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1.
J Virol ; 94(17)2020 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-32522855

RESUMO

The human adenovirus (HAdV) protein IX (pIX) is a minor component of the capsid that acts in part to stabilize the hexon-hexon interactions within the mature capsid. Virions lacking pIX have a reduced DNA packaging capacity and exhibit thermal instability. More recently, pIX has been developed as a platform for presentation of large polypeptides, such as fluorescent proteins or large targeting ligands, on the viral capsid. It is not known whether such modifications affect the natural ability of pIX to stabilize the HAdV virion. In this study, we show that addition of large polypeptides to pIX does not alter the natural stability of virions containing sub-wild-type-sized genomes. However, similar virions containing wild-type-sized genomes tend to genetically rearrange, likely due to selective pressure caused by virion instability as a result of compromised pIX function.IMPORTANCE Human adenovirus capsid protein IX (pIX) is involved in stabilizing the virion but has also been developed as a platform for presentation of various polypeptides on the surface of the virion. Whether such modifications affect the ability of pIX to stabilize the virion is unknown. We show that addition of large polypeptides to pIX can reduce both the DNA packaging capacity and the heat stability of the virion, which provides important guidance for the design of pIX-modified vectors.


Assuntos
Adenovírus Humanos/genética , Adenovírus Humanos/fisiologia , Proteínas do Capsídeo/metabolismo , Capsídeo/metabolismo , Empacotamento do DNA/fisiologia , Peptídeos/metabolismo , Vírion/metabolismo , Proteínas do Capsídeo/genética , Linhagem Celular , DNA Viral , Vetores Genéticos , Genoma Viral , Humanos , Ligantes , Vírion/genética
2.
PLoS Pathog ; 15(12): e1008175, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31809525

RESUMO

A key step in replication of human cytomegalovirus (HCMV) in the host cell is the generation and packaging of unit-length genomes into preformed capsids. The enzymes involved in this process are the terminases. The HCMV terminase complex consists of two terminase subunits, the ATPase pUL56 and the nuclease pUL89. A potential third component pUL51 has been proposed. Even though the terminase subunit pUL89 has been shown to be essential for DNA packaging and interaction with pUL56, it is not known how pUL89 mechanistically achieves sequence-specific DNA binding and nicking. To identify essential domains and invariant amino acids vis-a-vis nuclease activity and DNA binding, alanine substitutions of predicted motifs were analyzed. The analyses indicated that aspartate 463 is an invariant amino acid for the nuclease activity, while argine 544 is an invariant aa for DNA binding. Structural analysis of recombinant protein using electron microscopy in conjunction with single particle analysis revealed a curvilinear monomer with two distinct domains connected by a thinner hinge-like region that agrees well with the predicted structure. These results allow us to model how the terminase subunit pUL89's structure may mediate its function.


Assuntos
Citomegalovirus/química , Empacotamento do DNA/fisiologia , Proteínas Virais/química , Citomegalovirus/genética , Conformação Proteica , Relação Estrutura-Atividade , Proteínas Virais/genética
3.
Proc Natl Acad Sci U S A ; 115(50): E11614-E11622, 2018 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-30487222

RESUMO

The Gam protein of transposable phage Mu is an ortholog of eukaryotic and bacterial Ku proteins, which carry out nonhomologous DNA end joining (NHEJ) with the help of dedicated ATP-dependent ligases. Many bacteria carry Gam homologs associated with either complete or defective Mu-like prophages, but the role of Gam in the life cycle of Mu or in bacteria is unknown. Here, we show that MuGam is part of a two-component bacterial NHEJ DNA repair system. Ensemble and single-molecule experiments reveal that MuGam binds to DNA ends, slows the progress of RecBCD exonuclease, promotes binding of NAD+-dependent Escherichia coli ligase A, and stimulates ligation. In vivo, Gam equally promotes both precise and imprecise joining of restriction enzyme-digested linear plasmid DNA, as well as of a double-strand break (DSB) at an engineered I-SceI site in the chromosome. Cell survival after the induced DSB is specific to the stationary phase. In long-term growth competition experiments, particularly upon treatment with a clastogen, the presence of gam in a Mu lysogen confers a distinct fitness advantage. We also show that the role of Gam in the life of phage Mu is related not to transposition but to protection of genomic Mu copies from RecBCD when viral DNA packaging begins. Taken together, our data show that MuGam provides bacteria with an NHEJ system and suggest that the resulting fitness advantage is a reason that bacteria continue to retain the gam gene in the absence of an intact prophage.


