Use of Genomic Exclusion to Isolate Heat-Sensitive Mutants in Tetrahymena

We have used the abnormal form of conjugation known as "genomic exclusion" to isolate a collection of heat-sensitive mutants of Tetrahymena pyriformis, syngen 1. Growth at room temperature in bacterized medium and no growth at 40 degrees C in the same medium was the criterion used for the isolation. The mutant strains were tested for growth in pure (axenic) culture in proteose peptone medium; of the 31 strains which grew normally at room temperature and not at 40 degrees C in that medium, 21 also failed to grow at 37 degrees C. Preliminary results of complementation tests suggest that most, if not all, the mutations are recessive and that a variety of genes was affected. A detailed genetic analysis was performed on one mutant (H9). The results are all consistent with the idea that the heat-sensitive phenotype of this mutant is determined by a single recessive mutation, designated ts-2. Heterozygotes ts-2/+ yield heat-sensitive segregants during vegetative growth; we interpret this finding as another example of allelic exclusion, a phenomenon universally encountered among heterozygotes in syngen 1 of T. pyriformis. Our results are discussed in the context of some questions of current interest in Tetrahymena genetics.     

Identification of Genomic Regions Required for DNA Replication during Drosophila Embryogenesis

A collection of Drosophila deficiency stocks was examined by bromodeoxyuridine (BrdU) labeling of embryos to analyze the DNA replication patterns in late embryogenesis. This permitted us to screen 34% of the genome for genes that when absent in homozygous deficiencies affect the cell cycle or DNA replication. We found three genomic intervals that when deleted result in cessation of DNA replication in the embryo, 39D2-3;E2-F1, 51E and 75C5-7;F1. Embryos deleted for the 75C5-7;F1 region stop DNA replication at the time in embryogenesis when a G(1) phase is added to the mitotic cell cycle and the larval tissues begin to become polytene. Thus, this interval may contain a gene controlling these cell cycle transitions. DNA replication arrests earlier in embryos homozygous for deletions for the other two regions. Analysis of the effects of deletions in the 39D2-3;E2-F1 region on DNA replication showed that the block to DNA replication correlates with deletion of the histone genes. We were able to identify a single, lethal complementation group in 51E, l(2)51Ec, that is responsible for the cessation of replication observed in this interval. Deficiencies that removed one of the Drosophila cdc2 genes and the cyclin A gene had no effect on replication during embryogenesis. Additionally, our analysis identified a gene, pimples, that is required for the proper completion of mitosis in the post-blastoderm divisions of the embryo.     

Defective Micronuclei and Genomic Exclusion in Selected C* Subclones of Tetrahymena1

SYNOPSIS. C* is a structurally heterogeneous clone containing normal and crinkled cells which are amicronucleate. Selection for structurally normal subclones did not result in the genesis of a diploid cell line. The stem cell of C* appears to be aneuploid with about 4 chromosomes instead of the usual 10, and from this line cells with fewer chromosomes or without micronuclei are generated. Only cells containing a portion of the micronucleus are viable. Amicronucleate cells die. They also mate very poorly. Consequently, little difference is observed between subclones having different proportions of amicronucleate cells in their ability to generate viable offspring by genomic exclusion. Our observations are discussed in terms of the separate functions of micronucleus and macronucleus and ways in which the nuclei seem to interact.     

Dynamic Exchange of Two Essential DNA Polymerases during Replication and after Fork Arrest

The replisome is a multiprotein machine responsible for the faithful replication of chromosomal and plasmid DNA. Using single-molecule super-resolution imaging, we characterized the dynamics of three replisomal proteins in live Bacillus subtilis cells: the two replicative DNA polymerases, PolC and DnaE, and a processivity clamp loader subunit, DnaX. We quantified the protein mobility and dwell times during normal replication and following replication fork stress using damage-independent and damage-dependent conditions. With these results, we report the dynamic and cooperative process of DNA replication based on changes in the measured diffusion coefficients and dwell times. These experiments show that the replication proteins are all highly dynamic and that the exchange rate depends on whether DNA synthesis is active or arrested. Our results also suggest coupling between PolC and DnaX in the DNA replication process and indicate that DnaX provides an important role in synthesis during repair. Furthermore, our results suggest that DnaE provides a limited contribution to chromosomal replication and repair in vivo.     

