Yeast artificial chromosome cloning

Yeast artificial chromosome (YAC) cloning systems enable the cloning of DNA stretches of 50 to well over 2000 kb. This makes it possible to study large intact regions of DNA in detail, by restriction mapping the YAC to produce a physical map and by examining the YAC for coding sequences or genes. YACs are important for their ability to clone the complete sequences of large genes or gene complexes that exceed the size limit for cloning in conventional bacterial cloning vectors like plasmids (up to 10 kb), bacteriophage (15 kb), and cosmids (50 kb). A major advantage of cloning in yeast, a eukaryotc. is that many sequences that are unstable, underrepresented, or absent when cloned into prokaryotic systems, remain stable and intact in YAC clones. It is possible to reinlroduce YACs intact into mammalian cells where the introduced mammalian genes are expressed and used to study the functions of genes in the context of flanking sequences. The correct prolein processing mechanisms are present in the mammalian cells to ensure that a viable protein product is produced.     

The dnaK gene of Escherichia coli functions in initiation of chromosome replication.

A newly isolated dnaK mutant of Escherichia coli, which contains the mutation dnaK111, has been found to be conditionally defective in initiation of DNA replication. Mutant cells that were transferred to high temperature exhibited residual DNA synthesis before the synthesis stopped completely. Analysis of the DNA synthesized at high temperature by hybridization with probe DNAs for detection of DNA replicated in the origin (oriC) and terminal (terC) regions has revealed that this mutant is unable to initiate a new round of DNA replication at high temperature after termination of the round in progress. The cells exposed to high temperature were subsequently capable of initiating DNA replication at low temperature in a synchronous manner. DNA synthesis of this mutant became temperature resistant upon inactivation of the rnh gene, similar to that of dnaA mutants, although cell growth of the dnaK mutant with the inactive rnh gene remained temperature sensitive. The dnaK mutation prevented DNA synthesis of lambda bacteriophage at high temperature even in the absence of the rnh gene function.     

Yeast comparative genetics. A new MEL15 alpha-galactosidase gene of Saccharomyces cerevisiae

To supplement the earlier identified European family of the highly homologous alpha-galactosidase MEL1-MEL11 genes and the African family of the divergent MEL12-MEL14 genes, a new MEL gene (MEL15) was found in several Saccharomyces cerevisiae strains isolated from maize dough in Ghana. Southern blotting and restriction enzyme analysis assigned the MEL15 gene to the African family and mapped it to chromosomes IV/XII, which migrate together in electrophoresis. Tetrad analysis ruled out the MEL15 location in the left arm of chromosome IV or the right arm of chromosome XII, which respectively contain the known MEL5 and MEL10 genes.     

SPA1: a gene important for chromosome segregation and other mitotic functions in S. cerevisiae

Human autoantibodies that recognize the spindle poles of mammals, plants, and insects were found to recognize two antigens in yeast. One of these proteins, called SPA1 (for Spindle Pole Antigen), is antigenically related to the spindle poles of a diverse set of organisms. The gene encoding SPA1 was cloned by immunoscreening a lambda gt11 yeast genomic DNA expression library with autoantibody probes. Mutational analysis of the SPA1 gene demonstrates that it is important for cell growth, chromosome segregation, and other cellular processes; spa1 mutants are viable but grow poorly at 30 degrees C, missegregate chromosomes at an increased frequency, and often contain deformed spindles. A significant fraction of spa1 mutant cells contain two or more nuclei, and others contain none; these abnormal cells may arise through a nuclear migration defect. Thus SPA1 represents a new fidelity gene that is important for chromosome segregation and other mitotic functions.     

Lipopolysaccharides of Vibrio cholerae: III. Biological functions

This review presents the salient features of the biological functions including the (i) endotoxic activities, (ii) antigenic properties, (iii) immunological responses to and (iv) phage receptor activities of the Vibrio cholerae lipopolysaccharides (LPS). The biological functions of the capsular polysaccharide (CPS) of V. cholerae have also been discussed briefly as a relevant topic. The roles of LPS and other extracellular polysaccharides in the (i) intestinal adherence and virulence of the vibrios and (ii) the biofilm formation by the organisms have been analysed on the basis of the available data. Every effort has been made to bring out, wherever applicable, the lacunae in our knowledge. The need for the continuous serogroup surveillance and monitoring of the environmental waters and the role of LPS in the designing of newer cholera vaccines has been discussed briefly in conclusion.     

Yeast RNA polymerase III: A zinc metalloenzyme

Atomic absorption spectroscopy has been used to demonstrate that zinc is associated with yeast RNA polymerase III. The enzyme purified by DNA-Sepharose chromatography gives a single predominant protein band in polyacrylamide gel electrophoresis and contains 0.7 gram-atoms of zinc per 100,000 grams of protein. The zinc is tightly associated with the enzyme and cannot be removed by passing the protein through a column of Chelex-100 resin under conditions where free zinc is quantitatively removed. Inhibition by the chelating agent 1,10-phenanthroline demonstrates that the zinc is essential to the catalytic process. The enzyme is inhibited 50% at 0.1 mM and 100% at 1 mM 1,10-phenanthroline.     

PK3: A new chromosome enzyme marker for gene dosage studies in chromosome 15 imbalance

Summary Gene dosage studies yielded results consistent with the assignment of the locus for pyruvate kinase (PK 3) to chromosome 15. The activity of seven cytoplasmic enzymes has been determined in fibroblast extracts from six trisomy 15 lines and 16 normal control lines. The fibroblast extracts from the trisomic patients had pyruvate kinase activity 57% higher than fibroblast extracts from control lines, while other enzyme activities were within the normal range of activity.     

Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.

The recent determination of the complete sequence of chromosome III from the yeast Saccharomyces cerevisiae allows, for the first time, the investigation of the long range primary structure of a eukaryotic chromosome. We have found that, against a background G+C level of about 35%, there are two regions (one in each chromosome arm) in which G+C values rise to over 50%. This effect is seen in silent sites within genes, but not in noncoding intergenic sequences. The variation in G+C content is not related to differential selection of synonymous codons, and probably reflects mutational biases. That the intergenic regions do not exhibit the same phenomenon is particularly interesting, and suggests that they are under substantial constraint. The yeast chromosome may be a model of the structure of the human genome, since there is evidence that it is also a mosaic of long regions of different base compositions, reflected in wide variation of G+C content at silent sites among genes. Two possible causes of this regional effect, replication timing, and recombination frequency, are discussed.     

Yeast pyruvate carboxylase: gene isolation

To improve our understanding of pyruvate carboxylase (PC)(EC 6.4.1.1) structure and the evolution of the biotin-dependent carboxylases we have isolated and sequenced a yeast (Saccharomyces cerevisiae) genomic DNA fragment encoding PC. The identity of the cloned gene was confirmed by comparing the encoded protein with the sequence of a 26 amino acid biotin-containing peptide isolated from yeast PC. The yeast PC sequence is homologous (43% amino acid homology) to the rat PC sequence, although the carboxyl-terminus was found to be 44 residues from the biotinyl-lysine whereas in all biotin carboxylases sequenced to date the biotin is 35 residues from the carboxyl-terminus.     

The murine Bin1 gene functions early in myogenesis and defines a new region of synteny between mouse chromosome 18 and human chromosome 2

We cloned and functionally characterized the murine Bin1 gene as a first step to investigate its physiological roles in differentiation, apoptosis, and tumorigenesis. The exon-intron organization of the >/=55-kb gene is similar to that of the human gene. Consistent with a role for Bin1 in apoptosis, the promoter included a functional consensus motif for activation by NF-kappaB, an important regulator of cell death. A muscle regulatory module defined in the human promoter that includes a consensus recognition site for myoD family proteins was not conserved in the mouse promoter. However, Bin1 is upregulated in embryonic development by E10.5 in myotomes, the progenitors of skeletal muscle, supporting a role in myogenesis and suggesting that the mouse and human genes may be controlled somewhat differently during development. In C2C12 myoblasts antisense Bin1 prevents induction of the cell cycle kinase inhibitor p21WAF1, suggesting that it acts at an early time during the muscle differentiation program. Interspecific mouse backcross mapping located the Bin1 locus between Mep1b and Apc on chromosome 18. Since the human gene was mapped previously to chromosome 2q14, the location of Bin1 defines a previously unrecognized region of synteny between human chromosome 2 and mouse chromosome 18.     

Human elastin gene: new evidence for localization to the long arm of chromosome 7.

In this study we have utilized human elastin cDNAs in molecular hybridizations to establish the chromosomal location of the human elastin gene. First, in situ hybridizations were performed with metaphase chromosomes from phytohemagglutinin-stimulated human peripheral blood lymphocytes. In three separate experiments using two different regions of human elastin cDNAs, the distribution of grains was found to be concentrated on the long arm of chromosome 7 within the [q11.1-21.1] region, and the peak number of grains coincided with the locus 7q11.2. Second, hybridizations with a panel of human-rodent cell hybrids showed concordance with human chromosome 7. Third, PCR analyses with elastin-specific primers of DNA from a hybrid cell line containing chromosome 7 as the only human chromosome yielded a product of the expected size, while DNA containing human chromosome 2, but not chromosome 7, did not result in a product. The results indicate that the human elastin gene is located in the proximal region of the long arm of chromosome 7. The precise localization of the elastin gene in the human genome is useful in establishing genetic linkage between inheritance of an allele with a mutated elastin gene and a heritable disorder.     

New protein functions in yeast chromosome VIII.

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.     

Yeast artificial chromosome segregation from host chromosomes with similar lengths.

We propose a new method for segregation of yeast artificial chromosomes (YACs) from endogenous yeast chromosomes with similar lengths. The method is based on recently developed PNA-assisted rare cleavage (PARC) of genomic DNA. We apply the PARC procedure to YAC-containing samples of yeast DNA in such a way that host chromosomes, which electrophoretically comigrate with the chosen YACs, are selectively digested while YACs remain intact. These data demonstrate that a pool of appropriate PNAs can be used as an efficient tool for the PARC-based isolation of intact purified YACs directly from the host cells.     

Ribonuclease III: new sense from nuisance.

RNases play an important role in the processing of precursor RNAs, creating the mature, functional RNAs. The ribonuclease III family currently is one of the most interesting families of endoribonucleases. Surprisingly, RNase III is involved in the maturation of almost every class of prokaryotic and eukaryotic RNA. We present an overview of the various substrates and their processing. RNase III contains one of the most prominent protein domains used in RNA-protein recognition, the double-stranded RNA binding domain (dsRBD). Progress in the understanding of this domain is summarized. Furthermore, RNase III only recently emerged as a key player in the new exciting biological field of RNA silencing, or RNA interference. The eukaryotic RNase III homologues which are likely involved in this process are compared with the other members of the RNase III family.