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PubMed2000

Chromosome replication, nucleoid segregation and cell division in archaea.

Recent progress in cell cycle analysis of archaea has included the identification of putative chromosome replication origins, novel DNA polymerases and an unusual mode of cell cycle organization featuring multiple copies of the chromosome and asymmetric cell divisions. Genome sequence data indicate that in crenarchaea, the 'ubiquitous' FtsZ/MinD-based prokaryotic cell division apparatus is absent and division therefore must occur by unique, as-yet-unidentified mechanisms. The evolutionary and functional relationships between the archaeal Cdc6 protein and bacterial and eukaryal replication initiation factors are discussed.

Archaea↗

PubMed1987

Replication origin (oric) on the complementary DNA strand of Escherichia coli phage G4: biological properties of mutants.

Phage G4 origin of complementary DNA strand synthesis (oric) consists of three stable secondary loop structures. In a cloned 274-bp DNA fragment that is active as an ori in the filamentous phage cloning vector R199, insertion mutants have been constructed by introducing EcoRI and HindIII linkers at the base of loop III. The in vivo activity of these oric mutants (conversion of single-strand form to replicative form in the presence of rifampicin) was significantly reduced (50-70%) but not completely abolished. Nucleotide sequences and/or potential secondary structure of loop III centered at the AvaII site are therefore an important functional part of oric.

Base Sequence↗

PubMed1993

BPV-4 induces amplification and activation of 'silent' BPV-1 in a sub-line of C127 cells.

BPV-4-induced malignant transformation of C127 mouse fibroblasts in vitro is the result of a 'hit and run' mechanism. Viral DNA is lost on continued subculture of transformed cell lines without loss of any malignant characteristics. The DNA from these cells harbours specific amplified sequences. Two such amplified fragments of approximately 10 kb and 12 kb were molecularly cloned and designated HL-10 and HL-12 respectively. HL-10 transformed C127 cells efficiently and therefore encodes a transforming function, whereas the 12 kb clone did not. Heteroduplexes showed that HL-12 was homologous to HL-10 except for two additional tandem copies of an approximately 1.7 kb sequence. Sequence analysis of HL-10 revealed that the clone contained a 5.2 kb region from BPV-1 including the transforming ORFs. Transformation studies have shown differences between HL-10 and BPV-1, indicating that the host flanking sequences may contribute to the transforming potential of the BPV-1 ORFs. The BPV-1 DNA was associated with sequences homologous to murine autonomously replicating sequences (ARS) implicated in the establishment of multiple tandem DNA repeats. As the parental cells contain the set of sequences amplified in transformed cells in single copy and show none of the characteristics of transformed cells, we conclude that BPV-4 has activated these sequences by amplification and rearrangement. These phenomena may be mediated through an interaction between BPV-4 proteins and the BPV-1 origin of DNA replication or via the ARS region.

Animals↗

PubMed1985

Comparison of 10 IncP plasmids: homology in the regions involved in plasmid replication.

We have examined the DNA homology in the replication regions of 10 IncP plasmids independently isolated from several different countries. Two regions of RK2, the best-studied plasmid of this group, are required for vegetative DNA replication: the origin of replication (oriV) and the trfA region, which codes for a gene product necessary for replication. Six of nine IncP plasmids studied were identical to RK2 in the oriV and trfA regions as shown by Southern hybridization. Three P plasmids, R751, R772, and R906, showed weaker homology with the RK2 trfA, region and hybridized to different-sized HaeII fragments than the other six plasmids. R751, R772, and R906 hybridized to the region of the RK2 replication origin which expresses P incompatibility but differed markedly from RK2 and the other six plasmids in the GC-rich region of the origin required for replication. These data indicate that the P-group plasmids can be divided into two subgroups: IncP alpha, which includes the RK2-like plasmids, and IncP beta which includes the R751-like plasmids.

DNA Replication↗

PubMed1984

Dispersive segregation of nucleosomes during replication of simian virus 40 chromosomes.

