Requirement of the Poly(A) Tail in Coronavirus Genome Replication

The graphical abstract represents the synthesis of size engineered ZnS QDs for conjugating anti-viral drug (MPA) and its safe and effective delivery against cytoplasmically replicating dengue virus 2.

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Snapshots of a Non-Canonical RdRP in Action

Viruses ◽

10.3390/v13071260 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1260

Author(s):

Diego S. Ferrero ◽

Michela Falqui ◽

Nuria Verdaguer

Keyword(s):

Metal Ion ◽

Rna Viruses ◽

Ion Binding ◽

Genome Replication ◽

Metal Ion Binding ◽

Insect Virus ◽

X Ray ◽

Template Strand ◽

Nucleotide Incorporation ◽

Elongation Process

RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.

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Developmental differences in genome replication program and origin activation

Nucleic Acids Research ◽

10.1093/nar/gkaa1124 ◽

2020 ◽

Vol 48 (22) ◽

pp. 12751-12777

Author(s):

Cathia Rausch ◽

Patrick Weber ◽

Paulina Prorok ◽

David Hörl ◽

Andreas Maiser ◽

...

Keyword(s):

Dna Replication ◽

Single Molecule ◽

Embryonic Stem ◽

S Phase ◽

Developmental Differences ◽

Centromeric Heterochromatin ◽

Genome Replication ◽

Origin Activation ◽

Spatio Temporal ◽

Mes Cells

Abstract To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.

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Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

Genes ◽

10.3390/genes12040480 ◽

2021 ◽

Vol 12 (4) ◽

pp. 480

Author(s):

Lin Tao ◽

Xiaoyun He ◽

Yanting Jiang ◽

Yufang Liu ◽

Yina Ouyang ◽

...

Keyword(s):

Signaling Pathway ◽

Litter Size ◽

Luteal Phase ◽

Antigen Processing ◽

Osteoclast Differentiation ◽

Follicular Phase ◽

Comparative Genomic ◽

Genome Replication ◽

Viral Genome Replication ◽

Transcriptomic Level

The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.

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Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

Nature Methods ◽

10.1038/s41592-019-0394-y ◽

2019 ◽

Vol 16 (5) ◽

pp. 429-436 ◽

Cited By ~ 21

Author(s):

Carolin A. Müller ◽

Michael A. Boemo ◽

Paolo Spingardi ◽

Benedikt M. Kessler ◽

Skirmantas Kriaucionis ◽

...

Keyword(s):

Genome Replication

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Structure and assembly of double-headed Sendai virus nucleocapsids

Communications Biology ◽

10.1038/s42003-021-02027-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Na Zhang ◽

Hong Shan ◽

Mingdong Liu ◽

Tianhao Li ◽

Rui Luo ◽

...

Keyword(s):

Electron Microscopy ◽

Measles Virus ◽

Sendai Virus ◽

Nipah Virus ◽

Mumps Virus ◽

Genome Replication ◽

Direct Visualization ◽

Closed State ◽

Cryo Electron Microscopy ◽

Negative Sense

AbstractParamyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.

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Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽

10.3390/v11111042 ◽

2019 ◽

Vol 11 (11) ◽

pp. 1042

Author(s):

Cheepudom ◽

Lin ◽

Lee ◽

Meng

Keyword(s):

Plant Cell Wall ◽

Hydrolytic Enzymes ◽

Thermobifida Fusca ◽

Genome Replication ◽

Putative Orfs ◽

Base Pairs ◽

Double Stranded Dna ◽

Virion Morphogenesis ◽

Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

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