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The FEBS Journal Jun 2015The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is... (Review)
Review
The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.
Topics: Animals; Chromatin Assembly and Disassembly; DNA; DNA, Superhelical; Energy Metabolism; Genetic Phenomena; Genetics; Genome; History, 20th Century; History, 21st Century; Humans; Nucleic Acid Conformation
PubMed: 25903461
DOI: 10.1111/febs.13307 -
Essays in Biochemistry Apr 2019This collection of reviews focuses on the most exciting areas of DNA packaging at the current time. Many of the new discoveries are driven by the development of...
This collection of reviews focuses on the most exciting areas of DNA packaging at the current time. Many of the new discoveries are driven by the development of molecular or imaging techniques, and these are providing insights into the complex world of chromatin. As these new techniques continue to improve, we will be able to answer many of the questions we have now, while likely raising many new ones.
Topics: Animals; DNA; DNA Packaging; Histones; Nucleosomes; RNA
PubMed: 31015379
DOI: 10.1042/EBC20190040 -
Cold Spring Harbor Perspectives in... Sep 2013Poxviruses are large, enveloped viruses that replicate in the cytoplasm and encode proteins for DNA replication and gene expression. Hairpin ends link the two strands of... (Review)
Review
Poxviruses are large, enveloped viruses that replicate in the cytoplasm and encode proteins for DNA replication and gene expression. Hairpin ends link the two strands of the linear, double-stranded DNA genome. Viral proteins involved in DNA synthesis include a 117-kDa polymerase, a helicase-primase, a uracil DNA glycosylase, a processivity factor, a single-stranded DNA-binding protein, a protein kinase, and a DNA ligase. A viral FEN1 family protein participates in double-strand break repair. The DNA is replicated as long concatemers that are resolved by a viral Holliday junction endonuclease.
Topics: DNA Packaging; DNA Replication; DNA, Viral; DNA-Binding Proteins; Genome, Viral; Models, Biological; Poxviridae
PubMed: 23838441
DOI: 10.1101/cshperspect.a010199 -
Advances in Anatomy, Embryology, and... 2017Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic... (Review)
Review
Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome. The capsid shell of HSV-1 is built from four structural proteins: a major capsid protein, VP5, which forms the capsomers (hexons and pentons), the triplex consisting of VP19C and VP23 found between the capsomers, and VP26 which binds to VP5 on hexons but not pentons. In addition, the dodecameric pUL6 portal complex occupies 1 of the 12 capsid vertices, and the capsid vertex specific component (CVSC), a heterotrimer complex of pUL17, pUL25, and pUL36, binds specifically to the triplexes adjacent to each penton. The capsid is assembled in the nucleus where the viral genome is packaged into newly assembled closed capsid shells. Cleavage and packaging of replicated, concatemeric viral DNA requires the seven viral proteins encoded by the UL6, UL15, UL17, UL25, UL28, UL32, and UL33 genes. Considerable advances have been made in understanding the structure of the herpesvirus capsid and the function of several of the DNA packaging proteins by applying biochemical, genetic, and structural techniques. This review is a summary of recent advances with respect to the structure of the HSV-1 virion capsid and what is known about the function of the seven packaging proteins and their interactions with each other and with the capsid shell.
Topics: Animals; Capsid; DNA Packaging; Herpesviridae; Humans; Viral Proteins; Virion; Virus Assembly
PubMed: 28528442
DOI: 10.1007/978-3-319-53168-7_6 -
Virus Research May 2013Tailed bacteriophages and herpesviruses package DNA inside the viral capsid by a powerful molecular motor. This packaging machine is composed of the portal protein,... (Review)
Review
Tailed bacteriophages and herpesviruses package DNA inside the viral capsid by a powerful molecular motor. This packaging machine is composed of the portal protein, which provides a gate for DNA entry, the large terminase subunit whose ATPase activity fuels DNA translocation, and most frequently, a small terminase subunit that recognizes the viral packaging site. Here we review the mechanisms how the virulent Bacillus subtilis phage SPP1 packages DNA into a preformed procapsid. Encapsidation of the SPP1 DNA follows a processive unidirectional headful mechanism that starts with the recognition and cleavage of a unique genomic sequence (pac) by the viral terminase. The viral genome is then translocated through the central channel of the portal protein found at a single vertex of the procapsid. Packaging is terminated by an endonucleolytic cleavage of the concatemeric DNA substrate, following by disassembly of the packaging motor and closure of the portal system by the gatekeepers preventing leakage of the viral genome. Recent advances are providing new molecular insights on the mechanisms that ensure precise coordination of these critical steps required to accomplish the packaging encapsidation cycle.