The distribution of preformed ("old") histone octamers between the two arms of DNA replication forks was analyzed in simian virus 40(SV40)-infected cells following treatment with cycloheximide to prevent nucleosome assembly from nascent histones. Viral chromatin synthesized in the presence of cycloheximide was shown to be deficient in nucleosomes. Replicating SV40 DNA (wild-type 800 and capsid assembly mutant, tsB11) was radiolabeled in either intact cells or nuclear extracts supplemented with cytosol. Nascent nucleosomal monomers were then released by extensive digestion of isolated nuclei, nuclear extracts or isolated viral chromosomes with micrococcal nuclease. The labeled nucleosomal DNA was purified and found to hybridize to both strands of SV40 DNA restriction fragments taken from each side of the origin of DNA replication, whereas Okazaki fragments hybridized only to the strand representing the retrograde DNA template. In addition, isolated, replicating SV40 chromosomes were digested with two strand-specific exonucleases that excised nascent DNA from either the forward or the retrograde side of replication forks. Pretreatment of cells with cycloheximide did not result in an excess of prenucleosomal DNA on either side of replication forks, but did increase the amount of internucleosomal DNA. These data are consistent with a dispersive model for nucleosome segregation in which "old" histone octamers are distributed to both arms of DNA replication forks.

Centrifugation, Density Gradient↗

PubMed2026

Ori-Finder-Arch: An Updated Web Server for the Annotation and Visualization of Archaeal Replication Origins.

Archaea are promising chassis organisms in biotechnology, and the accurate annotation of their chromosomal replication origins (oriCs) is the key to unlocking their full potential. However, the existing Ori-Finder 2 web server suffers from low accuracy, slow speed, and limited scalability. In this study, we present Ori-Finder-Arch, an updated web server for high-performance oriC prediction in archaea. This pipeline integrates HMMER-based replication initiation protein (RIP) annotation, refined consensus motif recognition, and GC profile-based DNA unwinding element (DUE) detection. On a benchmark set of experimentally validated oriCs, Ori-Finder-Arch achieved a recall of 95.6% and a precision of 86.0%, substantially outperforming Ori-Finder 2 (62.2% and 63.6%, respectively), while running 4.75 times faster and supporting diverse assembly levels. When applied to the available archaeal assemblies, it successfully annotated 17,472 oriCs. Meanwhile, the web server provides interactive visualizations at different levels. In conclusion, Ori-Finder-Arch offers an efficient, accurate, and user-friendly platform for advanced studies of archaeal DNA replication initiation and synthetic biology applications, and is freely available at https://tubic.org/Ori-Finder-Arch/ and https://tubic.tju.edu.cn/Ori-Finder-Arch/.

Archaea↗

PubMed1987

[Excision of the plasmid containing the inserted human satellite DNA from Chinese hamster chromosomes after fusion of hamster and human cells].

Fusion of the Chinese hamster stably transformed Tk+ cells containing chromosomally integrated plasmid with a fragment of human satellite III DNA (HS3), with mitomycin C-treated human cells (B-lymphoma, line Raji) results in amplification and excision of heterogeneous plasmid material from hamster chromosomes. Some of these plasmids contain HS3. Functional activity of HS3 in the initiation of DNA replication is shown in transient transfection experiments. The results indicate that mitomycin C induces in human cells some trans-acting factors (possibly proteins) activating a replication origin within HS3 DNA and leading to plasmid replication in situ and their excision from chromosomes.

Animals↗

PubMed1991

Mapping eukaryotic replication origins in vivo by size analysis of purified nascent DNA strands.

A simple and efficient method for the mapping of eukaryotic replication origins was tested. The method is based on differential labeling of newly synthesized DNA with BrdUrd and subsequent separation of heavy nascent strands from parental DNA by conventional alkaline sucrose and neutral CsCl isopycnic gradient centrifugation. Purified nascent DNA is then size-fractionated on alkaline agarose gels and analyzed by sequential hybridization to specific probes of known location on the DNA segment of interest. Evaluation of the hybridization results allows: (i) determination of the direction of replication fork movement and (ii) location of the initiation site of DNA synthesis. Taking SV40 and polyoma virus as model systems, we demonstrate the feasibility of this procedure. It applicability to the location of chromosomal replication origins is discussed.

Blotting, Southern↗

PubMed2002

Hyper-phosphorylation of the adeno-associated virus Rep78 protein inhibits terminal repeat binding and helicase activity.