Assuntos
Bacteriófago mu/metabolismo , Reparo do DNA por Junção de Extremidades/fisiologia , DNA Ligases/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Proteínas Virais/metabolismo , Bacteriófago mu/genética , Bacteriófago mu/crescimento & desenvolvimento , DNA Ligases/química , Empacotamento do DNA/fisiologia , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Proteínas de Ligação a DNA/química , Escherichia coli/genética , Proteínas de Escherichia coli/química , Exodesoxirribonuclease V/metabolismo , Cinética , Modelos Biológicos , Modelos Moleculares , Estrutura Quaternária de Proteína , Homologia Estrutural de Proteína , Proteínas Virais/química
4.
J Virol ; 93(22)2019 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-31462565

RESUMO

We present the genome sequences of Salmonella enterica tailed phages Sasha, Sergei, and Solent. These phages, along with Salmonella phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related Proteus 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 Siphoviridae 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 pac 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%.IMPORTANCE 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.


Assuntos
Empacotamento do DNA/genética , Fagos de Salmonella/genética , Salmonella/virologia , Empacotamento do DNA/fisiologia , Replicação do DNA , DNA Viral/genética , Genoma/genética , Genoma Viral/genética , Genômica/métodos , Filogenia , Salmonella/genética , Salmonella/metabolismo , Siphoviridae/genética , Siphoviridae/metabolismo , Proteínas Virais/genética , Vírion/genética
5.
Angew Chem Int Ed Engl ; 57(7): 1748-1756, 2018 02 12.
Artigo em Inglês | MEDLINE | ID: mdl-29078032

RESUMO

Rapid technological advances enabling the construction of designer gene networks, biosynthetic pathways, and even entire genomes are moving the fields of genetics and genomics from descriptive to synthetic applications. Following the synthesis of small viral genomes, advances in DNA assembly and rewriting have enabled the hierarchical synthesis of bacterial genomes, such as Mycoplasma genitalium, as well as recoding of the Escherichia coli genome by reducing the number of codons from 64 to 57. The field has advanced to the point of synthesizing an entire eukaryotic genome. The Synthetic Yeast Genome Project (Sc2.0) is underway and aims to rewrite all 16 Saccharomyces cerevisiae chromosomes by 2018; to date, 6.5 chromosomes have been designed and synthesized. Using bottom-up assembly and applying genome-wide alterations will improve our understanding of genome structure and function. This approach will not only provide a platform for systematic studies of eukaryotic chromosomes but will also generate diverse "streamlined" strains that are potentially suitable for medical and industrial applications. Herein, we review the current state of synthetic genome research and discuss potential applications of this emerging technology.


Assuntos
DNA/síntese química , Genes Sintéticos , Genômica , Bacteriófagos/genética , DNA/metabolismo , Empacotamento do DNA/fisiologia , Genoma Bacteriano , Genoma Fúngico , Genoma Viral , Mycobacterium/genética , Saccharomyces cerevisiae/genética
6.
J Virol ; 89(20): 10569-79, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26269173

RESUMO

UNLABELLED: Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as "molecular staples" at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging. IMPORTANCE: Many dsDNA viruses have morphogenic pathways utilizing an intermediate capsid, known as a procapsid. These procapsids are assembled from a coat protein having the HK97 fold in a reaction driven by scaffolding proteins or delta domains. Maturation of the capsid occurs during DNA packaging. Bacteriophage HK97 uniquely stabilizes its capsid during maturation by intercapsomer cross-linking, but most virus capsids are stabilized by alternate means. Here we show that the I domain that is inserted into the coat protein of bacteriophage P22 is important in the process of proper procapsid assembly. Specifically, the I domain allows for stabilizing interactions across the capsid 2-fold axis of symmetry via a D-loop. When amino acid residues at the tip of the D-loop are mutated, aberrant assembly products, including tubes, are formed instead of procapsids, consequently phage production is affected, indicating the importance of stabilizing interactions during the assembly and maturation reactions.


