromosomes duplicated, paired, and segregated properly in meiosis. Moreover, their structure, as deduced from mobilities in orthogonal field gels, did not change with continued mitotic growth or after passage through meiosis, indicating that they did not give rise to isochromosomes or suffer large deletions or additions. Thus, in S. cerevisiae the close spacing of centromeres and telomeres on a DNA molecule of chromosomal size does not markedly alter the efficiency with which it is maintained. Taken together these data suggest that there is a size threshold below which stable propagation of linear chromosomes is no longer possible.     

Folded chromosomes of Saccharomyces cerevisiae

Folded chromosome phenotypes have been examined and compared in four cell-division-cycle (cdc) mutants during transitions between cycling and non-cycling states. The two start mutants, cdc 28 and cdc 25, can undergo G₀ arrest at the restrictive temperature. Arrest at start, defined by the cdc 28 and cdc 25 block points, is distinguishable from G₀ arrest. Arrest at the cdc 28 and cdc 25 block points can also be distinguished from each other: folded chromosomes appear to be destabilized at the cdc 25 block, but are stable at the cdc 28 arrest point. On the other hand, folded chromosomes from cdc 28 in sporulation medium at the restrictive temperature appear unstable, while chromosomes from cdc 25 are stable. The G₁ arrest mutants, cdc 4 and cdc 7, can undergo G₀ arrest at the restrictive temperature. In sporulation medium no meiotic replication form is detected at the restrictive temperature, although incorporation of labeled precursors into nuclear DNA does take place. A schematic model incorporating these various findings is presented.     

Distribution of telomere-associated sequences on natural chromosomes in Saccharomyces cerevisiae.

Pulsed-field gel electrophoresis was used to examine the distribution of telomere-associated sequences on individual chromosomes in four strains of Saccharomyces cerevisiae. The pattern of X and Y' distribution was different for each strain. At least one chromosome in each strain lacked Y', and in some strains, chromosome I, the smallest yeast chromosome, lacked detectable amounts of both X and Y'.     

On the origin of telocentric chromosomes in mammals

The origin of mammalian telocentric chromosomes is considered under the classical (fusion) and fission hypotheses using both theoretical analyses of the mechanisms proposed under the two hypotheses, and the published chromosomal data for 723 mammal species. Telocentrics are defined on the basis of short arm size (S_w) as chromosomes with S_w < 0·1(Imai, 1976). The fusion hypothesis lacks adequate models for producing these telocentrics, but their origin is readily understood under the fission hypothesis. Based on these analyses, I propose a cyclical model of chromosome change, symbolized:

in which T, A, and $\text{M}$ are, respectively, telocentric, acrocentric, and meta-, submeta- and subtelocentric chromosomes. The chief elements of this model are centric fission $\text{(}\text{M}\text{→ T + T)}$, tandem growth of constitutive heterochromatin (T → A), and pericentric inversion $\text{(A →}\text{M}\text{)}$. Under this model, therefore, mammalian karyotypes have an overall tendency, with occasional reversals, to evolve higher numbers of both chromosomes and chromosome arms.     

Physical dissection and characterization of chromosomes V and VIII of Saccharomyces cerevisiae.

Chromosomes V and VIII of S. cerevisiae were dissected and ordered clone banks were constructed and characterized. Each bank contains almost the entire chromosome from the left to the right telomere except for a small gap in each case. The size of the banks constructed is in good agreement with the physical length of these chromosomes, 580 kb, estimated by pulsed-field gel electrophoresis. The remaining gap in the ordered clone bank of chromosome V was found to be only 1.6 kb in length and to contain a 1.5 kb-long portion of one of the two Ty elements located in tandem. The gap in the bank of chromosome VIII was 6.4 kb in length and contained four copies of the CUP1 gene. A genomic restriction map analysis of the corresponding region of chromosome VIII revealed that a unit of about 2 kb in length harbouring the CUP1 gene was repeated ten times in strain DC5 rho degrees which was used for the bank construction. A 588.5 kb-long high resolution physical map for chromosome V and a 585.6 kb-long one for chromosome VIII have thus been established.     