The replication (Rep) proteins of adeno-associated virus (AAV) play prominent roles in regulation of viral DNA replication, RNA transcription, assembly of an infectious virion and establishment of the provirus. We have previously demonstrated that all four Rep proteins are phosphorylated on serine residues [Virology 23 (1997) 332-336]. Reversible phosphorylation may provide a mechanism for regulating Rep protein function. To test this hypothesis, we used the phosphatase inhibitor okadaic acid (OA) to obtain hyper-phosphorylated Rep proteins. OA treatment of AAV- and adenovirus (Ad)-infected cells and baculovirus-infected insect cells at a concentration of 100 nM resulted in a significant increase in Rep protein phosphorylation. This concentration suggests that protein phosphatase 2A (PP2A) is one of the enzymes involved in regulation of Rep phosphorylation. The increased phosphorylation occurred primarily on serine residues with a detectable amount of phosphate on threonine. Hyper-phosphorylation of Rep78 resulted in reduced binding to the AAV origin of DNA replication. Hyper-phosphorylated Rep78 also had diminished helicase activity. These results suggest that regulated phosphorylation of Rep78 plays a role in controlling Rep functions in the virus replication cycle.

Cell Line↗

PubMed2000

Cdc7p-Dbf4p becomes famous in the cell cycle.

Great insight into the molecular details of cell cycle regulation has been obtained in the past decade. However, most of the progress has been in defining the regulation of the family of cyclin-dependent kinases (CDKs). Recent studies of a myriad of eukaryotic organisms have defined both the regulation and substrates of Cdc7p kinase, which forms a CDK-cyclin-like complex with Dbf4p, is necessary for the initiation of DNA replication and has been conserved in evolution. This kinase is also required for the induction of mutations after DNA damage and for commitment to recombination in the meiotic cell cycle. However, less is known about the role of the kinase in these processes. In a manner similar to CDKs, Cdc7p is activated by a regulatory subunit, Dbf4, the levels of which fluctuate during the cell cycle. One or more subunits of the conserved MCM helicase complex at chromosomal origins of DNA replication are substrates for the kinase during S phase. Phosphorylation of the MCM complex by Cdc7p-Dbf4p might activate DNA replication by unwinding DNA. Therefore, activation of Cdc7p is required for DNA replication. Given that Cdc7p-Dbf4 kinase is overexpressed in many neoplastic cells and tumors, it might be an important early biomarker during cancer progression.

Animals↗

PubMed1987

The origin of cells: a symbiosis between genes, catalysts, and membranes.

The gap between early molecular evolution and the origin of the first cell may have been bridged by a photoheterotrophic obcell, consisting of genes and ribosomes attached to the outer surface of a phospholipid vesicle containing a light-driven proton pump and a proton-driven pyrophosphate synthase. I argue that the obcell was the substratum for the origin of DNA replication; DNA segregation by the growth and division of the peptidoglycan murein; periplasmic solute-binding proteins; bioenergetics, including the F0F1 proton-driven ATP synthase; active transport of calcium; and facilitated diffusion of nutrients across membranes, and that it played the major role in the replacement of ribozymes by protein catalysts. Curved growth of the peptidoglycan and a mutation causing septum formation produced the first true cell. Evolution of porins, sodium extrusion and potassium import, conversion of the facilitated diffusion proteins to active pumps, and the evolution of intermediary metabolism, carbon and nitrogen fixation, and of substrate level phosphorylation, completed the origin of the first negibacterial eubacterium, from which all other cells evolved, and from which they have inherited most of their major catalytic properties--with the notable exceptions of reverse transcriptase, RNA splicing, and methanogenesis, all of which I believe evolved very much later.

Animals↗

PubMed2004

Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection.