Assuntos
Bacteriófago P22/química , Proteínas do Capsídeo/química , Capsídeo/química , DNA Viral/química , Vírion/química , Montagem de Vírus/fisiologia , Bacteriófago P22/genética , Bacteriófago P22/metabolismo , Capsídeo/metabolismo , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/metabolismo , Reagentes de Ligações Cruzadas/química , DNA/química , DNA/metabolismo , Empacotamento do DNA/fisiologia , DNA Viral/metabolismo , Expressão Gênica , Modelos Moleculares , Fenantrolinas/química , Dobramento de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Salmonella typhimurium/virologia , Vírion/genética , Vírion/metabolismo
7.
Biophys J ; 109(8): 1663-75, 2015 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-26488657

RESUMO

Viral terminase enzymes serve as genome packaging motors in many complex double-stranded DNA viruses. The functional motors are multiprotein complexes that translocate viral DNA into a capsid shell, powered by a packaging ATPase, and are among the most powerful molecular motors in nature. Given their essential role in virus development, the structure and function of these biological motors is of considerable interest. Bacteriophage λ-terminase, which serves as a prototypical genome packaging motor, is composed of one large catalytic subunit tightly associated with two DNA recognition subunits. This protomer assembles into a functional higher-order complex that excises a unit length genome from a concatemeric DNA precursor (genome maturation) and concomitantly translocates the duplex into a preformed procapsid shell (genome packaging). While the enzymology of λ-terminase has been well described, the nature of the catalytically competent nucleoprotein intermediates, and the mechanism describing their assembly and activation, is less clear. Here we utilize analytical ultracentrifugation to determine the thermodynamic parameters describing motor assembly and define a minimal thermodynamic linkage model that describes the effects of salt on protomer assembly into a tetrameric complex. Negative stain electron microscopy images reveal a symmetric ring-like complex with a compact stem and four extended arms that exhibit a range of conformational states. Finally, kinetic studies demonstrate that assembly of the ring tetramer is directly linked to activation of the packaging ATPase activity of the motor, thus providing a direct link between structure and function. The implications of these results with respect to the assembly and activation of the functional packaging motor during a productive viral infection are discussed.


Assuntos
Empacotamento do DNA , DNA Viral , Termodinâmica , Adenosina Trifosfatases/metabolismo , Bacteriófagos/enzimologia , Empacotamento do DNA/fisiologia , DNA Viral/metabolismo , Endodesoxirribonucleases/metabolismo , Microscopia Eletrônica , Modelos Biológicos , Conformação de Ácido Nucleico , Cloreto de Sódio/metabolismo
8.
Proc Natl Acad Sci U S A ; 109(49): 20000-5, 2012 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-23169641

RESUMO

Tailed bacteriophages and herpes viruses use powerful ATP-driven molecular motors to translocate their viral genomes into a preformed capsid shell. The bacteriophage T4 motor, a pentamer of the large terminase protein (gp17) assembled at the portal vertex of the prohead, is the fastest and most powerful known, consistent with the need to package a ~170-kb viral genome in approximately 5 min. Although much is known about the mechanism of DNA translocation, very little is known about how ATP modulates motor-DNA interactions. Here, we report single-molecule measurements of the phage T4 gp17 motor by using dual-trap optical tweezers under different conditions of perturbation. Unexpectedly, the motor pauses randomly when ATP is limiting, for an average of 1 s, and then resumes translocation. During pausing, DNA is unpackaged, a phenomenon so far observed only in T4, where some of the packaged DNA is slowly released. We propose that the motor pauses whenever it encounters a subunit in the apo state with the DNA bound weakly and incorrectly. Pausing allows the subunit to capture ATP, whereas unpackaging allows scanning of DNA until a correct registry is established. Thus, the "pause-unpackaging" state is an off-translocation recovery state wherein the motor, sometimes by taking a few steps backward, can bypass the impediments encountered along the translocation path. These results lead to a four-state mechanochemical model that provides insights into the mechanisms of translocation of an intricately branched concatemeric viral genome.


