scholarly journals On the opportunistic nature of transcription and replication initiation in the metazoan genome

BioEssays ◽  
2011 ◽  
Vol 34 (2) ◽  
pp. 119-125 ◽  
Author(s):  
Joana Sequeira-Mendes ◽  
María Gómez
Keyword(s):  
Replication Initiation ◽  
Metazoan Genome ◽  
Transcription And Replication

scholarly journals Role of the influenza virus heterotrimeric RNA polymerase complex in the initiation of replication

2006 ◽  
Vol 87 (11) ◽  
pp. 3373-3377 ◽  
Author(s):  
Tao Deng ◽  
Jane L. Sharps ◽  
George G. Brownlee
Keyword(s):  
Influenza Virus ◽  
Rna Polymerase ◽  
Replication Initiation ◽  
Polymerase Complex ◽  
Virus Rna ◽  
Initiation Of Replication ◽  
Rna Genome ◽  
Transcription And Replication

Both transcription and replication of the influenza virus RNA genome are catalysed by a virus-specific RNA polymerase. Recently, an in vitro assay, based on the synthesis of pppApG, for the initiation of replication by recombinant RNA polymerase in the absence of added primer was described. Here, these findings are extended to show that adenosine, AMP and ADP can each substitute for ATP in reactions catalysed by either recombinant ribonucleoprotein or RNA polymerase complexes with either model virion RNA (vRNA) or cRNA promoters. The use of either adenosine or AMP, rather than ATP, provides a convenient, sensitive and easy assay of replication initiation. Moreover, no pppApG was detected when a PB1–PA dimer, rather than the trimeric polymerase, was used to catalyse synthesis, contrasting with a previous report using baculovirus-expressed influenza RNA polymerase. Overall, it is suggested that the heterotrimeric polymerase is essential for the initiation of replication.

scholarly journals The Marburg Virus 3′ Noncoding Region Structurally and Functionally Differs from That of Ebola Virus

2009 ◽  
Vol 83 (9) ◽  
pp. 4508-4519 ◽  
Author(s):  
Sven Enterlein ◽  
Kristina M. Schmidt ◽  
Michael Schümann ◽  
Dominik Conrad ◽  
Verena Krähling ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Ebola Virus ◽  
Gene Mutations ◽  
Replication Initiation ◽  
Marburg Virus ◽  
Noncoding Region ◽  
Nontranslated Region ◽  
Transcription And Replication

ABSTRACT We have previously shown that the first transcription start signal (TSS) of Zaire Ebola virus (ZEBOV) is involved in formation of an RNA secondary structure regulating VP30-dependent transcription activation. Interestingly, transcription of Marburg virus (MARV) minigenomes occurs independently of VP30. In this study, we analyzed the structure of the MARV 3′ noncoding region and its influence on VP30 necessity. Secondary structure formation of the TSS of the first gene was experimentally determined and showed substantial differences from the structure formed by the ZEBOV TSS. Chimeric MARV minigenomes mimicking the ZEBOV-specific RNA secondary structure were neither transcribed nor replicated. Mapping of the MARV genomic replication promoter revealed that the region homologous to the sequence involved in formation of the regulatory ZEBOV RNA structure is part of the MARV promoter. The MARV promoter is contained within the first 70 nucleotides of the genome and consists of two elements separated by a spacer region, comprising the TSS of the first gene. Mutations within the spacer abolished transcription activity and led to increased replication, indicating competitive transcription and replication initiation. The second promoter element is located within the nontranslated region of the first gene and consists of a stretch of three UN5 hexamers. Recombinant full-length MARV clones, in which the three conserved U residues were substituted, could not be rescued, underlining the importance of the UN5 hexamers for replication activity. Our data suggest that differences in the structure of the genomic replication promoters might account for the different transcription strategies of Marburg and Ebola viruses.

The kinases HipA and HipA7 phosphorylate different substrate pools inEscherichia colito promote multidrug tolerance

2018 ◽  
Vol 11 (547) ◽  
pp. eaat5750 ◽  
Author(s):  
Maja Semanjski ◽  
Elsa Germain ◽  
Katrin Bratl ◽  
Andreas Kiessling ◽  
Kenn Gerdes ◽  
...  
Keyword(s):  
Growth Inhibition ◽  
Replication Initiation ◽  
Translation Inhibition ◽  
Inhibition Of Growth ◽  
High Copy Number Plasmid ◽  
Primary Determinant ◽  
Multidrug Tolerance ◽  
Endogenous Substrates ◽  
Ribosomal Protein L11 ◽  
Transcription And Replication