T7 RNA polymerase selectively transcribes T7 genes during infection but is also involved in DNA replication, maturation and packaging. T7 lysozyme is an amidase that cuts a bond in the peptidoglycan layer of the cell wall, but it also binds T7 RNA polymerase and inhibits transcription, and it stimulates replication and packaging of T7 DNA. To better understand the roles of these two proteins during T7 infection, mutants of each were constructed or selected and their biochemical and physiological behavior analyzed. The amidase activity of lysozyme is needed for abrupt lysis and release of phage particles but appears to have no role in replication and packaging. The interaction between polymerase and lysozyme stimulates both replication and packaging. Polymerase mutants that gain the ability to grow normally in the absence of an interaction with lysozyme still fail to shut down late transcription and, remarkably, have become hypersensitive to inhibition when lysozyme is able to bind. These lysozyme-hypersensitive polymerases behave without lysozyme similarly to wild-type polymerase with lysozyme: both remain longer at the promoter before establishing a lysozyme-resistant elongation complex and both increase the length of pausing when elongation complexes encounter an eight-base recognition sequence involved in DNA packaging. Replication origins contain T7 promoters, but the role of T7 RNA polymerase in initiating replication is not understood well enough to more than speculate how the lysozyme-polymerase interaction stimulates replication. Maturation and packaging is apparently initiated through interaction between prohead-terminase complexes and transcription elongation complexes paused at the sequence TATCTGT(T/A), well conserved at the right-end of the concatemer junction of T7-like phages. A model that is consistent with the structure of an elongation complex and a large body of mutational and biochemical data is proposed to explain sequence-specific pausing and potential termination at the consensus recognition sequence (C/T)ATCTGT(T/A).

Amidohydrolases↗

PubMed1991

Replication of adenovirus type 4 DNA by a purified fraction from infected cells.

An extract from Adenovirus type 4 infected HeLa cells was fractionated by ion-exchange and DNA affinity chromatography. One fraction, which bound tightly to single stranded DNA, contained predominantly a protein of apparent molecular weight 65,000 and three less abundant proteins. Immunological cross-reactivity with adenovirus type 2 proteins confirmed the presence of preterminal protein and indicated that the abundant species was the virus coded DNA binding protein. This fraction contained an aphidicolin resistant DNA polymerase activity and in the presence of a linearised plasmid containing the adenovirus type 4 origin of DNA replication efficient transfer of dCMP onto preterminal protein, indicative of initiation, was observed. Furthermore, addition of all four deoxyribonucleotide triphosphates and an ATP regenerating system resulted in the elongation of initiated molecules to generate plasmid molecules covalently attached to preterminal protein. Adenovirus type 4 DNA binding protein was extensively purified from crude adenovirus-4 infected HeLa extract by immunoaffinity chromatography using a monoclonal antibody raised against adenovirus type 2 DNA binding protein. A low level of initiation of DNA replication was detected in the fraction depleted of DNA binding protein but activity was restored by addition of purified DNA binding protein. DNA binding protein therefore plays an important role in the initiation of Ad4 DNA replication.

Adenovirus E2 Proteins↗

PubMed1981

Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA.

Transcription of ColE1 DNA by RNA polymerase in vitro starts at two sites in a region required for maintenance of the plasmid. Certain transcripts that start at one of the sites can be cleaved by RNase H and then act as primers for DNA replication. Transcription from the other site produces a RNA approximately 108 nucleotides long (species I or RNA I). Transcripts analogous to the primer and RNA I of ColE1 are produced when p15A or small derivatives of two other ColE1-compatible plasmids, CloDF13 and RSF1030, are used as template. If purified RNA I is added to the transcription reaction containing RNase H, formation of primer is inhibited. Each RNA I can inhibit primer formation by the plasmid that specifies it but has no effect on primer formation by heterologous templates. Thus, the inhibition of primer formation by RNA I is incompatibility specific. Because RNA I does not inhibit initiation or propagation of transcription or the processing of preformed precursors, the step that is sensitive to inhibition is probably formation of the hybrid between the primer precursor and the template. This hybrid is the required substrate for RNase H. Experiments with recombinant plasmids show the region that determines the specificity of response to RNA I to be greater than 300 base pairs upstream of the origin of DNA replication.

Base Composition↗

PubMed1995

On the nature of replication origins in higher eukaryotes.

Establishing whether DNA replication in higher eukaryotic cells is regulated by genetic replicators has been one of the more challenging problems in cell biology. Several important replicon-mapping techniques have been developed in the past decade that have opened up new windows on replication origins. In the past few years, the application of these strategies has identified a large number of origins in a variety of different loci and organisms. Comparison of sequence motifs and chromosomal milieu, as well as genetic manipulation, should begin to uncover the secrets of these illusive regulatory elements.