A Novel Replication Arrest Pathway in Response to DNA Damage

DNA damage has been shown to regulate DNA replication both by inhibition of origin utilization, and by slowing of replication progression. We have recently reported another mechanism by which DNA damage affects replication, in which the presence of damaged DNA inhibits, in trans, the initiation of chromosomal replication. This inhibition occurs by blocking the association of the processivity clamp PCNA with undamaged chromatin. This inhibitory activity is not due to sequestration of replication factors by the damaged DNA, rather, it acts through generation of a diffusible inhibitor of PCNA loading. The activation of this pathway is independent of canonical checkpoint signaling, and, in fact, results in activation of the checkpoint. This novel pathway may therefore represent an amplification step to stop cell cycle progression in response to lower levels of DNA damage.     

Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication

UVA radiation (320–400 nm) is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS), such as singlet oxygen (¹O₂) and hydrogen peroxide (H₂O₂), which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of ¹O₂ by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1) to several hours (replication fork velocity and origin firing). The quenching of ¹O₂ by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen.     

Replication of the linear mitochondrial DNA of Tetrahymena pyriformis.

1. Electron micrographs of the linear mtDNA from Tetrahymena pyriformis strain GL show linear molecules with a duplex 'eye' of variable size in the middle. This indicates that replication of this DNA starts near the middle of the molecule and proceeds bidirectionally to the ends, as previously shown for the mtDNA of strain ST (Arnberg, A.C., Van Bruggen, E.F.J., Clegg, R.A., Upholt, W.B. and Borst, P. (1974) Biochim. Biophys. Acta 361, 266-276). The mtDNAs of these two strains have little base sequence homology beyond the ribosomal RNA cistron (Goldbach, R.W., Bollen-De Boer, J.E., Van Bruggen, E.F.J. and Borst, P. (1978) Biochim. Biophys. Acta 521, 187-197). 2. Electron micrographs of mtDNA from strain ST, spread under non-denaturing conditions, contain only molecules with fully duplex ends. mtDNA spread under conditions of early denaturation contains duplex loops on one end (40% of all molecules) or both ends (37%). The loops are stable to partial denaturation and vary in size from 0.15 to approximately 1.0 micron, most loops measuring 0.25--0.40 micron. No loops are formed with single-stranded DNA under analogous conditions and we conclude from this result that loop formation is based on the presence of straight, rather than inverted, duplications near the ends. 3. When full-length 3H-labelled mtDNA from strain ST, 32P-labelled at the 5'-termini with T4 polynucleotide kinase, was sedimented in alkaline sucrose gradients, greater than 70% of the 3H and less than 30% of the 32P cosedimented with full-length molecules; the remaining 32P sedimented heterogeneously and predominantly with the DNA less than 10% the size of intact single strands. Brief incubations of full-length mtDNA with DNA polymerase I from Escherichia coli and labelled dNTPs at 15 degrees C did not lead to preferential labelling of terminal EcoRI fragments of the DNA. From these results we infer that the DNA contains nicks or gaps near the termini and that these are not bordered by free 3'-OH groups. 4. A model is presented in which straight sequence repetitions at the termini of Tetrahymena pyriformis mtDNA are involved in the later stages of replication. This model can also account for the pronounced terminal heterogeneity previously observed in this DNA.     

Correlation between the Shortened Period of Cell Pairing during Genomic Exclusion and the Block in Posttransfer Nuclear Development in Tetrahymena thermophia.

The duration of pairing in crosses of the micronuclearly defective strain A^*V and the amicronuclear strain BI3840 of Tetrahymena thermophila is shorter than that in normal conjugation. In controls, pairing takes about 620 min at 30°C and 60 min more at 28°C. In contrast pairing of crosses of the A^*strain took 470 min at 30°C and 490 min at 28°C, and that of crosses of BI3840 strain took 440 min at 30°C. The course of nuclear development in the tester strain crossed with the A^*strain was similar to that in the control until the 3rd prezygotic division. Unilateral transfer of the pronuclei occurred later than on reciprocal transfer in control crosses; posttransfer divisions in hemikarya was completely blocked in over 90% of the cases examined. Defective cell contact in crosses of the A^*V strain and an amicronuclear BI3840 strain may be correlated with block in nuclear division and in macronuclear development, since unfertilized cells from triplet conjugation remain haploid and develop normally.     

