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Journal articles on the topic 'RNA ; Proteins ; DNA replication'

Author: Grafiati

Published: 4 June 2021

Last updated: 16 February 2022

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1

ZDRAVKOVIĆ, S., M. V. SATARIĆ, and D. VUKOVIĆ. "MODULATION AND DEMODULATION IN DNA MOLECULE." Modern Physics Letters B 20, no. 11 (2006): 607–15. http://dx.doi.org/10.1142/s0217984906010706.

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In this paper, we consider the transformation of a breather type soliton in DNA into its demodulated version due to the strong impact of proteins associated with some sequences of DNA chain. These proteins are, for example, RNA polymerase responsible for the formation of m-RNA or initiation protein complex indispensable for chromosome replication.

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2

Wiedmer, Andreas, Pu Wang, Jing Zhou, et al. "Epstein-Barr Virus Immediate-Early Protein Zta Co-Opts Mitochondrial Single-Stranded DNA Binding Protein To Promote Viral and Inhibit Mitochondrial DNA Replication." Journal of Virology 82, no. 9 (2008): 4647–55. http://dx.doi.org/10.1128/jvi.02198-07.

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ABSTRACT Disruption of cellular metabolic processes and usurpation of host proteins are hallmarks of herpesvirus lytic infection. Epstein-Barr virus (EBV) lytic replication is initiated by the immediate-early protein Zta. Zta is a multifunctional DNA binding protein that stimulates viral gene transcription, nucleates a replication complex at the viral origin of lytic replication, and inhibits cell cycle proliferation. To better understand these functions and identify cellular collaborators of Zta, we purified an epitope-tagged version of Zta in cells capable of supporting lytic replication. FL

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3

Ohba, R., K. Matsumoto, and Y. Ishimi. "Induction of DNA replication by transcription in the region upstream of the human c-myc gene in a model replication system." Molecular and Cellular Biology 16, no. 10 (1996): 5754–63. http://dx.doi.org/10.1128/mcb.16.10.5754.

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An important relationship between transcription and initiation of DNA replication in both eukaryotes and prokaryotes has been suggested. In an attempt to understand the molecular mechanism of this interaction, we examined whether transcription can induce DNA replication in vitro by constructing a system in which both replication and transcription were combined. Relaxed circular DNA possessing a replication initiation zone located upstream of the human c-myc gene and a T7 promoter near the P1 promoter of the gene was replicated in the presence of T7 RNA polymerase. In our model system, replicat

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4

Barton, Deborah A., Elke F. Roovers, Quentin Gouil, et al. "Live Cell Imaging Reveals the Relocation of dsRNA Binding Proteins Upon Viral Infection." Molecular Plant-Microbe Interactions® 30, no. 6 (2017): 435–43. http://dx.doi.org/10.1094/mpmi-02-17-0035-r.

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Viral infection triggers a range of plant responses such as the activation of the RNA interference (RNAi) pathway. The double-stranded RNA binding (DRB) proteins DRB3 and DRB4 are part of this pathway and aid in defending against DNA and RNA viruses, respectively. Using live cell imaging, we show that DRB2, DRB3, and DRB5 relocate from their uniform cytoplasmic distribution to concentrated accumulation in nascent viral replication complexes (VRC) that develop following cell invasion by viral RNA. Inactivation of the DRB3 gene in Arabidopsis by T-DNA insertion rendered these plants less able to

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Guogas, Laura, James Hogle, and Lee Gehrke. "Origins of Life and the RNA World: Evolution of RNA-Replicase Recognition." Symposium - International Astronomical Union 213 (2004): 321–24. http://dx.doi.org/10.1017/s0074180900193489.

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Central to understanding the origin of life is the elucidation of the first replication mechanism. The RNA World hypothesis suggests that the first self-replicating molecules were RNAs and that DNA later superceded RNA as the genetic material. RNA viruses were not subjected to the same evolutionary pressures as cellular organisms; consequently, they likely possess remnants of earlier replication strategies. Our laboratory investigates how members of the RNA virus family Bromoviridae can have structurally distinct 3' end tags yet are specifically recognized by conserved replication enzymes. Thi

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6

Kavanaugh, Gina, Runxiang Zhao, Yan Guo, et al. "Enhancer of Rudimentary Homolog Affects the Replication Stress Response through Regulation of RNA Processing." Molecular and Cellular Biology 35, no. 17 (2015): 2979–90. http://dx.doi.org/10.1128/mcb.01276-14.

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Accurate replication of DNA is imperative for the maintenance of genomic integrity. We identified Enhancer of Rudimentary Homolog (ERH) using a whole-genome RNA interference (RNAi) screen to discover novel proteins that function in the replication stress response. Here we report that ERH is important for DNA replication and recovery from replication stress. ATR pathway activity is diminished in ERH-deficient cells. The reduction in ATR signaling corresponds to a decrease in the expression of multiple ATR pathway genes, including ATR itself. ERH interacts with multiple RNA processing complexes,

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Rogan, Peter K., Eliseos J. Mucaki, and Ben C. Shirley. "A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections." F1000Research 9 (August 7, 2020): 943. http://dx.doi.org/10.12688/f1000research.25390.1.

