We have been studying the evolution and function of DNA methylation in vertebrate animals using three related approaches. The first is to further characterise proteins that bind to methylated DNA. Such proteins can be viewed as 'receptors' of the methyl-CpG 'ligand' that mediate downstream consequences of DNA modification. The second approach involves CpG islands. These patches of non-methylated DNA coincide with most gene promoters, but their origin and functional significance have only recently become the subject of intensive study. The third approach is to trace the evolution of DNA methylation. Genomic methylation patterns of vertebrates are strikingly different from those of invertebrates. By studying methylation in animals that diverged from common ancestors near to the invertebrate/vertebrate boundary, we will assess the possibility that changes in DNA methylation contributed causally to the evolution of the complex vertebrate lineage.
NF-kappa B is a dimeric protein that serves to initiate gene transcription in higher eukaryotic cells in response to mainly pathogenic stimuli. Its activity is controlled by a third inhibitory subunit, called I kappa B. When I kappa B is bound, NF-kappa B cannot bind to DNA or enter the nucleus but is stored in a latent cytoplasmic form. Upon stimulation of cells I kappa B is released, which allows the activation of NF-kappa B. We have analyzed the molecular mechanism underlying the removal of I kappa B-alpha. Distinct extracellular stimuli lead to a phosphorylation of I kappa B-alpha of serines 32 and 36 by a yet unidentified kinase. These modifications do not directly dissociate I kappa B from NF-kappa B but render the inhibitor highly susceptible for proteolytic degradation by, presumably, the proteasome. In this paper, we report for the first time that higher molecular mass forms of I kappa B-alpha occur under conditions that lead to a phosphorylation of I kappa B-alpha and activation of NF-kappa B. These I kappa B-alpha variants had discrete molecular masses and were most prominent in cells overexpressing I kappa B-alpha, suggesting the covalent modification of I kappa B-alpha by ubiquitin conjugation. The proteasome inhibitor Cbz-Ile-Glu(O-t-Bu)-Ala-leucinal (PSI), which stabilizes the phospho form of I kappa B-alpha, only slightly increased the amount of conjugates indicating that the conjugation of I kappa B-alpha with ubiquitin was the rate-limiting step in I kappa B-alpha degradation, and not its phosphorylation or proteolysis. Our data suggest that conjugation of I kappa B-alpha with ubiquitin is an intermediate reaction in the phosphorylation-controlled degradation of I kappa B-alpha and the subsequent activation of NF-kappa B.
The 5' cap structure of RNA polymerase II transcripts and the poly(A) tail found at the 3' end of most mRNAs have been demonstrated to play multiple roles in gene expression and its regulation. In the first part of this review we will concentrate on the role played by the cap in pre-mRNA splicing and how it may contribute to efficient and specific substrate recognition. In the second half, we will discuss the roles that polyadenylation has been demonstrated to play in RNA metabolism and will concentrate in particular on an elegant mechanism where regulation of polyadenylation is used to control gene expression.
ABSTRACT There is increasing interest in studying how specific metabolic activities within the nucleus are organised into functional domains. The best known example is the nucleolus where rRNA genes are transcribed and rRNA processed and assembled into ribosomal subunits. Other subnuclear domains have been known for many years through morphological studies but are only recently being analysed at the molecular level. Here we focus on an evolutionarily conserved nuclear domain, called the coiled body, which contains splicing snRNPs. We review recent literature on the coiled body and discuss a possible model for its biological function.
The multiple origins of eukaryotic chromosomes vary in the time of their initiation during S phase. In the chromosomes of Saccharomyces cerevisiae the presence of a functional telomere causes nearby origins to delay initiation until the second half of S phase. The key feature of telomeres that causes the replication delay is the telomeric sequence (C(1-3)A/G(1-3)T) itself and not the proximity of the origin to a DNA end. A second group of late replicating origins has been found at an internal position on chromosome XIV. Four origins, spanning approximately 140 kb, initiate replication in the second half of S phase. At least two of these internal origins maintain their late replication time on circular plasmids. Each of these origins can be separated into two functional elements: those sequences that provide origin function and those that impose late activation. Because the assay for determining replication time is costly and laborious, it has not been possible to analyze in detail these 'late' elements. We report here the development of two new assays for determining replication time. The first exploits the expression of the Escherichia coli dam methylase in yeast and the characteristic period of hemimethylation that transiently follows the passage of a replication fork. The second uses quantitative hybridization to detect two-fold differences in the amount of specific restriction fragments as a function of progress through S phase. The novel aspect of this assay is the creation in vivo of a non-replicating DNA sequence by site-specific pop-out recombination. This non-replicating fragment acts as an internal control for copy number within and between samples. Both of these techniques are rapid and much less costly than the more conventional density transfer experiments that require CsCl gradients to detect replicated DNA. With these techniques it should be possible to identify the sequences responsible for late initiation, to search for other late replicating regions in the genome, and to begin to analyze the effect that altering the temporal program has on chromosome function.
