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1.
Mol Cell ; 84(14): 2601-2617.e12, 2024 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-38925115

RESUMO

The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4)2 tetramers on DNA for replication-independent chromatin assembly. The molecular architecture of the HIRA/Hir complex and its mode of histone deposition have remained unknown. Here, we report the cryo-EM structure of the S. cerevisiae Hir complex with Asf1/H3/H4 at 2.9-6.8 Å resolution. We find that the Hir complex forms an arc-shaped dimer with a Hir1/Hir2/Hir3/Hpc2 stoichiometry of 2/4/2/4. The core of the complex containing two Hir1/Hir2/Hir2 trimers and N-terminal segments of Hir3 forms a central cavity containing two copies of Hpc2, with one engaged by Asf1/H3/H4, in a suitable position to accommodate a histone (H3/H4)2 tetramer, while the C-terminal segments of Hir3 harbor nucleic acid binding activity to wrap DNA around the Hpc2-assisted histone tetramer. The structure suggests a model for how the Hir/Asf1 complex promotes the formation of histone tetramers for their subsequent deposition onto DNA.


Assuntos
Proteínas de Ciclo Celular , Microscopia Crioeletrônica , Chaperonas de Histonas , Histonas , Ligação Proteica , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Histonas/metabolismo , Histonas/química , Histonas/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/ultraestrutura , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/genética , Chaperonas de Histonas/metabolismo , Chaperonas de Histonas/química , Chaperonas de Histonas/genética , Modelos Moleculares , Chaperonas Moleculares/metabolismo , Chaperonas Moleculares/química , Chaperonas Moleculares/genética , Multimerização Proteica , Sítios de Ligação , Fatores de Transcrição/metabolismo , Fatores de Transcrição/química , Fatores de Transcrição/genética , Domínios e Motivos de Interação entre Proteínas
2.
Mol Cell ; 83(4): 574-588.e11, 2023 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-36731470

RESUMO

Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.


Assuntos
RNA Polimerase II , Proteínas de Saccharomyces cerevisiae , RNA Polimerase II/metabolismo , Microscopia Crioeletrônica , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Regiões Promotoras Genéticas , Transcrição Gênica , Complexo Mediador/genética , Iniciação da Transcrição Genética
3.
Mol Cell ; 82(3): 660-676.e9, 2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-35051353

RESUMO

Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.


Assuntos
RNA Polimerase II/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimologia , Iniciação da Transcrição Genética , Microscopia Crioeletrônica , Regulação Fúngica da Expressão Gênica , Modelos Moleculares , Regiões Promotoras Genéticas , Conformação Proteica , RNA Polimerase II/genética , RNA Polimerase II/ultraestrutura , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/ultraestrutura , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/ultraestrutura , Relação Estrutura-Atividade , Fatores de Tempo , Elongação da Transcrição Genética , Fatores de Transcrição TFII/genética , Fatores de Transcrição TFII/metabolismo
4.
Nucleic Acids Res ; 2024 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-39287137

RESUMO

RNA polymerase II (pol II) initiates transcription from transcription start sites (TSSs) located ∼30-35 bp downstream of the TATA box in metazoans, whereas in the yeast Saccharomyces cerevisiae, pol II scans further downstream TSSs located ∼40-120 bp downstream of the TATA box. Previously, we found that removal of the kinase module TFIIK (Kin28-Ccl1-Tfb3) from TFIIH shifts the TSS in a yeast in vitro system upstream to the location observed in metazoans and that addition of recombinant Tfb3 back to TFIIH-ΔTFIIK restores the downstream TSS usage. Here, we report that this biochemical activity of yeast TFIIK in TSS scanning is attributable to the Tfb3 RING domain at the interface with pol II in the pre-initiation complex (PIC): especially, swapping Tfb3 Pro51-a residue conserved among all fungi-with Ala or Ser as in MAT1, the metazoan homolog of Tfb3, confers an upstream TSS shift in vitro in a similar manner to the removal of TFIIK. Yeast genetic analysis suggests that both Pro51 and Arg64 of Tfb3 are required to maintain the stability of the Tfb3-pol II interface in the PIC. Cryo-electron microscopy analysis of a yeast PIC lacking TFIIK reveals considerable variability in the orientation of TFIIH, which impairs TSS scanning after promoter opening.