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Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N1), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expressio

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Rogan, Peter K., Eliseos J. Mucaki, and Ben C. Shirley. "A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections." F1000Research 9 (January 6, 2021): 943. http://dx.doi.org/10.12688/f1000research.25390.2.

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Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N2), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expressio

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Dudas, Kathleen C., and Kenneth N. Kreuzer. "UvsW Protein Regulates Bacteriophage T4 Origin-Dependent Replication by Unwinding R-Loops." Molecular and Cellular Biology 21, no. 8 (2001): 2706–15. http://dx.doi.org/10.1128/mcb.21.8.2706-2715.2001.

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ABSTRACT The UvsW protein of bacteriophage T4 is involved in many aspects of phage DNA metabolism, including repair, recombination, and recombination-dependent replication. UvsW has also been implicated in the repression of origin-dependent replication at late times of infection, when UvsW is normally synthesized. Two well-characterized T4 origins, ori(uvsY) andori(34), are believed to initiate replication through an R-loop mechanism. Here we provide both in vivo and in vitro evidence that UvsW is an RNA-DNA helicase that catalyzes the dissociation of RNA from origin R-loops. Two-dimensional g

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Johnson, Kyle L., and L. Andrew Ball. "Induction and Maintenance of Autonomous Flock House Virus RNA1 Replication." Journal of Virology 73, no. 10 (1999): 7933–42. http://dx.doi.org/10.1128/jvi.73.10.7933-7942.1999.

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The nodavirus flock house virus (FHV) has a bipartite, positive-sense, RNA genome that encodes the catalytic subunit of the RNA replicase and the viral capsid protein precursor on separate genomic segments (RNA1 and RNA2, respectively). RNA1 can replicate autonomously when transfected into permissive cells, allowing study of the kinetics of RNA1 replication in the absence of either RNA2 or capsid proteins. However, RNA1 replication ceases ca. 3 days after transfection despite the presence of replication-competent RNA. We examined this inhibition by inducing the expression of RNA1 in cells from

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Englund, P. T., E. E. C. Agbo, M. E. Lindsay, et al. "RNAi libraries and kinetoplast DNA." Biochemical Society Transactions 33, no. 6 (2005): 1409–12. http://dx.doi.org/10.1042/bst0331409.

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African trypanosomes have a remarkable mitochondrial DNA termed kDNA (kinetoplast DNA) that contains several thousands of topologically interlocked DNA rings. Because of its highly unusual structure, kDNA has a complex replication mechanism. Our approach to understanding this mechanism is to identify the proteins involved and to characterize their function. So far approx. 30 candidate proteins have been discovered and we predict that there are over 100. To identify genes for more kDNA replication proteins, we are using an RNA interference library, which is the first forward genetic approach us

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Gopinath, K., B. Dragnea, and C. Kao. "Interaction between Brome Mosaic Virus Proteins and RNAs: Effects on RNA Replication, Protein Expression, and RNA Stability." Journal of Virology 79, no. 22 (2005): 14222–34. http://dx.doi.org/10.1128/jvi.79.22.14222-14234.2005.

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ABSTRACT Brome mosaic virus (BMV) RNA replication has been examined in a number of systems, including Saccharomyces cerevisiae. We developed an efficient T-DNA-based gene delivery system using Agrobacterium tumefaciens to transiently express BMV RNAs in Nicotiana benthamiana. The expressed RNAs can systemically infect plants and provide material to extract BMV replicase that can perform template-dependent RNA-dependent RNA synthesis in vitro. We also expressed the four BMV-encoded proteins from nonreplicating RNAs and analyzed their effects on BMV RNA accumulation. The capsid protein that coin

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Roller, R. J., A. L. McCormick, and B. Roizman. "Cellular proteins specifically bind single- and double-stranded DNA and RNA from the initiation site of a transcript that crosses the origin of DNA replication of herpes simplex virus 1." Proceedings of the National Academy of Sciences 86, no. 17 (1989): 6518–22. http://dx.doi.org/10.1073/pnas.86.17.6518.

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The small-component origins of herpes simplex virus 1 DNA synthesis are transcribed late in infection by an RNA with heterogeneous initiation sites approximately 290-360 base pairs from the origins. We report that cellular proteins react with a labeled RNA probe representing the 5' terminus of a subset of this RNA but not with the complementary strand of this RNA. The proteins form two complexes. Complex 2 was formed by all nuclear extracts tested, whereas complex 1 was invariably formed by proteins present only in nuclear extracts of mock-infected cells. Complex 1 protects a contiguous stretc

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Gillian, Anne Lynn, Stephen C. Schmechel, Jonathan Livny, Leslie A. Schiff та Max L. Nibert. "Reovirus Protein ςNS Binds in Multiple Copies to Single-Stranded RNA and Shares Properties with Single-Stranded DNA Binding Proteins". Journal of Virology 74, № 13 (2000): 5939–48. http://dx.doi.org/10.1128/jvi.74.13.5939-5948.2000.