The removal of introns from precursor messenger RNAs occurs in a large complex, the spliceosome, that contains many proteins and five small nuclear RNAs (snRNAs). The snRNAs interact with the intron-containing substrate RNA and with each other to form a dynamic network of RNA interactions that define the intron and promote splicing. There is evidence that protein splicing factors play important roles in regulating RNA interactions in the spliceosome. PRP8 is a highly conserved protein that is associated in particles with the U5 snRNA and directly binds the substrate RNA in spliceosomes. UV crosslinking has been used to map the binding sites, and shows extensive interaction between PRP8 protein and the 5' exon prior to the first step of splicing and with the 3' splice site region subsequently. It is proposed that PRP8 protein may stabilize fragile interactions between the U5 snRNA and exon sequences at the splice sites, to anchor and align them in the catalytic centre of the spliceosome.
DNA replication is a pivotal event in the cell cycle and, as a consequence, is tightly controlled in eukaryotic cells. The initiation of DNA replication is dependent upon the completion of mitosis and upon the commitment to complete the cell cycle made during G(1). Characterisation of the protein factors required for initiating DNA replication is essential to understand how the cell cycle is regulated. Recent results indicate that initiation complexes assemble in multiple stages during the cell cycle. First, origins are bound by the multisubunit origin recognition complex (ORC) which is essential for DNA replication in vivo. ORC, present at little more than one complete complex per replication origin, binds to origins immediately after initiation in the previous cell cycle. ORC binding occurs by the recognition of a bipartite sequence that includes the essential ARS consensus sequence (ACS) and the functionally important B1 element adjacent to the ACS. A novel pre-replicative complex (pre-RC) assembles at origins at the end of mitosis in actively cycling cells and remains at origins until DNA replication initiates. Finally, Dbf4, which is periodically synthesised at the end of G(1), interacts with replication origins. Dbf4-origin interaction requires an intact ACS strongly suggesting that interaction occurs through ORC. Dbf4 interacts with and is required for the activation of the Cdc7 protein kinase and together, Dbf4 and Cdc7 are required for the G(1)-S transition. Separate regions of Dbf4 are required for Cdc7- and origin-interaction suggesting that Dbf4 may act to recruit Cdc7 to replication origins where phosphorylation of some key component may cause origin firing.
Recent experiments suggest that active polymerases are concentrated in large structures, 'factories', within eukaryotic nuclei. Data concerning the structure of these factories is reviewed.
Myc is a nuclear phosphoprotein which controls cellular proliferation, most likely by regulating gene activity, The finding that the neuronal model cell line PC12 lacks the Myc DNA binding partner, the Max protein, and the demonstration that Myc is a repressor of gene activity as well as a transactivator, lead to models for Myc action in regulating cell growth.
The Wilms' tumour suppressor gene (WT1) encodes a protein(s) with 4 zinc fingers that is essential for the development of the genitourinary system. A considerable body of evidence exists to support the idea that WT1 binds DNA and functions as a transcription factor. However, we have shown recently by confocal microscopy and immunoprecipitation studies that a significant proportion of WT1 is associated with splice factors in kidney cell lines, fetal tissues and transfected Cos cells. Different isoforms of WT1 are produced by an alternative splice that leads to the presence or absence of a 3 amino acid insertion (KTS) between zinc fingers 3 and 4. We have shown that these different forms localise differently in the nucleus. The +KTS form mainly localises with splice factors, the -KTS form mainly with transcription factors. Here we propose a model to account for these different localisations. Also, we discuss the possible significance of these findings.