Construction of a dual chain pseudotetrameric chicken avidin by combining two circularly permuted avidins

Two distinct circularly permuted forms of chicken avidin were designed with the aim of constructing a fusion avidin containing two biotin-binding sites in one polypeptide. The old N and C termini of wild-type avidin were connected to each other via a glycine/serine-rich linker, and the new termini were introduced into two different loops. This enabled the creation of the desired fusion construct using a short linker peptide between the two different circularly permuted subunits. The circularly permuted avidins (circularly permuted avidin 5 --> 4 and circularly permuted avidin 6 --> 5) and their fusion, pseudotetrameric dual chain avidin, were biologically active, i.e. showed biotin binding, and also displayed structural characteristics similar to those of wild-type avidin. Dual chain avidin facilitates the development of dual affinity avidins by allowing adjustment of the ligand-binding properties in half of the binding sites independent of the other half. In addition, the subunit fusion strategy described in this study can be used, where applicable, to modify oligomeric proteins in general.     

G+C content variation along and among Saccharomyces cerevisiae chromosomes.

Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these questions. Our results indicate that open reading frames (ORFs) with similar G+C contents at silent codon positions are significantly clustered on chromosomes. This clustering can be explained by very short range correlations of silent-site G+C contents at neighboring ORFs. ORFs of high silent-site G+C content are disproportionately concentrated on shorter chromosomes, which causes a negative relationship between chromosome length and G+C content. Contrary to previous reports, there is no correlation between gene density and silent-site G+C content in yeast. Chromosome III is atypical in many regards, and possible reasons for this are discussed.     

Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae

Meiotic reciprocal recombination (crossing over) was examined in the outermost 60-80 kb of almost all Saccharomyces cerevisiae chromosomes. These sequences included both repetitive gene-poor subtelomeric heterochromatin-like regions and their adjacent unique gene-rich euchromatin-like regions. Subtelomeric sequences underwent very little crossing over, exhibiting approximately two- to threefold fewer crossovers per kilobase of DNA than the genomic average. Surprisingly, the adjacent euchromatic regions underwent crossing over at twice the average genomic rate and contained at least nine new recombination "hot spots." These results prompted an analysis of existing genetic mapping data, which showed that meiotic reciprocal recombination rates were on average greater near chromosome ends exclusive of the subtelomeres. Thus, the distribution of crossovers in S. cerevisiae appears to resemble that found in several higher eukaryotes where the outermost chromosomal regions show increased crossing over.     

Multiple sites for double-strand breaks in whole meiotic chromosomes of Saccharomyces cerevisiae.

We present a scheme for locating double-strand breaks (DSBs) in meiotic chromosomes of Saccharomyces cerevisiae, based on the separation of large DNA molecules by pulsed field gel electrophoresis. Using a rad50S mutant, in which DSBs are not processed, we show that DSBs are widely induced in S. cerevisiae chromosomes during meiosis. Some of the DSBs accumulate at certain preferred sites. We present general profiles of DSBs in chromosomes III, V, VI and VII. A map of the 12 preferred sites on chromosome III is presented. At least some of these sites correlate with known 'hot spots' for meiotic recombination. The data are discussed in view of current models of meiotic recombination and chromosome segregation.     

Construction of xylose-assimilating Saccharomyces cerevisiae

The xylose reductase gene originating from Pichia stipitis was subcloned on an expression vector with the enolase promoter and terminator from Saccharomyces cerevisiae. The transformants of S. cerevisiae harboring the resultant plasmids produced xylose reductase constitutively at a rate about 3 times higher than P. stipitis, but could not assimilate xylose due to the deficient conversion of xylitol to xylulose. The xylitol dehydrogenase gene was also isolated from the gene library of P. stipitis by plaque hybridization using a probe specific for its N-terminal amino acid sequence. The gene transferred into S. cerevisiae was well expressed. Furthermore, high expressions of the xylose reductase and xylitol dehydrogenase genes in S. cerevisiae were achieved by introducing both genes on the same or coexisting plasmids. The transformants could grow on a medium containing xylose as the sole carbon source, but ethanol production from xylose was less than that by P. stipitis and a significant amount of xylitol was excreted into the culture broth.     