5.
Cell ; 143(2): 275-87, 2010 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-20946985

RESUMO

Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. Here, we present the cryo-electron microscopic (cryo-EM) structure of filamentous actin (F-actin) in the presence of phosphate, with the visualization of some α-helical backbones and large side chains. A complete atomic model based on the EM map identified intermolecular interactions mediated by bound magnesium and phosphate ions. Comparison of the F-actin model with G-actin monomer crystal structures reveals a critical role for bending of the conserved proline-rich loop in triggering phosphate release following ATP hydrolysis. Crystal structures of G-actin show that mutations in this loop trap the catalytic site in two intermediate states of the ATPase cycle. The combined structural information allows us to propose a detailed molecular mechanism for the biochemical events, including actin polymerization and ATPase activation, critical for actin filament dynamics.


Assuntos
Actinas/química , Músculo Esquelético/química , Fosfatos/metabolismo , Actinas/ultraestrutura , Trifosfato de Adenosina/metabolismo , Animais , Microscopia Crioeletrônica , Cristalografia por Raios X , Modelos Moleculares , Músculo Esquelético/metabolismo , Coelhos
6.
BMC Vet Res ; 20(1): 381, 2024 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-39187880

RESUMO

Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis and causes a persistent infection that can leave cattle with no symptoms. Many countries have been able to successfully eradicate BLV through improved detection and management methods. However, with the increasing novel molecular detection methods there have been few efforts to standardize these results at global scale. This study aimed to determine the interlaboratory accuracy and agreement of 11 molecular tests in detecting BLV. Each qPCR/ddPCR method varied by target gene, primer design, DNA input and chemistries. DNA samples were extracted from blood of BLV-seropositive cattle and lyophilized to grant a better preservation during shipping to all participants around the globe. Twenty nine out of 44 samples were correctly identified by the 11 labs and all methods exhibited a diagnostic sensitivity between 74 and 100%. Agreement amongst different assays was linked to BLV copy numbers present in samples and the characteristics of each assay (i.e., BLV target sequence). Finally, the mean correlation value for all assays was within the range of strong correlation. This study highlights the importance of continuous need for standardization and harmonization amongst assays and the different participants. The results underscore the need of an international calibrator to estimate the efficiency (standard curve) of the different assays and improve quantitation accuracy. Additionally, this will inform future participants about the variability associated with emerging chemistries, methods, and technologies used to study BLV. Altogether, by improving tests performance worldwide it will positively aid in the eradication efforts.


Assuntos
Leucose Enzoótica Bovina , Vírus da Leucemia Bovina , Provírus , Vírus da Leucemia Bovina/isolamento & purificação , Vírus da Leucemia Bovina/genética , Animais , Bovinos , Leucose Enzoótica Bovina/diagnóstico , Leucose Enzoótica Bovina/virologia , Leucose Enzoótica Bovina/sangue , Provírus/genética , Provírus/isolamento & purificação , Reação em Cadeia da Polimerase/veterinária , Reação em Cadeia da Polimerase/métodos , Sensibilidade e Especificidade , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Reação em Cadeia da Polimerase em Tempo Real/métodos , DNA Viral/sangue
7.
J Phys Ther Sci ; 36(9): 530-536, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39239416

RESUMO

[Purpose] This study aimed to test whether a combination of specific postures and movements can increase trunk muscle activity in older adults. [Participants and Methods] Forty-six community-dwelling older adults (mean age: 83.9 ± 4.5 years) were living independently without the need for nursing care. The thicknesses of the external oblique, internal oblique, and transversus abdominis muscles were measured during the following three tasks: task I, natural sitting posture; task II, specific sitting posture to promote activity of the deep trunk muscles; and task III, task II plus a pushing down motion using both upper limbs. During each task, an ultrasound imaging device was used to measure the thicknesses of the external oblique, internal oblique, and transversus abdominis muscles on both the left and right sides according to the time required for expiration. [Results] Significant differences were found in the thicknesses of the internal oblique and transversus abdominis muscles between tasks II and III. Among the three muscles, the transversus abdominis showed the highest increase in thickness. [Conclusion] High activity of the trunk muscles, especially the transverse abdominis, can be achieved via specific sitting positions/tasks and further manipulations to increase the intra-abdominal pressure in both upper limbs.