The eukaryotic cell nucleus is a highly dynamic organelle. This is illustrated most dramatically during mitosis, when the nuclear envelope breaks down, the nuclear lamina disassembles, chromosomes condense, and a microtubule-based spindle apparatus distributes sister chromatids to the dividing daughter cells. Many of these dramatic changes in nuclear architecture and microtubule organization are controlled by phosphorylation and dephosphorylation events. Whereas the cardinal role of cyclin-dependent kinases (CDKs) in the regulation of mitosis is well established, there is now clear evidence for the requirement of additional mitotic protein kinases. Studies into the regulation of CDKs and other mitotic kinases have revealed that these enzymes undergo cell cycle dependent changes in subcellular distribution, suggesting that localization may contribute to regulating their activities. This article describes some recent findings relating to the nucleocytoplasmic translocation of CDK/cyclin complexes at the onset of mitosis. In addition, it summarizes recent information on two novel human protein kinases which have been implicated in the control of mitotic progression.
Base excision-repair, which is required for correction of spontaneous hydrolytic and oxidative damage to DNA as well as lesions inflicted by alkylating agents, is a relatively well understood repair pathway. Mammalian factors involved in this pathway are reviewed, with emphasis on current uncertainties.Most DNA replication and repair enzymes in mammalian cell nuclei, e.g. DNA polymerases alpha, beta, delta, and epsilon, have direct counterparts in yeast. In contrast, the abundant enzymes in mammalian cell nuclei that bind and are activated specifically by DNA strand interruptions, poly(ADP-ribose) polymerase and DNA-dependent protein kinase, have not been detected in yeast; nor has p53, which is elevated in response to DNA strand breaks, We have found a family of four distinct DNA ligases in human cell nuclei, whereas only a single DNA ligase has been detected in yeast. It would appear that the cellular responses to DNA strand breaks may differ markedly between higher and lower eukaryotes.
ABSTRACT Bidirectional molecular trafficking between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complexes (NPCs), ∼120 megadalton supramolecular assemblies embedded in the double-membraned nuclear envelope. Significant progress has been made in elucidating the three-dimensional (3-D) architecture of the NPC, and in identifying, characterizing, and cloning and sequencing NPC proteins. Several of these have now been localized within the 3-D structure of the NPC. Nevertheless, there still remain major questions relating to the conformation, molecular composition and functional roles of distinct NPC components. Here we review recent structural studies from our group and others which have contributed toward dissecting the molecular architecture of the NPC. We also present our results on the molecular characterization of some NPC components, and on the elucidation of their functional roles in mediated nucleocytoplasmic transport.
Apoptotic cell death is characterized by a dramatic morphological transformation during which apparently healthy cells suddenly initiate a comprehensive program of motility changes and degradative activities that culminates in disassembly of the cell into membrane-enclosed vesicles. The mechanism of the cellular changes during this spectacular execution phase of apoptosis is just now yielding to biochemical analysis, In our laboratory, we have applied a novel in vitro system to the study of these events. In this system, nuclei isolated from healthy cells undergo the characteristic changes of apoptosis rapidly and synchronously. Using this system we have identified the first substrates for interleukin-1 beta-converting enzyme (ICE)-like proteinases during apoptotic execution. One of these, the nuclear enzyme poly (ADP-ribose) polymerase is cleaved very early in the apoptotic process. A second class of proteins, the nuclear lamins, is cleaved later in the pathway. Lamin cleavage requires a second ICE-related proteinase, and is essential for the complete dissolution of nuclei into apoptotic bodies. Studies with our cell-free extracts reveal that the various proteinases and nucleases that operate during the execution phase of apoptosis do so largely in independent parallel biochemical pathways. However, all of these pathways require the action of ICE-related proteinases for their initiation.
ABSTRACT Yeast chromosomes may lack the linker histone Hl (normally required to compact 10 nm beads-on-a-string fiber into the 30 nm fiber) and there is no cytological evidence for higher order fiber structure but they do contain regions which correspond to euchromatin and heterochromatin of higher eukaryotes. Both euchromatin and heterochromatin contain nucleosomal particles (composed of two molecules each of histones H2A, H2B, H3 and H4), however histones have been shown to regulate genes in these regions in quite different ways. The mechanisms by which such regulation occurs are the topic of this paper.
The E2F1 transcription factor, in co-operation with DP1, controls the expression of several S-phase specific genes. This activity is most likely responsible for the oncogenic and S-phase inducing properties of E2F1, suggesting that this transcription factor plays a key role in regulating the cell cycle. The transcriptional activation functions of E2F1 are resident in a small C-terminal domain which can independently activate transcription. Here we review the protein-protein interactions which impinge upon and regulate this activation domain and put forward some models on their mechanism of action.