Topics: Bacillus Phages; Bacillus subtilis; DNA Packaging; DNA, Viral
PubMed: 23419885
DOI: 10.1016/j.virusres.2013.01.021 -
Annual Review of Virology Nov 2015Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and... (Review)
Review
Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and translocase activities. TerL, following endonucleolytic cleavage of immature viral DNA concatemer recognized by TerS, assembles into a pentameric ring motor on the prohead's portal vertex and uses ATP hydrolysis energy for DNA translocation. TerL's N-terminal ATPase is connected by a hinge to the C-terminal endonuclease. Inchworm models propose that modest domain motions accompanying ATP hydrolysis are amplified, through changes in electrostatic interactions, into larger movements of the C-terminal domain bound to DNA. In phage ϕ29, four of the five TerL subunits sequentially hydrolyze ATP, each powering translocation of 2.5 bp. After one viral genome is encapsidated, the internal pressure signals termination of packaging and ejection of the motor. Current focus is on the structures of packaging complexes and the dynamics of TerL during DNA packaging, endonuclease regulation, and motor mechanics.
Topics: DNA Packaging; DNA Viruses; DNA, Viral; Viral Proteins; Virus Assembly
PubMed: 26958920
DOI: 10.1146/annurev-virology-100114-055212 -
Viruses Jan 2024In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive... (Review)
Review
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.
Topics: DNA, Viral; Bacteriophage T4; Fluorescence; Virus Assembly; DNA Packaging; Endodeoxyribonucleases
PubMed: 38399968
DOI: 10.3390/v16020192 -
Nature Reviews. Microbiology Aug 2011Tailed bacteriophages use nanomotors, or molecular machines that convert chemical energy into physical movement of molecules, to insert their double-stranded DNA genomes... (Review)
Review
Tailed bacteriophages use nanomotors, or molecular machines that convert chemical energy into physical movement of molecules, to insert their double-stranded DNA genomes into virus particles. These viral nanomotors are powered by ATP hydrolysis and pump the DNA into a preformed protein container called a procapsid. As a result, the virions contain very highly compacted chromosomes. Here, I review recent progress in obtaining structural information for virions, procapsids and the individual motor protein components, and discuss single-molecule in vitro packaging reactions, which have yielded important new information about the mechanism by which these powerful molecular machines translocate DNA.
Topics: Adenosine Triphosphate; Bacteriophages; Capsid; Cryoelectron Microscopy; DNA Packaging; DNA, Viral; Molecular Motor Proteins
PubMed: 21836625
DOI: 10.1038/nrmicro2632 -
Journal of Virology Nov 2019We present the genome sequences of tailed phages Sasha, Sergei, and Solent. These phages, along with phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly...
We present the genome sequences of tailed phages Sasha, Sergei, and Solent. These phages, along with phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. We show that it uses a site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. We also show that its packaging series initiates with double-stranded DNA cleavages that are scattered across a 170-bp region and that its headful measuring device has a precision of ±1.8%. The 9NA-like phages are clearly highly related to each other but are not closely related to any other known phage type. This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head. There is increasing interest in the biology of phages because of their potential for use as antibacterial agents and for their ecological roles in bacterial communities. 9NA-like phages that infect two bacterial genera have been identified to date, and related phages infecting additional Gram-negative bacterial hosts are likely to be found in the future. This work provides a foundation for the study of these phages, which will facilitate their study and potential use.
Topics: DNA Packaging; DNA Replication; DNA, Viral; Genome; Genome, Viral; Genomics; Phylogeny; Salmonella; Salmonella Phages; Siphoviridae; Viral Proteins; Virion
PubMed: 31462565
DOI: 10.1128/JVI.00848-19 -
Current Opinion in Virology Jun 2019During the assembly of dsDNA viruses such as the tailed bacteriophages and herpesviruses, the viral chromosome is compacted to near crystalline density inside a... (Review)
Review
During the assembly of dsDNA viruses such as the tailed bacteriophages and herpesviruses, the viral chromosome is compacted to near crystalline density inside a preformed head shell. DNA translocation is driven by powerful ring ATPase motors that couple ATP binding, hydrolysis, and release to force generation and movement. Studies of the motor of the bacteriophage phi29 have revealed a complex mechanochemistry behind this process that slows as the head fills. Recent studies of the physical behavior of packaging DNA suggest that surprisingly long-time scales of relaxation of DNA inside the head and jamming phenomena during packaging create the physical need for regulation of the rate of packaging. Studies of DNA packaging in viral systems have, therefore, revealed fundamental insight into the complex behavior of DNA and the need for biological systems to accommodate these physical constraints.
Topics: Adenosine Triphosphate; Bacteriophages; DNA Packaging; DNA, Viral; Models, Molecular; Translocation, Genetic; Viral Proteins; Virus Assembly; Viruses
PubMed: 31003199
DOI: 10.1016/j.coviro.2019.03.002