Replicator dominance in a eukaryotic chromosome.

Replicators are genetic elements that control initiation at an origin of DNA replication (ori). They were first identified in the yeast Saccharomyces cerevisiae as autonomously replicating sequences (ARSs) that confer on a plasmid the ability to replicate in the S phase of the cell cycle. The DNA sequences required for ARS function on a plasmid have been defined, but because many sequences that participate in ARS activity are not components of chromosomal replicators, a mutational analysis of the ARS1 replicator located on chromosome IV of S. cerevisiae was performed. The results of this analysis indicate that four DNA elements (A, B1, B2 and B3) are either essential or important for ori activation in the chromosome. In a yeast strain containing two closely spaced and identical copies of the ARS1 replicator in the chromosome, only one is active. The mechanism of replicator repression requires the essential A element of the active replicator. This element is the binding site for the origin recognition complex (ORC), a putative initiator protein. The process that determines which replicator is used, however, depends entirely upon flanking DNA sequences.     

Integrated functional visualization of eukaryotic genomes

Background  

Increasing amounts of data from large scale whole genome analysis efforts demands convenient tools for manipulation, visualization and investigation. Whole genome plots offer an intuitive window to the analysis. We describe two applications that enable users to easily plot and explore whole genome data from their own or other researchers' experiments.     

Animal locomotion: a new spin on bat flight

Biologists and engineers have long struggled to understand the hovering flight of insects, birds, and bats. The enormous diversity of these groups would suggest they fly using a variety of mechanisms, but a new study shows that hovering bats use the same aerodynamic mechanisms as do moths and other insects.     

Ring chromosome 16: a new case

A 46,XX,r(16) "de novo" karyotype is reported in a 4 7/12-year-old girl. In spite of the mild cranio-facial dysmorphism without visceral malformations in r(16) patients, the proband's phenotype is similar to the other four previous case reports. This could support the hypothesis of a specific "r(16) syndrome".     

EGF receptor signaling: putting a new spin on eye development

The coordinated polarization of cells within an epithelium is required for the development and function of some tissues. Recent work has shown that the EGF receptor signaling pathway plays a key role in establishing epithelial polarity in the compound eye of Drosophila.     

Basic mechanism of eukaryotic chromosome segregation

We now have firm evidence that the basic mechanism of chromosome segregation is similar among diverse eukaryotes as the same genes are employed. Even in prokaryotes, the very basic feature of chromosome segregation has similarities to that of eukaryotes. Many aspects of chromosome segregation are closely related to a cell cycle control that includes stage-specific protein modification and proteolysis. Destruction of mitotic cyclin and securin leads to mitotic exit and separase activation, respectively. Key players in chromosome segregation are SMC-containing cohesin and condensin, DNA topoisomerase II, APC/C ubiquitin ligase, securin-separase complex, aurora passengers, and kinetochore microtubule destabilizers or regulators. In addition, the formation of mitotic kinetochore and spindle apparatus is absolutely essential. The roles of principal players in basic chromosome segregation are discussed: most players have interphase as well as mitotic functions. A view on how the centromere/kinetochore is formed is described.     

Isochore chromosome maps of eukaryotic genomes

Analytical DNA ultracentrifugation revealed that eukaryotic genomes are mosaics of isochores: long DNA segments (>300 kb on average) relatively homogeneous in G+C. Important genome features are dependent on this isochore structure, e.g. genes are found predominantly in the GC-richest isochore classes. However, no reliable method is available to rigorously partition the genome sequence into relatively homogeneous regions of different composition, thereby revealing the isochore structure of chromosomes at the sequence level. Homogeneous regions are currently ascertained by plain statistics on moving windows of arbitrary length, or simply by eye on G+C plots. On the contrary, the entropic segmentation method is able to divide a DNA sequence into relatively homogeneous, statistically significant domains. An early version of this algorithm only produced domains having an average length far below the typical isochore size. Here we show that an improved segmentation method, specifically intended to determine the most statistically significant partition of the sequence at each scale, is able to identify the boundaries between long homogeneous genome regions displaying the typical features of isochores. The algorithm precisely locates classes II and III of the human major histocompatibility complex region, two well-characterized isochores at the sequence level, the boundary between them being the first isochore boundary experimentally characterized at the sequence level. The analysis is then extended to a collection of human large contigs. The relatively homogeneous regions we find show many of the features (G+C range, relative proportion of isochore classes, size distribution, and relationship with gene density) of the isochores identified through DNA centrifugation. Isochore chromosome maps, with many potential applications in genomics, are then drawn for all the completely sequenced eukaryotic genomes available.     