In Drosophila, over 50 genes have been identified in which loss-of-function mutations lead to excess cell proliferation in the embryo, in the central nervous system, imaginal discs or hematopoietic organs of the larva, or in the adult gonads. Twenty-two of these genes have been cloned and characterized at the molecular level, and nine of them show clear homology to mammalian genes. Most of these mammalian genes had not been previously implicated in cell proliferation control. Overgrowth in some of the mutants involves conversion to a cell type that, in normal development, shows more cell proliferation than the original cell type. Thus the neurogenic mutants, including Notch, show conversion of epidermal cells to neuroblasts, leading to the 'neurogenic' phenotype of excess nervous tissue. The ovarian tumor mutants show conversion of the female germ line to a cell type resembling the male germ line, which undergoes more proliferation than the female germ line. Mutations of the fat locus cause hyperplastic overgrowth of imaginal discs, in which the epithelial structure is largely intact. The predicted fat protein product is a giant relative of cadherins, supporting indications from human cancer that cadherins play an important role in tumor suppression. Mutations in the lethal(2)giant larvae and lethal(1)discs large genes cause neoplastic overgrowth of imaginal discs as well as the larval brain. The dlg gene encodes a membrane-associated guanylate kinase homolog that is localized at septate junctions between epithelial cells. This protein is a member of a family of homologs that also includes two proteins found at mammalian tight junctions (ZO-1 and ZO-2) and a protein found at mammalian synaptic junctions (PSD-95/SAP90). Genes in which mutations cause blood cell overproduction include aberrant immune response-8, which encodes the RpS6 ribosomal protein and hopscotch, which encodes a putative non-receptor protein tyrosine kinase. The gene products identified by ovarian tumor mutants do not show clear amino acid sequence homology to known proteins. Drosophila provides an opportunity to rapidly identify and characterize tumor suppressor genes, many of which have mammalian homologs that might also be involved in cell proliferation control and tumor suppression.
In order for cells to respond to their environment, a series of regulated molecular events has to take place. External signalling molecules bind to cellular receptors and thereby trigger the activation of multiple intracellular pathways, which modify cellular phenotypes. The cell-surface receptors for a wide range of polypeptide hormones possess protein tyrosine kinase activity, which is induced by binding of the appropriate extracellular ligand. Tyrosine phosphorylation can act as a molecular switch, by initiating the recruitment of cytoplasmic effector molecules containing Src homology (SH) 2 domains, to activated receptors. These SH2-containing proteins, in turn, regulate intracellular signalling pathways. Here, we discuss the role of tyrosine phosphorylation in triggering signalling pathways, as well as the functions of SH2 domains, which mediate these events through phosphotyrosine-dependent protein-protein interactions.
SUMMARY The fission yeast cut5+ (identical to rad4+) gene is essential for S phase. Its temperature-sensitive (ts) mutation causes mitosis while S phase is inhibited: dependence of mitosis upon the completion of S phase is abolished. If DNA is damaged in mutant cells, however, cell division is arrested. Thus the checkpoint control system for DNA damage is functional, while that for DNA synthesis inhibition is not in the cut5 mutants. Transcription of the cut5+ gene is not under the direct control of cdc10+, which encodes a transcription factor for the START of cell cycle. The transcript level does not change during the cell cycle. The protein product has four distinct domains and is enriched in the nucleus. Its level does not alter during the cell cycle. The N-domain is important for cut5 protein function: it is essential for complementation of ts cut5 mutations and its overexpression blocks cell division. Furthermore, it resembles the N-terminal repeat domain of proto-oncoprotein Ect2, which, in the C-domain, contains a regulator-like sequence for small G proteins. We discuss a hypothesis that the cut5 protein is an essential component of the checkpoint control system for the completion of DNA synthesis. The restraint of mitosis until the completion of S phase is mediated by the cut5 protein, which can sense the state of chromosome duplication and negatively interacts with M phase regulators such as cdc25 and cdc2.
Major checkpoints that gate progression through the cell cycle function at the G1/S transition, entry into mitosis and exit from mitosis. Cells use feedback mechanisms to inhibit passage through these checkpoints in response to growth control signals, incomplete DNA replication or spindle assembly. In many organisms, transition points seem to involve regulation of the activity of cyclin-dependent kinases (cdks) not only through their interactions with various cyclins, but also by phosphorylation-dephosphorylation cycles acting on the kinase activity of the cdks. These phosphorylation cycles are modulated by the regulation of the opposing kinases and phosphatases that act on cdks and form feedback loops. In this article, we discuss the role of positive and negative feedback loops in cell cycle timing and checkpoints, focusing more specifically on the regulation of the dual specificity cdc25 phosphatase.