Recombination between genes located on nonhomologous chromosomes in Saccharomyces cerevisiae

We constructed strains of Saccharomyces cerevisiae that contained two different mutant alleles of either the leu2 gene or the ura3 gene. These repeated genes were located on nonhomologous chromosomes; the two ura3^- alleles were located on chromosomes V and XII and the two leu2^- alleles were located on chromosomes III and XII. Genetic interactions between the two mutant copies of a gene were detected by the generation of either Leu⁺ or Ura⁺ revertants. Both spontaneous and ultraviolet irradiation-induced revertants were examined. By genetic and physical analysis, we have shown that Leu⁺ or Ura⁺ revertants can arise by a variety of different genetic interactions. The most common type of genetic interaction is the nonreciprocal transfer of information from one repeat to the other. We also detected reciprocal recombination between repeated genes, resulting in reciprocally translocated chromosomes.     

Temperate Bacillus bacteriophage SP16 genome is circularly permuted and terminally redundant.

The physical nature of temperate Bacillus bacteriophage SP16 DNA was analyzed by electron microscopy, exonuclease digestion, denaturation-renaturation experiments, and restriction enzyme analysis. The SP16 genome is a linear molecule 60.0 +/- 2.0 kilobases in length without cohesive ends. Electron micrographs of denatured and renatured SP16 DNA showed that the DNA is circularly permuted. The genome possesses terminal redundancy, as demonstrated by electron microscopy of exonuclease III-digested DNA.     

Amyloid fibril formation by circularly permuted and C-terminally deleted mutants

The natural N- and C-termini, i.e., the given order of secondary structure segments, are critical for protein folding and stability, as shown by several studies using circularly permuted proteins, mutants that have their N- and C-termini linked and are then digested at another site to create new termini. A previous work showed that circularly permuted mutants of sperm whale myoglobin (Mb) are functional, have native-like folding and bind heme, but are less stable than the wild-type protein and aggregate. The ability of wild-type myoglobin to form amyloid fibrils has been established recently, and because circularly permuted mutations are destabilizing, we asked whether these permutations would also affect the rate of amyloid fibril formation. Our investigations revealed that, indeed, the circularly permuted mutants formed cytotoxic fibrils at a rate higher than that of the wild-type. To further investigate the role of the C-terminus in the overall stability of the protein, we investigated two C-terminally deleted mutant, Mb(1-123) and Mb(1-99), and found that Mb(1-123) formed cytotoxic fibrils at a higher rate than that of the wild-type while Mb(1-99) formed cytotoxic fibrils at a similar rate than that of the wild-type. Collectively, our findings show that the native position of both the N-and C-termini is important for the precise structural architecture of myoglobin.     

Absence of circularly permuted and largely redundant sequences in the genome of visna virus.

A previous study of the infectivity of visna virus proviral DNA suggested that the genetic information of the virus is distributed over at least two of the RNA subunits. Because the genetic complexity of visna virus corresponds to the size of one subunit, this result may imply that sequence redundancies exist within each subunit. In the present article we have examined this question by constructing a map of the large RNase T1-resistant oligonucleotides of the viral genome. Our principal results are as follows: (i) all 36S RNA subunits have the same genetic content regardless of their polyadenylic acid [poly(A)] content; (ii) the poly(A) tract is present at the 3' end of the molecule; and (iii) the recoveries of 19 large RNase T1-resistant oligonucleotides from poly(A)-tagged RNA fragments of various sizes demonstrate that the oligonucleotides are organized in the same linear order within all subunits. Our results, therefore, exclude the existence of large sequence redundancies in the genome of visna virus.     