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ABSTRACT Reovirus nonstructural protein ςNS interacts with reovirus plus-strand RNAs in infected cells, but little is known about the nature of those interactions or their roles in viral replication. In this study, a recombinant form of ςNS was analyzed for in vitro binding to nucleic acids using gel mobility shift assays. Multiple units of ςNS bound to single-stranded RNA molecules with positive cooperativity and with each unit covering about 25 nucleotides at saturation. The ςNS protein did not bind preferentially to reovirus RNA over nonreovirus RNA in competition experiments but did bind p

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15

del Solar, Gloria, Rafael Giraldo, María Jesús Ruiz-Echevarría, Manuel Espinosa, and Ramón Díaz-Orejas. "Replication and Control of Circular Bacterial Plasmids." Microbiology and Molecular Biology Reviews 62, no. 2 (1998): 434–64. http://dx.doi.org/10.1128/mmbr.62.2.434-464.1998.

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SUMMARY An essential feature of bacterial plasmids is their ability to replicate as autonomous genetic elements in a controlled way within the host. Therefore, they can be used to explore the mechanisms involved in DNA replication and to analyze the different strategies that couple DNA replication to other critical events in the cell cycle. In this review, we focus on replication and its control in circular plasmids. Plasmid replication can be conveniently divided into three stages: initiation, elongation, and termination. The inability of DNA polymerases to initiate de novo replication makes

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Franz, Kate M., William J. Neidermyer, Yee-Joo Tan, Sean P. J. Whelan, and Jonathan C. Kagan. "STING-dependent translation inhibition restricts RNA virus replication." Proceedings of the National Academy of Sciences 115, no. 9 (2018): E2058—E2067. http://dx.doi.org/10.1073/pnas.1716937115.

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In mammalian cells, IFN responses that occur during RNA and DNA virus infections are activated by distinct signaling pathways. The RIG-I–like-receptors (RLRs) bind viral RNA and engage the adaptor MAVS (mitochondrial antiviral signaling) to promote IFN expression, whereas cGAS (cGMP–AMP synthase) binds viral DNA and activates an analogous pathway via the protein STING (stimulator of IFN genes). In this study, we confirm that STING is not necessary to induce IFN expression during RNA virus infection but also find that STING is required to restrict the replication of diverse RNA viruses. The ant

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Kumar, Naveen, Sanjay Barua, Riyesh Thachamvally, and Bhupendra Nath Tripathi. "Systems Perspective of Morbillivirus Replication." Journal of Molecular Microbiology and Biotechnology 26, no. 6 (2016): 389–400. http://dx.doi.org/10.1159/000448842.

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Systems biology refers to system-wide changes in biological components such as RNA/DNA (genomics), protein (proteomics) and lipids (lipidomics). In this review, we provide comprehensive information about morbillivirus replication. Besides discussing the role of individual viral/host proteins in virus replication, we also discuss how systems-level analyses could improve our understanding of morbillivirus replication, host-pathogen interaction, immune response and disease resistance. Finally, we discuss how viroinformatics is likely to provide important insights for understanding genome-genome,

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Neerukonda, Sabari Nath. "Interplay between RNA Viruses and Promyelocytic Leukemia Nuclear Bodies." Veterinary Sciences 8, no. 4 (2021): 57. http://dx.doi.org/10.3390/vetsci8040057.

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Promyelocytic leukemia nuclear bodies (PML NBs) are nuclear membrane-less sub structures that play a critical role in diverse cellular pathways including cell proliferation, DNA damage, apoptosis, transcriptional regulation, stem cell renewal, alternative lengthening of telomeres, chromatin organization, epigenetic regulation, protein turnover, autophagy, intrinsic and innate antiviral immunity. While intrinsic and innate immune functions of PML NBs or PML NB core proteins are well defined in the context of nuclear replicating DNA viruses, several studies also confirm their substantial roles i

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Jiang, Min, Xie Xie, Xuefeng Zhu, et al. "The mitochondrial single-stranded DNA binding protein is essential for initiation of mtDNA replication." Science Advances 7, no. 27 (2021): eabf8631. http://dx.doi.org/10.1126/sciadv.abf8631.

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We report a role for the mitochondrial single-stranded DNA binding protein (mtSSB) in regulating mitochondrial DNA (mtDNA) replication initiation in mammalian mitochondria. Transcription from the light-strand promoter (LSP) is required both for gene expression and for generating the RNA primers needed for initiation of mtDNA synthesis. In the absence of mtSSB, transcription from LSP is strongly up-regulated, but no replication primers are formed. Using deep sequencing in a mouse knockout model and biochemical reconstitution experiments with pure proteins, we find that mtSSB is necessary to res

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Sullivan, Michael L., and Paul Ahlquist. "A Brome Mosaic Virus Intergenic RNA3 Replication Signal Functions with Viral Replication Protein 1a To Dramatically Stabilize RNA In Vivo." Journal of Virology 73, no. 4 (1999): 2622–32. http://dx.doi.org/10.1128/jvi.73.4.2622-2632.1999.