Assuntos
Bacteriófago T4/fisiologia , Empacotamento do DNA/fisiologia , Modelos Biológicos , Proteínas Motores Moleculares/metabolismo , Proteínas Virais/metabolismo , Montagem de Vírus/fisiologia , Trifosfato de Adenosina/metabolismo , Cinética , Simulação de Dinâmica Molecular , Pinças Ópticas
9.
Proc Natl Acad Sci U S A ; 109(50): 20419-24, 2012 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-23185020

RESUMO

Viral genome packaging into capsids is powered by high-force-generating motor proteins. In the presence of all packaging components, ATP-powered translocation in vitro expels all detectable tightly bound YOYO-1 dye from packaged short dsDNA substrates and removes all aminoacridine dye from packaged genomic DNA in vivo. In contrast, in the absence of packaging, the purified T4 packaging ATPase alone can only remove up to ∼1/3 of DNA-bound intercalating YOYO-1 dye molecules in the presence of ATP or ATP-γ-S. In sufficient concentration, intercalating dyes arrest packaging, but rare terminase mutations confer resistance. These distant mutations are highly interdependent in acquiring function and resistance and likely mark motor contact points with the translocating DNA. In stalled Y-DNAs, FRET has shown a decrease in distance from the phage T4 terminase C terminus to portal consistent with a linear motor, and in the Y-stem DNA compression between closely positioned dye pairs. Taken together with prior FRET studies of conformational changes in stalled Y-DNAs, removal of intercalating compounds by the packaging motor demonstrates conformational change in DNA during normal translocation at low packaging resistance and supports a proposed linear "DNA crunching" or torsional compression motor mechanism involving a transient grip-and-release structural change in B form DNA.


Assuntos
Empacotamento do DNA/fisiologia , DNA Viral/metabolismo , Montagem de Vírus/fisiologia , Trifosfato de Adenosina/metabolismo , Bacteriófago T4/genética , Bacteriófago T4/metabolismo , Benzoxazóis , Sítios de Ligação , DNA Viral/química , Endodesoxirribonucleases/genética , Endodesoxirribonucleases/metabolismo , Transferência Ressonante de Energia de Fluorescência , Corantes Fluorescentes , Genes Virais , Substâncias Intercalantes , Modelos Moleculares , Proteínas Motores Moleculares/metabolismo , Mutagênese Sítio-Dirigida , Mutação , Conformação de Ácido Nucleico , Compostos de Quinolínio , Especificidade por Substrato
10.
Biochemistry ; 53(48): 7459-70, 2014 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-25335823

RESUMO

Integration host factor (IHF) is an Escherichia coli protein involved in (i) condensation of the bacterial nucleoid and (ii) regulation of a variety of cellular functions. In its regulatory role, IHF binds to a specific sequence to introduce a strong bend into the DNA; this provides a duplex architecture conducive to the assembly of site-specific nucleoprotein complexes. Alternatively, the protein can bind in a sequence-independent manner that weakly bends and wraps the duplex to promote nucleoid formation. IHF is also required for the development of several viruses, including bacteriophage lambda, where it promotes site-specific assembly of a genome packaging motor required for lytic development. Multiple IHF consensus sequences have been identified within the packaging initiation site (cos), and we here interrogate IHF-cos binding interactions using complementary electrophoretic mobility shift (EMS) and analytical ultracentrifugation (AUC) approaches. IHF recognizes a single consensus sequence within cos (I1) to afford a strongly bent nucleoprotein complex. In contrast, IHF binds weakly but with positive cooperativity to nonspecific DNA to afford an ensemble of complexes with increasing masses and levels of condensation. Global analysis of the EMS and AUC data provides constrained thermodynamic binding constants and nearest neighbor cooperativity factors for binding of IHF to I1 and to nonspecific DNA substrates. At elevated IHF concentrations, the nucleoprotein complexes undergo a transition from a condensed to an extended rodlike conformation; specific binding of IHF to I1 imparts a significant energy barrier to the transition. The results provide insight into how IHF can assemble specific regulatory complexes in the background of extensive nonspecific DNA condensation.