A transposase strategy for creating libraries of circularly permuted proteins

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.     

Meiotic exchange within and between chromosomes requires a common Rec function in Saccharomyces cerevisiae.

We used haploid yeast cells that express both the MATa and MAT alpha mating-type alleles and contain the spo13-1 mutation to characterize meiotic recombination within single, unpaired chromosomes in Rec+ and Rec- Saccharomyces cerevisiae. In Rec+ haploids, as in diploids, intrachromosomal recombination in the ribosomal DNA was detected in 2 to 6% of meiotic divisions, and most events were unequal reciprocal sister chromatid exchange (SCE). By contrast, intrachromosomal recombination between duplicated copies of the his4 locus occurred in approximately 30% of haploid meiotic divisions, a frequency much higher than that reported in diploids; only about one-half of the events were unequal reciprocal SCE. The spo11-1 mutation, which virtually eliminates meiotic exchange between homologs in diploid meiosis, reduced the frequency of intrachromosomal recombination in both the ribosomal DNA and the his4 duplication during meiosis by 10- to greater than 50-fold. This Rec- mutation affected all forms of recombination within chromosomes: unequal reciprocal SCE, reciprocal intrachromatid exchange, and gene conversion. Intrachromosomal recombination in spo11-1 haploids was restored by transformation with a plasmid containing the wild-type SPO11 gene. Mitotic intrachromosomal recombination frequencies were unaffected by spo11-1. This is the first demonstration of a gene product required for recombination between homologs as well as recombination within chromosomes during meiosis.     

产虫草素酿酒酵母工程菌株的构建与发酵优化

虫草素作为药用真菌蛹虫草的主要活性成分,具有抗肿瘤、抗病毒等多种生理功能。现阶段虫草素主要通过蛹虫草液体发酵生产,但发酵周期长、生产强度低,制约了其大规模开发利用。文中在酿酒酵母Saccharomyces cerevisiae S288C中异源表达虫草素合成关键基因ScCNS1和ScCNS2,成功构建了产虫草素的酵母工程菌SHC16,发酵240 h虫草素产量可达67.32 mg/L;基因表达分析显示,发酵后期磷酸戊糖途径、嘌呤代谢及虫草素合成途径关键酶编码基因ZWF1、PRS4、ADE4、ScCNS1及ScCNS2表达水平显著上调。进一步地,通过优化发酵培养基组成,确定以50 g/L葡萄糖为初始底物结合一次补料、添加5 mmol/L Cu2+和1.0 g/L腺嘌呤为最适培养基组成。基于此在5 L搅拌发酵罐中开展补料分批发酵,144 h虫草素产量达到137.27 mg/L,生产强度达0.95 mg/(L·h),较未优化发酵体系提高240%。     

A fully active variant of dihydrofolate reductase with a circularly permuted sequence.

The amino acid sequence of mouse dihydrofolate reductase was permuted circularly at the level of the gene. By transposing the 3'-terminal half of the coding sequence to its 5' terminus, the naturally adjacent amino and carboxyl termini of the native protein were fused, and one of the flexible peptide loops at the protein surface was cleaved. The steady-state kinetic constants, the dissociation constants of folate analogues, and the degree of activation by both mercurials and salt as well as the resistance toward digestion by trypsin were almost indistinguishable from those of a recombinant wild-type protein. Judged by these criteria, the circularly permuted variant has the same active site and overall structure as the wild-type enzyme. The only significant difference was the lower stability toward guanidinium chloride and the lower solubility of the circularly permuted variant. This behavior may be due to moving a mononucleotide binding fold from the interior of the sequence to the carboxyl terminus. Thus, dihydrofolate reductase requires neither the natural termini nor the cleaved loop for stability, for the conformational changes that accompany catalysis as well as the binding of inhibitors, and for the folding process.