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ABSTRACT Brome mosaic virus (BMV), a positive-strand RNA virus in the alphavirus-like superfamily, encodes two RNA replication proteins. The 1a protein has putative helicase and RNA-capping domains, whereas 2a contains a polymerase-like domain. Saccharomyces cerevisiae expressing 1a and 2a is capable of replicating a BMV RNA3 template produced by in vivo transcription of a DNA copy of RNA3. Although insufficient for RNA3 replication, the expression of 1a protein alone results in a dramatic and specific stabilization of the RNA3 template in yeast. As one step toward understanding 1a-induced sta

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Li, Yue, Yu Sun, Jane C. Hines, and Dan S. Ray. "Identification of New Kinetoplast DNA Replication Proteins in Trypanosomatids Based on Predicted S-Phase Expression and Mitochondrial Targeting." Eukaryotic Cell 6, no. 12 (2007): 2303–10. http://dx.doi.org/10.1128/ec.00284-07.

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ABSTRACT Trypanosomatid parasites contain an unusual form of mitochondrial DNA (kinetoplast DNA [kDNA]) consisting of a catenated network of several thousand minicircles and a smaller number of maxicircles. Many of the proteins involved in the replication and division of kDNA are likely to have no counterparts in other organisms and would not be identified by similarity to known replication proteins in other organisms. A new kDNA replication protein conserved in kinetoplastids has been identified based on the presence of posttranscriptional regulatory sequences associated with S-phase gene exp

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Bansho, Yohsuke, Taro Furubayashi, Norikazu Ichihashi, and Tetsuya Yomo. "Host–parasite oscillation dynamics and evolution in a compartmentalized RNA replication system." Proceedings of the National Academy of Sciences 113, no. 15 (2016): 4045–50. http://dx.doi.org/10.1073/pnas.1524404113.

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To date, various cellular functions have been reconstituted in vitro such as self-replication systems using DNA, RNA, and proteins. The next important challenges include the reconstitution of the interactive networks of self-replicating species and investigating how such interactions generate complex ecological behaviors observed in nature. Here, we synthesized a simple replication system composed of two self-replicating host and parasitic RNA species. We found that the parasitic RNA eradicates the host RNA under bulk conditions; however, when the system is compartmentalized, a continuous osci

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Nayak, Ramnath, and David J. Pintel. "Positive and Negative Effects of Adenovirus Type 5 Helper Functions on Adeno-Associated Virus Type 5 (AAV5) Protein Accumulation Govern AAV5 Virus Production." Journal of Virology 81, no. 5 (2006): 2205–12. http://dx.doi.org/10.1128/jvi.02312-06.

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ABSTRACT Full replication of adeno-associated virus type 5 (AAV5) is sustained by adenovirus type 5 (Ad5) helper functions E1a, E1b, E2a, E4Orf6, and virus-associated (VA) RNA; however, their combined net enhancement of AAV5 replication was comprised of both positive and negative individual effects. Although Ad5 E4Orf6 was required for AAV5 genomic DNA replication, it also functioned together with E1b to degrade de novo-expressed, preassembled AAV5 capsid proteins and Rep52 in a proteosome-dependent manner. VA RNA enhanced accumulation of AAV5 protein, overcoming the degradative effects of E4O

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McGlynn, Peter. "Helicases that underpin replication of protein-bound DNA in Escherichia coli." Biochemical Society Transactions 39, no. 2 (2011): 606–10. http://dx.doi.org/10.1042/bst0390606.

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A pre-requisite for successful cell division in any organism is synthesis of an accurate copy of the genetic information needed for survival. This copying process is a mammoth task, given the amount of DNA that must be duplicated, but potential blocks to replication fork movement also pose a challenge for genome duplication. Damage to the template inhibits the replication machinery but proteins bound to the template such as RNA polymerases also present barriers to replication. This review discusses recent results from Escherichia coli that shed light on the roles of helicases in overcoming pro

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Grigoras, Ioana, Tatiana Timchenko, and Bruno Gronenborn. "Transcripts encoding the nanovirus master replication initiator proteins are terminally redundant." Journal of General Virology 89, no. 2 (2008): 583–93. http://dx.doi.org/10.1099/vir.0.83352-0.

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The multicomponent single-stranded DNA plant nanoviruses encode unique master replication initiator (Rep) proteins. We have mapped the 5′ and 3′ termini of the corresponding polyadenylated mRNAs from faba bean necrotic yellows virus (FBNYV) and subterranean clover stunt virus and found that these are terminally redundant by up to about 160 nt. Moreover, the origin of viral DNA replication is transcribed into RNA that is capable of folding into extended secondary structures. Other nanovirus genome components, such as the FBNYV DNA encoding the protein Clink or an FBNYV DNA encoding a non-essent

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Muñoz-Gómez, Ana J., Marc Lemonnier, Sandra Santos-Sierra, Alfredo Berzal-Herranz, and Ramón Díaz-Orejas. "RNase/Anti-RNase Activities of the Bacterial parD Toxin-Antitoxin System." Journal of Bacteriology 187, no. 9 (2005): 3151–57. http://dx.doi.org/10.1128/jb.187.9.3151-3157.2005.