Assuntos
Bacteriófago lambda/genética , Bacteriófago lambda/fisiologia , Empacotamento do DNA/fisiologia , Fatores Hospedeiros de Integração/fisiologia , Montagem de Vírus/fisiologia , DNA Viral/química , DNA Viral/fisiologia , Ensaio de Desvio de Mobilidade Eletroforética , Escherichia coli/genética , Escherichia coli/virologia , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos , Genoma Viral , Fatores Hospedeiros de Integração/química , Modelos Moleculares , Conformação de Ácido Nucleico , Nucleoproteínas/química , Nucleoproteínas/fisiologia , Conformação Proteica , Termodinâmica
11.
Exp Cell Res ; 318(12): 1448-55, 2012 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-22394510

RESUMO

Despite over 30 years of work, the fundamental structure of eukaryotic chromatin remains controversial. Here, we review the roots of this controversy in disparities between results derived from studies of chromatin in nuclei, chromatin isolated from nuclei, and chromatin reconstituted from defined components. Thanks to recent advances in imaging, modeling, and other approaches, it is now possible to recognize some unifying principles driving chromatin architecture at the level of the ubiquitous '30 nm' chromatin fiber. These suggest that fiber architecture involves both zigzag and bent linker motifs, and that such heteromorphic structures facilitate the observed high packing ratios. Interactions between neighboring fibers in highly compact chromatin lead to extensive interdigitation of nucleosomes and the inability to resolve individual fibers in compact chromatin in situ.


Assuntos
Montagem e Desmontagem da Cromatina/fisiologia , Cromatina/química , DNA/química , Conformação de Ácido Nucleico , Animais , Núcleo Celular/metabolismo , Cromatina/metabolismo , Cromatina/ultraestrutura , DNA/metabolismo , Empacotamento do DNA/genética , Empacotamento do DNA/fisiologia , Humanos , Modelos Biológicos , Modelos Moleculares
12.
Exp Cell Res ; 318(12): 1435-41, 2012 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-22475678

RESUMO

Work from several laboratories over the past 10-15 years has revealed that, within the interphase nucleus, chromosomes are organized into spatially distinct territories [T. Cremer, C. Cremer, Chromosome territories, nuclear architecture and gene regulation in mammalian cells, Nat. Rev. Genet. 2 (2001) 292-301 and T. Cremer, M. Cremer, S. Dietzel, S. Muller, I. Solovei, S. Fakan, Chromosome territories-a functional nuclear landscape, Curr. Opin. Cell Biol. 18 (2006) 307-316]. The overall compaction level and intranuclear location varies as a function of gene density for both entire chromosomes [J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague,W.A. Bickmore, Differences in the localization and morphology of chromosomes in the human nucleus, J. Cell Biol. 145 (1999) 1119-1131] and specific chromosomal regions [N.L. Mahy, P.E. Perry, S. Gilchrist, R.A. Baldock, W.A. Bickmore, Spatial organization of active and inactive genes and noncoding DNA within chromosome territories, J. Cell Biol. 157 (2002) 579-589] (Fig. 1A, A'). In prophase, when cyclin B activity reaches a high threshold, chromosome condensation occurs followed by Nuclear Envelope Breakdown (NEB) [1]. At this point vertebrate chromosomes appear as compact structures harboring an attachment point for the spindle microtubules physically recognizable as a primary constriction where the two sister chromatids are held together. The transition from an unshaped interphase chromosome to the highly structured mitotic chromosome (compare Figs. 1A and B) has fascinated researchers for several decades now; however a definite picture of how this process is achieved and regulated is not yet in our hands and it will require more investigation to comprehend the complete process. From a biochemical point of view a vertebrate mitotic chromosomes is composed of DNA, histone proteins (60%) and non-histone proteins (40%) [6]. I will discuss below what is known to date on the contribution of these two different classes of proteins and their co-operation in establishing the final mitotic chromosome structure.