嗜热四膜虫Ran结合蛋白1的表达对大小核分裂的影响

Ran是细胞内的一种具有GTP酶活性的功能蛋白,可以调节染色体稳定性、细胞核组建以及核质运输等多种细胞进程．Ran结合蛋白1（Ran-binding protein 1, Rbp1p ）是Ran的必要调控因子,促进Ran-GTP水解为Ran-GDP．本研究从嗜热四膜虫大核基因组中鉴定出1个保守的Ran结合蛋白基因RBP1(TTHERM_00158040, http://www.ciliate.org)．实时荧光定量PCR表明,RBP1在四膜虫营养生长和有性生殖过程中都有表达,且在有性生殖过程中表达水平提高．免疫荧光定位表明,在营养 生长期Rbp1p定位于细胞质中．过表达RBP1或敲减RBP1后,细胞生长速率下降,大核的无丝分裂异常,细胞分裂末期产生了无大核的异常细胞,同时过表达RBP1导致了多小核的产生．结果表明,Rbp1p影响四膜虫细胞核的分裂进程,它的正常表达对细胞增殖过程起到重要的调节作用．     

Specification of DNA Replication Origins and Genomic Base Composition in Fission Yeasts

In the “Replicon Theory”, Jacob, Brenner and Cuzin proposed the existence of replicators and initiators as the two major actors in DNA replication. Over the years, many protein components of initiators have been shown to be conserved in different organisms during evolution. By contrast, replicator DNA sequences (often referred to as replication origins) have diverged beyond possible comparison between eukaryotic genomes. Replication origins in the fission yeast Schizosaccharomyces pombe are made up of A + T-rich sequences that do not share any consensus elements. The information encoded in these replicators is interpreted by the Orc4 subunit of the ORC (origin recognition complex), which is unique among eukaryotes in that it contains a large domain harboring nine AT-hook subdomains that target ORC to a great variety of A + T-rich sequences along the chromosomes. Recently, the genomes of other Schizosaccharomyces species have been sequenced and the regions encompassing their replication origins have been identified. DNA sequence analysis and comparison of the organization of their Orc4 proteins have revealed species-specific differences that contribute to our understanding of how the specification of replication origins has evolved during the phylogenetic divergence of fission yeasts.     

Lamin A/C Depletion Enhances DNA Damage-Induced Stalled Replication Fork Arrest

The human LMNA gene encodes the essential nuclear envelope proteins lamin A and C (lamin A/C). Mutations in LMNA result in altered nuclear morphology, but how this impacts the mechanisms that maintain genomic stability is unclear. Here, we report that lamin A/C-deficient cells have a normal response to ionizing radiation but are sensitive to agents that cause interstrand cross-links (ICLs) or replication stress. In response to treatment with ICL agents (cisplatin, camptothecin, and mitomycin), lamin A/C-deficient cells displayed normal γ-H2AX focus formation but a higher frequency of cells with delayed γ-H2AX removal, decreased recruitment of the FANCD2 repair factor, and a higher frequency of chromosome aberrations. Similarly, following hydroxyurea-induced replication stress, lamin A/C-deficient cells had an increased frequency of cells with delayed disappearance of γ-H2AX foci and defective repair factor recruitment (Mre11, CtIP, Rad51, RPA, and FANCD2). Replicative stress also resulted in a higher frequency of chromosomal aberrations as well as defective replication restart. Taken together, the data can be interpreted to suggest that lamin A/C has a role in the restart of stalled replication forks, a prerequisite for initiation of DNA damage repair by the homologous recombination pathway, which is intact in lamin A/C-deficient cells. We propose that lamin A/C is required for maintaining genomic stability following replication fork stalling, induced by either ICL damage or replicative stress, in order to facilitate fork regression prior to DNA damage repair.     

A Rolling Circle Replication Mechanism Produces Multimeric Lariats of Mitochondrial DNA in Caenorhabditis elegans

Mitochondrial DNA (mtDNA) encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s) of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s) of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans.     

Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication

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