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ABSTRACT The bacterial parD toxin-antitoxin system of plasmid R1 encodes two proteins, the Kid toxin and its cognate antitoxin, Kis. Kid cleaves RNA and inhibits protein synthesis and cell growth in Escherichia coli. Here, we show that Kid promotes RNA degradation and inhibition of protein synthesis in rabbit reticulocyte lysates. These new activities of the Kid toxin were counteracted by the Kis antitoxin and were not displayed by the KidR85W variant, which is nontoxic in E. coli. Moreover, while Kid cleaved single- and double-stranded RNA with a preference for UAA or UAC triplets, KidR85W ma

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Morimatsu, Katsumi, Yun Wu, and Stephen C. Kowalczykowski. "RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus." Journal of Biological Chemistry 287, no. 42 (2012): 35621–30. http://dx.doi.org/10.1074/jbc.m112.397034.

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The repair of single-stranded gaps in duplex DNA by homologous recombination requires the proteins of the RecF pathway. The assembly of RecA protein onto gapped DNA (gDNA) that is complexed with the single-stranded DNA-binding protein is accelerated by the RecF, RecO, and RecR (RecFOR) proteins. Here, we show the RecFOR proteins specifically target RecA protein to gDNA even in the presence of a thousand-fold excess of single-stranded DNA (ssDNA). The binding constant of RecF protein, in the presence of the RecOR proteins, to the junction of ssDNA and dsDNA within a gap is 1–2 nm, suggesting th

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Oh, Jaewook, and Steven S. Broyles. "Host Cell Nuclear Proteins Are Recruited to Cytoplasmic Vaccinia Virus Replication Complexes." Journal of Virology 79, no. 20 (2005): 12852–60. http://dx.doi.org/10.1128/jvi.79.20.12852-12860.2005.

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ABSTRACT The initiation and termination of vaccinia virus postreplicative transcription have been reported to require cellular proteins, some of which are believed to be nuclear proteins. Vaccinia virus replicates in the cytoplasmic compartment of the cell, raising questions as to whether vaccinia virus has access to nuclear proteins. This was addressed here by following the fate of several nuclear proteins after infection of cells with vaccinia virus. The nuclear transcription factors YY1, SP1, and TATA binding protein were found to colocalize with virus replication complexes in the cytoplasm

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Gao, Yang, Dominique Kagele, Kate Smallenberg, and Gregory S. Pari. "Nucleocytoplasmic Shuttling of Human Cytomegalovirus UL84 Is Essential for Virus Growth." Journal of Virology 84, no. 17 (2010): 8484–94. http://dx.doi.org/10.1128/jvi.00738-10.

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ABSTRACT Human cytomegalovirus (HCMV) UL84 is a multifunctional protein that is the proposed initiator for lytic viral DNA synthesis. Recently it was shown that UL84 displays nucleocytoplasmic shuttling. The role of shuttling in lytic DNA replication and virus growth is unknown. We now show that expression of the nonshuttling UL84 mutant failed to complement oriLyt-dependent DNA replication in the transient assay under conditions where core replication and ancillary proteins were expressed under the control of their native promoters. However, constitutive expression of the core replication pro

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Mortusewicz, Oliver, Wera Roth, Na Li, M. Cristina Cardoso, Michael Meisterernst, and Heinrich Leonhardt. "Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites." Journal of Cell Biology 183, no. 5 (2008): 769–76. http://dx.doi.org/10.1083/jcb.200808097.

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The multifunctional nuclear protein positive cofactor 4 (PC4) is involved in various cellular processes including transcription, replication, and chromatin organization. Recently, PC4 has been identified as a suppressor of oxidative mutagenesis in Escherichia coli and Saccharomyces cerevisiae. To investigate a potential role of PC4 in mammalian DNA repair, we used a combination of live cell microscopy, microirradiation, and fluorescence recovery after photobleaching analysis. We found a clear accumulation of endogenous PC4 at DNA damage sites introduced by either chemical agents or laser micro

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Beck, Jürgen, Stefan Seitz, Chris Lauber, and Michael Nassal. "Conservation of the HBV RNA element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription." Proceedings of the National Academy of Sciences 118, no. 13 (2021): e2022373118. http://dx.doi.org/10.1073/pnas.2022373118.

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Hepadnaviruses, with the human hepatitis B virus as prototype, are small, enveloped hepatotropic DNA viruses which replicate by reverse transcription of an RNA intermediate. Replication is initiated by a unique protein-priming mechanism whereby a hydroxy amino acid side chain of the terminal protein (TP) domain of the viral polymerase (P) is extended into a short DNA oligonucleotide, which subsequently serves as primer for first-strand synthesis. A key component in the priming of reverse transcription is the viral RNA element epsilon, which contains the replication origin and serves as a templ

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Taneja, Poonam, Heinz-Peter Nasheuer, Hella Hartmann, Frank Grosse, Ellen Fanning, and Klaus Weisshart. "Timed interactions between viral and cellular replication factors during the initiation of SV40 in vitro DNA replication." Biochemical Journal 407, no. 2 (2007): 313–20. http://dx.doi.org/10.1042/bj20070794.