Assuntos
Montagem e Desmontagem da Cromatina/fisiologia , Cromossomos/metabolismo , Empacotamento do DNA/fisiologia , Mitose/genética , Vertebrados/genética , Animais , Núcleo Celular/genética , Núcleo Celular/metabolismo , Montagem e Desmontagem da Cromatina/genética , Segregação de Cromossomos/genética , Segregação de Cromossomos/fisiologia , Cromossomos/genética , Empacotamento do DNA/genética , Humanos , Modelos Biológicos , Vertebrados/metabolismo
13.
Electrophoresis ; 33(2): 352-65, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22222979

RESUMO

We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (i) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for the stabilization of structure and then (ii) determining effective radius by two-dimensional agarose gel electrophoresis (2D-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase the production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2D-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when the ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging.


Assuntos
Bacteriófago T3/química , Capsídeo/química , Empacotamento do DNA/fisiologia , Eletroforese em Gel de Ágar/métodos , Eletroforese em Gel Bidimensional/métodos , Bacteriófago T3/genética , Reagentes de Ligações Cruzadas/farmacologia , Empacotamento do DNA/efeitos dos fármacos , DNA Viral/química , Glutaral/farmacologia , Tamanho da Partícula , Cloreto de Sódio/farmacologia
14.
Biochemistry ; 50(7): 1125-7, 2011 Feb 22.
Artigo em Inglês | MEDLINE | ID: mdl-21241050

RESUMO

Here we explore the use of ethidium to determine relative affinities of different gene delivery vectors for DNA and describe an improved method for studying the interaction. Specifically, we investigate the binding of poly(amidoamine) dendrimers and show that the DNA-dendrimer-ethidium system is far from thermodynamic equilibrium. Moreover, dendrimer surface modification through PEGylation appears to make the interaction with DNA more reversible, which is favorable from the perspective of vector unpacking. Probing the nonequilibrium state of DNA during condensation processes is thus important for developing novel vectors, and further, it could also be useful in the study of chromatin folding.


Assuntos
DNA/metabolismo , Etídio/farmacologia , Técnicas de Transferência de Genes , Coloração e Rotulagem/métodos , DNA/análise , Empacotamento do DNA/efeitos dos fármacos , Empacotamento do DNA/fisiologia , Vetores Genéticos/metabolismo , Cinética , Modelos Biológicos , Modelos Moleculares , Modelos Teóricos , Conformação de Ácido Nucleico/efeitos dos fármacos , Titulometria/métodos
15.
Cell Rep ; 37(8): 110000, 2021 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-34818548

RESUMO

In human cells, generally a single mitochondrial DNA (mtDNA) is compacted into a nucleoprotein complex denoted the nucleoid. Each cell contains hundreds of nucleoids, which tend to cluster into small groups. It is unknown whether all nucleoids are equally involved in mtDNA replication and transcription or whether distinct nucleoid subpopulations exist. Here, we use multi-color STED super-resolution microscopy to determine the activity of individual nucleoids in primary human cells. We demonstrate that only a minority of all nucleoids are active. Active nucleoids are physically larger and tend to be involved in both replication and transcription. Inactivity correlates with a high ratio of the mitochondrial transcription factor A (TFAM) to the mtDNA of the individual nucleoid, suggesting that TFAM-induced nucleoid compaction regulates nucleoid replication and transcription activity in vivo. We propose that the stable population of highly compacted inactive nucleoids represents a storage pool of mtDNAs with a lower mutational load.


Assuntos
Replicação do DNA/fisiologia , DNA Mitocondrial/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteínas Mitocondriais/metabolismo , Fatores de Transcrição/metabolismo , Linhagem Celular , Empacotamento do DNA/fisiologia , Replicação do DNA/genética , DNA Mitocondrial/genética , Proteínas de Ligação a DNA/genética , Fibroblastos , Humanos , Microscopia/métodos , Mitocôndrias/metabolismo , Proteínas Mitocondriais/genética , Mutação , Nucleoproteínas/metabolismo , Fatores de Transcrição/genética
16.
Nat Commun ; 12(1): 6548, 2021 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-34772936