Amino Acid Sequence↗

PubMed1985

Common regulatory elements control gene expression from polyoma early and late promoters in cells transformed by chimeric plasmids.

In a previous report we showed that transcripts initiating from the late promoter of integrated polyoma plasmids could be detected at significant levels when neomycin resistance (neo) coding sequences were linked to this promoter. In this report we used chimeric plasmids that contain either a limited portion of the polyoma genome or deletions within the polyoma noncoding regulatory region to determine the sequence requirements for late promoter activity in this system. We observed no absolute requirement for either the polyoma early coding region or the origin of DNA replication for Neo-r colony formation. We were therefore able to independently assess the effects of deletions in the polyoma enhancer region on gene activity in both the early and late directions. We measured the ability of cells transfected with plasmids containing deletions in this region to form colonies in either semisolid or G418-containing medium under nonreplicative conditions. Our results indicate that either the PvuII 4 fragment, which contains the simian virus 40 core enhancer sequence, or a region from nucleotides 5099 to 5142, which contains the adenovirus type 5 E1A core enhancer sequence, can be deleted without significantly affecting gene expression in either direction. However, a deletion of nucleotides 5099 to 5172 reduced activities to similar extents in both directions, and a plasmid containing a larger deletion of nucleotides 5055 to 5182 showed a further reduction in activity. Although having no effect by itself, a second origin region deletion of nucleotides 5246 to 127 when present in these mutant backgrounds caused either a further reduction or elimination, respectively, of both G418 and agar colony-forming ability, suggesting the presence of an additional common regulatory element within this region. A comparison of 5' ends of neo transcripts present in cells transformed by these plasmids suggested that the reduction in activity was due to deletion of regulatory rather than structural elements of the late promoter. Our results indicate that the noncoding region of polyoma contains multiple complementing regulatory elements that control the level of both early and late gene expression.

Animals↗

PubMed1983

Biologic properties of viable deletion mutants of simian virus 40 (SV40) rescued from the cells of an SV40-induced hamster lymphocytic leukemia.

A lymphocytic leukemia induced by the oncogenic DNA simian virus 40 (SV40) in an inbred LSH/SsLak Syrian golden hamster was evoked to produce infectious SV40 by fusion of the leukemia cells with grivet monkey kidney (GMK) cells and by exposure of the leukemia cells to the chemical inducers mitomycin C and cycloheximide. Plaque-purified viable substrains of the rescued SV40 when studied by restriction endonuclease digestion of viral DNA were found to contain small deletions within the Hind III restriction fragment C. These deletions lay near the viral origin of DNA replication. Ten plaque-purified substrains of the rescued virus identified by immunofluorescence as being SV40 were found, when compared to the wild-type SV40, to replicate slowly and to form small plaques. Although these substrains transformed NIH/3T3 cells as efficiently as the wild-type SV40 in tissue culture, they were generally less oncogenic in vivo--7 of the 10 failed to induce tumors. The 3 oncogenic SV40-rescued substrains were not found to exhibit "lymphocytotropism," i.e., the capacity to infect and neoplastically transform preferentially hamster lymphocytes. Thus the hamster lymphocytic leukemia originally induced by the wild-type SV40 was most likely a chance-stochastic event rather than the result of tropism-determinism mediated by the virus, as is usually the case with leukemogenic RNA viruses.

Animals↗

PubMed2006

Autorepression of RctB, an initiator of Vibrio cholerae chromosome II replication.

The RctB protein binds to the origin of replication of Vibrio cholerae chromosome II (chrII) and is required for oriCIIVc-based replication. Here, we found that RctB acts as an autorepressor, inhibiting rctB transcription. Integration host factor promotes rctB transcription, while Dam and DnaA, factors required for replication of both V. cholerae chromosomes, influence RctB autorepression. Thus, RctB appears to regulate chrII replication as both an initiator and a transcription repressor, and its synthesis is modulated by factors that govern replication of both chromosomes.

Chromosomes, Bacterial↗