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The initiation of SV40 (simian virus 40) DNA replication requires the co-operative interactions between the viral Tag (large T-antigen), RPA (replication protein A) and Pol (DNA polymerase α-primase) on the template DNA. Binding interfaces mapped on these enzymes and expressed as peptides competed with the mutual interactions of the native proteins. Prevention of the genuine interactions was accomplished only prior to the primer synthesis step and blocked the assembly of a productive initiation complex. Once the complex was engaged in the synthesis of an RNA primer and its extension, the inter

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Paschalis, Vasileios, Emmanuelle Le Chatelier, Matthew Green, François Képès, Panos Soultanas, and Laurent Janniere. "Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity." Open Biology 7, no. 9 (2017): 170146. http://dx.doi.org/10.1098/rsob.170146.

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During Bacillus subtilis replication two replicative polymerases function at the replisome to collectively carry out genome replication. In a reconstituted in vitro replication assay, PolC is the main polymerase while the lagging strand DnaE polymerase briefly extends RNA primers synthesized by the primase DnaG prior to handing-off DNA synthesis to PolC. Here, we show in vivo that (i) the polymerase activity of DnaE is essential for both the initiation and elongation stages of DNA replication, (ii) its error rate varies inversely with PolC concentration, and (iii) its misincorporations are cor

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Nathan, Kavitha Ganesan, and Sunil K. Lal. "The Multifarious Role of 14-3-3 Family of Proteins in Viral Replication." Viruses 12, no. 4 (2020): 436. http://dx.doi.org/10.3390/v12040436.

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The 14-3-3 proteins are a family of ubiquitous and exclusively eukaryotic proteins with an astoundingly significant number of binding partners. Their binding alters the activity, stability, localization, and phosphorylation state of a target protein. The association of 14-3-3 proteins with the regulation of a wide range of general and specific signaling pathways suggests their crucial role in health and disease. Recent studies have linked 14-3-3 to several RNA and DNA viruses that may contribute to the pathogenesis and progression of infections. Therefore, comprehensive knowledge of host–virus

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Hines, Jane C., and Dan S. Ray. "A Second Mitochondrial DNA Primase Is Essential for Cell Growth and Kinetoplast Minicircle DNA Replication in Trypanosoma brucei." Eukaryotic Cell 10, no. 3 (2011): 445–54. http://dx.doi.org/10.1128/ec.00308-10.

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ABSTRACT The mitochondrial DNA of trypanosomes contains two types of circular DNAs, minicircles and maxicircles. Both minicircles and maxicircles replicate from specific replication origins by unidirectional theta-type intermediates. Initiation of the minicircle leading strand and also that of at least the first Okazaki fragment involve RNA priming. The Trypanosoma brucei genome encodes two mitochondrial DNA primases, PRI1 and PRI2, related to the primases of eukaryotic nucleocytoplasmic large DNA viruses. These primases are members of the archeoeukaryotic primase superfamily, and each of them

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Brieba. "Structure–Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System." Plants 8, no. 12 (2019): 533. http://dx.doi.org/10.3390/plants8120533.

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Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possib

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Gonsky, Jason, Eran Bacharach, and Stephen P. Goff. "Identification of Residues of the Moloney Murine Leukemia Virus Nucleocapsid Critical for Viral DNA Synthesis In Vivo." Journal of Virology 75, no. 6 (2001): 2616–26. http://dx.doi.org/10.1128/jvi.75.6.2616-2626.2001.

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ABSTRACT The nucleocapsid (NC) protein of retroviruses is a small nucleic acid-binding protein important in virion assembly and in the encapsidation of the viral RNA genome into the virion particle. Multiple single-amino-acid substitutions were introduced into the NC of Moloney murine leukemia virus to examine further its role in viral replication. Two residues were shown to play important roles in the early events of replication. Unlike viruses with previously characterized NC mutations, these viruses showed no impairment in the late events of replication. Viruses containing the substitutions

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Kyratsous, Christos A., and Saul J. Silverstein. "BAG3, a Host Cochaperone, Facilitates Varicella-Zoster Virus Replication." Journal of Virology 81, no. 14 (2007): 7491–503. http://dx.doi.org/10.1128/jvi.00442-07.