RESUMO

Multi-subunit ring-ATPases carry out a myriad of biological functions, including genome packaging in viruses. Though the basic structures and functions of these motors have been well-established, the mechanisms of ATPase firing and motor coordination are poorly understood. Here, using single-molecule fluorescence, we determine that the active bacteriophage T4 DNA packaging motor consists of five subunits of gp17. By systematically doping motors with an ATPase-defective subunit and selecting single motors containing a precise number of active or inactive subunits, we find that the packaging motor can tolerate an inactive subunit. However, motors containing one or more inactive subunits exhibit fewer DNA engagements, a higher failure rate in encapsidation, reduced packaging velocity, and increased pausing. These findings suggest a DNA packaging model in which the motor, by re-adjusting its grip on DNA, can skip an inactive subunit and resume DNA translocation, suggesting that strict coordination amongst motor subunits of packaging motors is not crucial for function.


Assuntos
Adenosina Trifosfatases/metabolismo , Empacotamento do Genoma Viral/fisiologia , Adenosina Trifosfatases/genética , Bacteriófago T4/genética , Bacteriófago T4/metabolismo , Empacotamento do DNA/genética , Empacotamento do DNA/fisiologia , DNA Viral/genética , Empacotamento do Genoma Viral/genética , Proteínas Virais/genética , Proteínas Virais/metabolismo , Montagem de Vírus/genética , Montagem de Vírus/fisiologia
17.
Biol Reprod ; 82(4): 769-77, 2010 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-20018907

RESUMO

Early preimplantation embryos are sensitive to external osmolarity and use novel mechanisms to accumulate organic osmolytes and thus control their cell volumes and maintain viability. However, these mechanisms are restricted to the cleavage stages of development, and it was unknown whether postcompaction embryos use organic osmolytes. Mouse embryos developing from the 8-cell stage formed blastocoel cavities in vitro at osmolarities up to 360 mOsM. Above this range, several putative organic osmolytes (alanine, glutamine, glycine, and beta-alanine) rescued blastocyst development, but several effective osmoprotectants in cleavage-stage embryos (such as betaine and proline) did not. At physiological osmolarities, each of these compounds resulted in significantly larger blastocysts. This was not due to increased cell numbers, which were unaffected in blastocysts by osmolarity in the range where blastocyst size was rescued by potential organic osmolytes, although cell number was decreased at higher osmolarities and was rescued by each osmolyte. The effective osmolytes were accumulated intracellularly by embryos developing in vitro from the 8-cell stage to blastocysts. However, unlike conventional organic osmolytes in somatic cells or those in cleavage-stage embryos, their intracellular concentrations were not increased with increasing external osmolarity. With the exception of beta-alanine, which is taken up via the beta-amino acid transport system, the effective osmolytes were transported by the B(0,+) system, which becomes highly active in blastocysts. The intracellular accumulation of these osmolytes in postcompaction embryos thus appears to support optimal development and blastocyst expansion at physiological osmolarities and may contribute to the embryo's ability to withstand stress.


Assuntos
Aminoácidos/farmacologia , Fase de Clivagem do Zigoto/efeitos dos fármacos , Desenvolvimento Embrionário/efeitos dos fármacos , Soluções Hipertônicas/efeitos adversos , Equilíbrio Hidroeletrolítico/efeitos dos fármacos , Alanina/farmacologia , Sistemas de Transporte de Aminoácidos/agonistas , Sistemas de Transporte de Aminoácidos/metabolismo , Animais , Células Cultivadas , Fase de Clivagem do Zigoto/fisiologia , Empacotamento do DNA/fisiologia , Relação Dose-Resposta a Droga , Técnicas de Cultura Embrionária , Feminino , Glutamina/farmacologia , Glicina/farmacologia , Soluções Hipertônicas/farmacologia , Camundongos , Compostos Orgânicos/farmacologia , Concentração Osmolar , Especificidade por Substrato , Equilíbrio Hidroeletrolítico/fisiologia , beta-Alanina/farmacologia
18.
Curr Opin Struct Biol ; 17(2): 237-43, 2007 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-17395453

RESUMO

Several symmetric and asymmetric reconstructions of bacteriophage particles have recently been determined using electron cryo-microscopy and image reconstruction, and X-ray crystal structures of phage particles and particle-associated gene products have also been solved. In the past two years, the asymmetric structures of four different phages, T7, epsilon15, P22 and phi29, were determined at resolutions sufficient to visualize details of the machinery for DNA packaging and delivery, as well as the organization of the double-stranded DNA within the particles. Invariably, the portals, through which DNA enters and leaves the particle, have 12-fold symmetry, occupy a pentavalent site in the capsid and, along with tail machine accessory proteins attached to it, are fixed in a specific orientation relative to the rest of the capsid.