The bacterial serine-threonine protein kinase HipA promotes multidrug tolerance by phosphorylating the glutamate-tRNA ligase (GltX), leading to a halt in translation, inhibition of growth, and induction of a physiologically dormant state (persistence). The HipA variant HipA7 substantially increases persistence despite being less efficient at inhibiting cell growth. We postulated that this phenotypic difference was caused by differences in the substrates targeted by both kinases. We overproduced HipA and HipA7 inEscherichia coliand identified their endogenous substrates by SILAC-based quantitative phosphoproteomics. We confirmed that GltX was the main substrate of both kinase variants and likely the primary determinant of persistence. When HipA and HipA7 were moderately overproduced from plasmids, HipA7 targeted only GltX, but HipA phosphorylated several additional substrates involved in translation, transcription, and replication, such as ribosomal protein L11 (RplK) and the negative modulator of replication initiation, SeqA. HipA7 showed reduced kinase activity compared to HipA and targeted a substrate pool similar to that of HipA only when produced from a high–copy number plasmid. The kinase variants also differed in autophosphorylation, which was substantially reduced for HipA7. When produced endogenously from the chromosome, HipA showed no activity because of inhibition by the antitoxin HipB, whereas HipA7 phosphorylated GltX and phage shock protein PspA. Initial testing did not reveal a connection between HipA-induced phosphorylation of RplK and persistence or growth inhibition, suggesting that other HipA-specific substrates were likely responsible for growth inhibition. Our results contribute to the understanding of HipA7 action and present a resource for elucidating HipA-related persistence.

scholarly journals Nature of a paramyxovirus replication promoter influences a nearby transcription signal

2005 ◽  
Vol 86 (1) ◽  
pp. 171-180 ◽  
Author(s):  
Diane Vulliémoz ◽  
Samuel Cordey ◽  
Geneviève Mottet-Osman ◽  
Laurent Roux
Keyword(s):  
Transcription Initiation ◽  
Sendai Virus ◽  
Initiation Site ◽  
Essential Elements ◽  
Replication Initiation ◽  
Start Site ◽  
Mrna Synthesis ◽  
Gene Start ◽  
Or Gene ◽  
Transcription And Replication

The genomic and antigenomic 3′ ends of the Sendai virus replication promoters are bi-partite in nature. They are symmetrically composed of leader or trailer sequences, a gene start (gs) or gene end (ge) site, respectively, and a simple hexameric repeat. Studies of how mRNA synthesis initiates from the first gene start site (gs1) have been hampered by the fact that gs1 is located between two essential elements of the replication promoter. Transcription initiation, then, is separated from the replication initiation site by only 56 nt on the genome, so that transcription and replication may sterically interfere with each other. In order to study the initiation of Sendai virus mRNAs without this possible interference, Sendai virus mini-genomes were prepared having tandem promoters in which replication takes place from the external one, whereas mRNA synthesis occurs from the internal one. Transcription now initiates at position 146 rather than position 56 relative to the genome 3′ end. Under these conditions, it was found that the frequency with which mRNA synthesis initiates depends, in an inverse fashion, on the strength of the external replication promoter. It was also found that the sequences essential for replication are not required for basic mRNA synthesis as long as there is an external replication promoter at which viral RNA polymerase can enter the nucleocapsid template. The manner in which transcription and replication initiations influence each other is discussed.

scholarly journals Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells

2019 ◽  
Author(s):  
Nina Kirstein ◽  
Alexander Buschle ◽  
Xia Wu ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
...  
Keyword(s):  
Dna Replication ◽  
Temporal Order ◽  
Replication Timing ◽  
S Phase ◽  
Replication Initiation ◽  
G1 Phase ◽  
Environmental Cues ◽  
Transcriptional Program ◽  
Active Transcription ◽  
Transcription And Replication

AbstractEukaryotic replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with replication initiation events obtained by Okazaki fragment sequencing. We demonstrate that MCM is displaced from early replicating, actively transcribed gene bodies, while ORC is mainly enriched at active TSS. Late replicating, H4K20me3 containing initiation zones display enhanced ORC and MCM levels. Furthermore, we find early RTDs being primarily enriched in ORC, compared to MCM, indicating that ORC levels are involved in organizing the temporal order of DNA replication. The organizational connection between active transcription and replication competence directly links changes in the transcriptional program to flexible replication patterns, which ensures the cell’s flexibility to respond to environmental cues.

A Novel Fluorescence-Based Screen for Inhibitors of the Initiation of DNA Replication in Bacteria

2019 ◽  
Vol 16 (3) ◽  
pp. 272-277 ◽  
Author(s):  
Rasmus N. Klitgaard ◽  
Anders Løbner-Olesen
Keyword(s):  
Dna Replication ◽  
High Throughput ◽  
Cyclic Peptide ◽  
Replication Initiation ◽  
False Positive Result ◽  
Over Expression ◽  
Initiator Protein ◽  
Dna Replication Initiation ◽  
Cellular Processes ◽  
Initiation Of Dna Replication

Background:One of many strategies to overcome antibiotic resistance is the discovery of compounds targeting cellular processes, which have not yet been exploited.Materials and Methods:Using various genetic tools, we constructed a novel high throughput, cellbased, fluorescence screen for inhibitors of chromosome replication initiation in bacteria.Results:The screen was validated by expression of an intra-cellular cyclic peptide interfering with the initiator protein DnaA and by over-expression of the negative initiation regulator SeqA. We also demonstrated that neither tetracycline nor ciprofloxacin triggers a false positive result. Finally, 400 extracts isolated mainly from filamentous actinomycetes were subjected to the screen.Conclusion:We concluded that the presented screen is applicable for identifying putative inhibitors of DNA replication initiation in a high throughput setup.

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