Pyrroloquinoline quinone: a new redox cofactor in eukaryotic enzymes

During the past decade pyrroloquinoline quinone has been shown to be a new redox cofactor for a range of bacterial alcohol dehydrogenases. Recent studies suggest that this cofactor may also be covalently bound to the active site of the eukaryotic copper amine oxidases. In this mini-review we present the evidence in support of pyrroloquinoline quinone as a novel eukaryotic cofactor. As a result of mechanistic advances during the last three years, together with a re-examination of previously existing data, a working model for the role of pyrroloquinoline quinone in enzyme-catalyzed amine oxidation reactions can be proposed.     

Ring-20 chromosome: a new syndrome]

A comparative study of five observations of a r (20) syndrome characterized by facial dysmorphism, the absence of severe malformations, and rather late onset of encephalopathy and seizures.     

Tolerating DNA damage during eukaryotic chromosome replication

In eukaryotes, the evolutionarily conserved RAD6/RAD18 pathway of DNA damage tolerance overcomes unrepaired DNA lesions that interfere with the progression of replication forks, helping to ensure the completion of chromosome replication and the maintenance of genome stability in every cell cycle. This pathway uses two different strategies for damage bypass: translesion DNA synthesis, which is carried out by specialized polymerases that can replicate across the lesions, and DNA damage avoidance, a process that relies on a switch to an undamaged-DNA template for synthesis past the lesion. In this review, we summarise the current knowledge on DNA damage tolerance mechanisms mediated by RAD6/RAD18 that are used by eukaryotic cells to cope with DNA lesions during chromosome replication.     

Prenyl proteins in eukaryotic cells: a new type of membrane anchor

Recent studies have indicated that eukaryotic cells contain proteins that are post-translationally modified by long-chain, thioether-linked prenyl groups. These proteins include yeast mating factors, ras proteins and nuclear lamins. The modification occurs on a cysteine residue near the C terminus and appears to initiate a set of additional protein modification reactions that promote attachment of the proteins to specific membranes.     

Chlorolissoclimides: new inhibitors of eukaryotic protein synthesis

Lissoclimides are cytotoxic compounds produced by shell-less molluscs through chemical secretions to deter predators. Chlorinated lissoclimides were identified as the active component of a marine extract from Pleurobranchus forskalii found during a high-throughput screening campaign to characterize new protein synthesis inhibitors. It was demonstrated that these compounds inhibit protein synthesis in vitro, in extracts prepared from mammalian and plant cells, as well as in vivo against mammalian cells. Our results suggest that they block translation elongation by inhibiting translocation, leading to an accumulation of ribosomes on mRNA. These data provide a rationale for the cytotoxic nature of this class of small molecule natural products.     

Letter: Electron microscopic visualization of the folded chromosome of Escherichia coli

The folded Escherichia coli chromosome has been analyzed in the electron microscope following the Kleinschmidt spreading technique. In all cases, the DNA molecule appears intact and supercoiled. In addition, the membrane-associated form of the chromosome shows DNA fibers attached to one or two membrane patches. The DNA molecule is intact, as evidenced by the absence of free ends. Two types of DNA coiling are generally observed: (1) spirals with about four to seven turns per spiral, and (2) stretched plectonemic supercoils, more abundant on the outside of the complex where the spreading has been more extensive.The released folded chromosome appears to be less compact; it extends over a larger area and frequently breaks with the spreading. The intact molecules which can be found show the DNA concentrated in few nueleation areas, with one or a few interconnecting DNA fibers. The folded DNA has very few or no single strand nicks, as evidenced by its extensive supertwisting at high ethidium bromide concentrations.     

Y chromosomal fertility genes of Drosophila: a new type of eukaryotic genes

The Y chromosomal fertility genes of Drosophila are required for sperm differentiation. They are active only in primary spermatocytes where they form giant lampbrush loops. The molecular structure of these genes was investigated and revealed an unusual composition of DNA. Short, tandemly repeated sequence clusters are interrupted by longer and more heterogeneous sequences, which probably all represent transposable elements. No indication of the presence of protein-coding regions has been found within the fertility genes. However, the lampbrush loops bind site-specific proteins recognized by immunofluorescence techniques. This, together with other experimental data, led to the hypothesis that the Y chromosomal genes have a function in binding chromosomal proteins. The data and arguments in support of this gene model are summarized in this paper.