Assuntos
Bacteriófagos/química , Bacteriófagos/fisiologia , Empacotamento do DNA/fisiologia , Fagos Bacilares/química , Fagos Bacilares/fisiologia , Fagos Bacilares/ultraestrutura , Bacteriófago P22/química , Bacteriófago P22/fisiologia , Bacteriófago P22/ultraestrutura , Bacteriófago T4/química , Bacteriófago T4/fisiologia , Bacteriófago T4/ultraestrutura , Bacteriófago T7/química , Bacteriófago T7/fisiologia , Bacteriófago T7/ultraestrutura , Bacteriófagos/ultraestrutura , Microscopia Crioeletrônica , Cristalografia por Raios X , DNA Viral/química , Imageamento Tridimensional , Modelos Moleculares , Montagem de Vírus
19.
J Virol ; 82(10): 5089-92, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18337584

RESUMO

The packaging of adenovirus (Ad) DNA into virions is dependent upon cis-acting sequences and trans-acting proteins. We studied the involvement of Ad packaging proteins in the serotype specificity of packaging. Both Ad5 and Ad17 IVa2 and L4-22K proteins complemented the growth of Ad5 IVa2 and L4-22K mutant viruses, respectively. In contrast, the Ad5 L1-52/55K protein complemented an Ad5 L1-52/55K mutant virus, but the Ad17 L1-52/55K protein did not. The analysis of chimeric proteins demonstrated that the N-terminal half of the Ad5 L1-52/55K protein mediated this function. Finally, we demonstrate that the L4-33K and L4-22K proteins have distinct functions during infection.


Assuntos
Adenoviridae/fisiologia , Empacotamento do DNA/fisiologia , Proteínas Virais/metabolismo , Adenoviridae/genética , Sequência de Aminoácidos , Células Cultivadas , Empacotamento do DNA/genética , Deleção de Genes , Teste de Complementação Genética , Humanos , Dados de Sequência Molecular , Alinhamento de Sequência , Especificidade por Substrato , Proteínas Virais/genética
20.
Reprod Fertil Dev ; 21(8): 952-63, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-19874719

RESUMO

A common theme in the evolution of sex chromosomes is the massive loss of genes on the sex-specific chromosome (Y or W), leading to a gene imbalance between males (XY) and females (XX) in a male heterogametic species, or between ZZ and ZW in a female heterogametic species. Different mechanisms have evolved to compensate for this difference in dosage of X-borne genes between sexes. In therian mammals, one of the X chromosomes is inactivated, whereas bird dosage compensation is partial and gene-specific. In therian mammals, hallmarks of the inactive X are monoallelic gene expression, late DNA replication and chromatin condensation. Platypuses have five pairs of X chromosomes in females and five X and five Y chromosomes in males. Gene expression analysis suggests a more bird-like partial and gene-specific dosage compensation mechanism. We investigated replication timing and chromosome condensation of three of the five X chromosomes in female platypus. Our data suggest asynchronous replication of X-specific regions on X(1), X(3) and X(5) but show significantly different condensation between homologues for X(3) only, and not for X(1) or X(5). We discuss these results in relation to recent gene expression analysis of X-linked genes, which together give us insights into possible mechanisms of dosage compensation in platypus.


Assuntos
Empacotamento do DNA/fisiologia , Período de Replicação do DNA/fisiologia , Ornitorrinco/genética , Cromossomo X/fisiologia , Animais , Células Cultivadas , Replicação do DNA/fisiologia , Mecanismo Genético de Compensação de Dose/fisiologia , Feminino , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Ornitorrinco/fisiologia , Cromossomo X/genética , Cromossomo X/metabolismo
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