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ABSTRACT Varicella-zoster virus (VZV) establishes a lifelong latent infection in the dorsal root ganglia of the host. During latency, a subset of virus-encoded regulatory proteins is detected; however, they are excluded from the nucleus. ORF29p, a single-stranded DNA binding protein, is one of these latency-associated proteins. We searched for cell proteins that interact with ORF29p and identified BAG3. BAG3, Hsp70/Hsc70, and Hsp90 colocalize with ORF29p in nuclear transcription/replication factories during lytic replication of VZV. Pharmacological intercession of Hsp90 activity with ansamycin

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Bell, Peter, Robert Brazas, Donald Ganem, and Gerd G. Maul. "Hepatitis Delta Virus Replication Generates Complexes of Large Hepatitis Delta Antigen and Antigenomic RNA That Affiliate with and Alter Nuclear Domain 10." Journal of Virology 74, no. 11 (2000): 5329–36. http://dx.doi.org/10.1128/jvi.74.11.5329-5336.2000.

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ABSTRACT Hepatitis delta virus (HDV), a single-stranded RNA virus, bears a single coding region whose product, the hepatitis delta antigen (HDAg), is expressed in two isoforms, small (S-HDAg) and large (L-HDAg). S-HDAg is required for replication of HDV, while L-HDAg inhibits viral replication and is required for the envelopment of the HDV genomic RNA by hepatitis B virus proteins. Here we have examined the spatial distribution of HDV RNA and proteins in infected nuclei, with particular reference to specific nuclear domains. We found that L-HDAg was aggregated in specific nuclear domains and t

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Lovett, Susan T. "DNA polymerase III protein, HolC, helps resolve replication/transcription conflicts." Microbial Cell 8, no. 6 (2021): 143–45. http://dx.doi.org/10.15698/mic2021.06.753.

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In Escherichia coli, DNA replication is catalyzed by an assembly of proteins, the DNA polymerase III holoenzyme. This complex includes the polymerase and proofreading subunits, the processivity clamp and clamp loader complex. The holC gene encodes an accessory protein (known as χ) to the core clamp loader complex and is the only protein of the holoenzyme that binds to single-strand DNA binding protein, SSB. HolC is not essential for viability although mutants show growth impairment, genetic instability and sensitivity to DNA damaging agents. In this study we isolate spontaneous suppressor muta

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Mazina, Olga M., Srinivas Somarowthu, Lyudmila Y. Kadyrova, et al. "Replication protein A binds RNA and promotes R-loop formation." Journal of Biological Chemistry 295, no. 41 (2020): 14203–13. http://dx.doi.org/10.1074/jbc.ra120.013812.

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Replication protein A (RPA), a major eukaryotic ssDNA-binding protein, is essential for all metabolic processes that involve ssDNA, including DNA replication, repair, and damage signaling. To perform its functions, RPA binds ssDNA tightly. In contrast, it was presumed that RPA binds RNA weakly. However, recent data suggest that RPA may play a role in RNA metabolism. RPA stimulates RNA-templated DNA repair in vitro and associates in vivo with R-loops, the three-stranded structures consisting of an RNA-DNA hybrid and the displaced ssDNA strand. R-loops are common in the genomes of pro- and eukar

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Nicolas, Armel, Nathalie Alazard-Dany, Coline Biollay, et al. "Identification of Rep-Associated Factors in Herpes Simplex Virus Type 1-Induced Adeno-Associated Virus Type 2 Replication Compartments." Journal of Virology 84, no. 17 (2010): 8871–87. http://dx.doi.org/10.1128/jvi.00725-10.

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ABSTRACT Adeno-associated virus (AAV) is a human parvovirus that replicates only in cells coinfected with a helper virus, such as adenovirus or herpes simplex virus type 1 (HSV-1). We previously showed that nine HSV-1 factors are able to support AAV rep gene expression and genome replication. To elucidate the strategy of AAV replication in the presence of HSV-1, we undertook a proteomic analysis of cellular and HSV-1 factors associated with Rep proteins and thus potentially recruited within AAV replication compartments (AAV RCs). This study resulted in the identification of approximately 60 ce

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Hu, Jianhong, Eugene Liu, and Rolf Renne. "Involvement of SSRP1 in Latent Replication of Kaposi's Sarcoma-Associated Herpesvirus." Journal of Virology 83, no. 21 (2009): 11051–63. http://dx.doi.org/10.1128/jvi.00907-09.

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ABSTRACT Kaposi's sarcoma-associated herpesvirus (also named human herpesvirus 8) is a γ-herpesvirus that undergoes both lytic and latent infection. During latent infection, two viral elements are required: latency-associated nuclear antigen (LANA), which functions as an origin binding protein, and the latent origin, which resides within the terminal repeats (TRs) of the viral genome. Previously, we identified two cis-elements within the TRs which are required for latent DNA replication: two LANA binding sites (LBS1 and LBS2 [LBS1/2]) and a GC-rich replication element (RE) upstream of LBS1/2.

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Wang, Fu-Zhang, Debasmita Roy, Edward Gershburg, Christopher B. Whitehurst, Dirk P. Dittmer, and Joseph S. Pagano. "Maribavir Inhibits Epstein-Barr Virus Transcription in Addition to Viral DNA Replication." Journal of Virology 83, no. 23 (2009): 12108–17. http://dx.doi.org/10.1128/jvi.01575-09.

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ABSTRACT Although many drugs inhibit the replication of Epstein-Barr virus (EBV) in cell culture systems, there is still no drug that is effective and approved for use in primary EBV infection. More recently, maribavir (MBV), an l-ribofuranoside benzimidazole, has been shown to be a potent and nontoxic inhibitor of EBV replication and to have a mode of action quite distinct from that of acyclic nucleoside analogs such as acyclovir (ACV) that is based primarily on MBV's ability to block the phosphorylation of target proteins by EBV and human cytomegalovirus protein kinases. However, since the a

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Price, B. D., P. Ahlquist, and L. A. Ball. "DNA-Directed Expression of an Animal Virus RNA for Replication-Dependent Colony Formation in Saccharomyces cerevisiae." Journal of Virology 76, no. 4 (2002): 1610–16. http://dx.doi.org/10.1128/jvi.76.4.1610-1616.2002.

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ABSTRACT To date, the insect nodavirus flock house virus (FHV) is the only virus of a higher eukaryote that has been shown to undergo a full replicative cycle and produce infectious progeny in the yeast Saccharomyces cerevisiae. The genome of FHV is composed of two positive-sense RNA segments: RNA1, encoding the RNA replicase, and RNA2, encoding the capsid protein precursor. When yeast cells expressing FHV RNA replicase were transfected with a chimeric RNA composed of a selectable gene flanked by the termini of RNA2, the chimeric RNA was replicated and transmitted to daughter cells indefinitel

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Seifer, Maria, Robert Hamatake, Marc Bifano, and David N. Standring. "Generation of Replication-Competent Hepatitis B Virus Nucleocapsids in Insect Cells." Journal of Virology 72, no. 4 (1998): 2765–76. http://dx.doi.org/10.1128/jvi.72.4.2765-2776.1998.

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ABSTRACT The double-stranded DNA genome of human hepatitis B virus (HBV) and related hepadnaviruses is reverse transcribed from a pregenomic RNA by a viral polymerase (Pol) harboring both priming and RNA- and DNA-dependent elongation activities. Although hepadnavirus replication occurs inside viral nucleocapsids, or cores, biochemical systems for analyzing this reaction are currently limited to unencapsidated Pols expressed in heterologous systems. Here, we describe cisand trans classes of replicative HBV cores, produced in the recombinant baculovirus system via coexpression of HBV core and Po

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Brüning, Jan-Gert, and Kenneth J. Marians. "Replisome bypass of transcription complexes and R-loops." Nucleic Acids Research 48, no. 18 (2020): 10353–67. http://dx.doi.org/10.1093/nar/gkaa741.

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Abstract The vast majority of the genome is transcribed by RNA polymerases. G+C-rich regions of the chromosomes and negative superhelicity can promote the invasion of the DNA by RNA to form R-loops, which have been shown to block DNA replication and promote genome instability. However, it is unclear whether the R-loops themselves are sufficient to cause this instability or if additional factors are required. We have investigated replisome collisions with transcription complexes and R-loops using a reconstituted bacterial DNA replication system. RNA polymerase transcription complexes co-directi

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Chen, Jianbo, Sheikh Abdul Rahman, Olga A. Nikolaitchik, et al. "HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein." Proceedings of the National Academy of Sciences 113, no. 2 (2015): E201—E208. http://dx.doi.org/10.1073/pnas.1518572113.

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Retroviruses package a dimeric genome comprising two copies of the viral RNA. Each RNA contains all of the genetic information for viral replication. Packaging a dimeric genome allows the recovery of genetic information from damaged RNA genomes during DNA synthesis and promotes frequent recombination to increase diversity in the viral population. Therefore, the strategy of packaging dimeric RNA affects viral replication and viral evolution. Although its biological importance is appreciated, very little is known about the genome dimerization process. HIV-1 RNA genomes dimerize before packaging

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Nevinsky, Georgy A. "How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities." International Journal of Molecular Sciences 22, no. 3 (2021): 1369. http://dx.doi.org/10.3390/ijms22031369.

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X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes—replication, restriction, integration

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Karakama, Yuko, Naoya Sakamoto, Yasuhiro Itsui, et al. "Inhibition of Hepatitis C Virus Replication by a Specific Inhibitor of Serine-Arginine-Rich Protein Kinase." Antimicrobial Agents and Chemotherapy 54, no. 8 (2010): 3179–86. http://dx.doi.org/10.1128/aac.00113-10.

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ABSTRACT Splicing of messenger RNAs is regulated by site-specific binding of members of the serine-arginine-rich (SR) protein family, and SR protein kinases (SRPK) 1 and 2 regulate overall activity of the SR proteins by phosphorylation of their RS domains. We have reported that specifically designed SRPK inhibitors suppressed effectively several DNA and RNA viruses in vitro and in vivo. Here, we show that an SRPK inhibitor, SRPIN340, suppressed in a dose-dependent fashion expression of a hepatitis C virus (HCV) subgenomic replicon and replication of the HCV-JFH1 clone in vitro. The inhibitory

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