8.
J Virol ; 96(17): e0094922, 2022 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-36037477

RESUMO

Epstein-Barr nuclear antigen 1 (EBNA1) is a multifunctional viral-encoded DNA-binding protein essential for Epstein-Barr virus (EBV) DNA replication and episome maintenance. EBNA1 binds to two functionally distinct elements at the viral origin of plasmid replication (oriP), termed the dyad symmetry (DS) element, required for replication initiation and the family of repeats (FR) required for episome maintenance. Here, we determined the cryo-electron microscopy (cryo-EM) structure of the EBNA1 DNA binding domain (DBD) from amino acids (aa) 459 to 614 and its interaction with two tandem sites at the DS and FR. We found that EBNA1 induces a strong DNA bending angle in the DS, while the FR is more linear. The N-terminal arm of the DBD (aa 444 to 468) makes extensive contact with DNA as it wraps around the minor groove, with some conformational variation among EBNA1 monomers. Mutation of variable-contact residues K460 and K461 had only minor effects on DNA binding but had abrogated oriP-dependent DNA replication. We also observed that the AT-rich intervening DNA between EBNA1 binding sites in the FR can be occupied by the EBNA1 AT hook, N-terminal domain (NTD) aa 1 to 90 to form a Zn-dependent stable complex with EBNA1 DBD on a 2×FR DNA template. We propose a model showing EBNA1 DBD and NTD cobinding at the FR and suggest that this may contribute to the oligomerization of viral episomes important for maintenance during latent infection. IMPORTANCE EBV latent infection is causally linked to diverse cancers and autoimmune disorders. EBNA1 is the viral-encoded DNA binding protein required for episomal maintenance during latent infection and is consistently expressed in all EBV tumors. The interaction of EBNA1 with different genetic elements confers different viral functions, such as replication initiation at DS and chromosome tethering at FR. Here, we used cryo-EM to determine the structure of the EBNA1 DNA-binding domain (DBD) bound to two tandem sites at the DS and at the FR. We also show that the NTD of EBNA1 can interact with the AT-rich DNA sequence between tandem EBNA1 DBD binding sites in the FR. These results provide new information on the mechanism of EBNA1 DNA binding at DS and FR and suggest a higher-order oligomeric structure of EBNA1 bound to FR. Our findings have implications for targeting EBNA1 in EBV-associated disease.


Assuntos
Antígenos Nucleares do Vírus Epstein-Barr/química , Herpesvirus Humano 4/química , Origem de Replicação , Sítios de Ligação , Microscopia Crioeletrônica , Replicação do DNA , Proteínas de Ligação a DNA/metabolismo , Infecções por Vírus Epstein-Barr , Antígenos Nucleares do Vírus Epstein-Barr/metabolismo , Antígenos Nucleares do Vírus Epstein-Barr/ultraestrutura , Herpesvirus Humano 4/metabolismo , Humanos , Infecção Latente , Plasmídeos , Replicação Viral
9.
Nature ; 544(7649): 196-201, 2017 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-28241144

RESUMO

The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.


Assuntos
Complexo Mediador/química , Complexo Mediador/metabolismo , RNA Polimerase II/química , RNA Polimerase II/ultraestrutura , Sítios de Ligação , Microscopia Crioeletrônica , Holoenzimas/química , Holoenzimas/metabolismo , Holoenzimas/ultraestrutura , Complexo Mediador/ultraestrutura , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , RNA Polimerase II/metabolismo , Schizosaccharomyces , Proteínas de Schizosaccharomyces pombe/química , Proteínas de Schizosaccharomyces pombe/metabolismo , Proteínas de Schizosaccharomyces pombe/ultraestrutura , Relação Estrutura-Atividade
10.
Mol Cell ; 59(1): 133-8, 2015 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-26073544

RESUMO

Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp downstream of the TATA box in metazoans, TSSs are located 40-120 bp downstream in S. cerevisiae. Promoter melting begins about 12 bp downstream in all eukaryotes, so Pol II is presumed to "scan" further downstream before starting transcription in yeast. Here we report that removal of the kinase complex TFIIK from TFIIH shifts the TSS in a yeast system upstream to the location observed in metazoans. Conversely, moving the normal TSS to an upstream location enables a high level of TFIIK-independent transcription in the yeast system. We distinguish two stages of the transcription initiation process: bubble formation by TFIIH, which fills the Pol II active center with single-stranded DNA, and subsequent scanning downstream, also driven by TFIIH, which requires displacement of the initial bubble. Omission of TFIIK uncouples the two stages of the process.


Assuntos
RNA Polimerase II/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Fator de Transcrição TFIIH/genética , Sítio de Iniciação de Transcrição/fisiologia , Sequência de Bases , Conformação de Ácido Nucleico , Regiões Promotoras Genéticas , Proteínas de Saccharomyces cerevisiae/metabolismo , Fator de Transcrição TFIIH/metabolismo , Transcrição Gênica/genética
11.
Retina ; 43(1): 34-41, 2023 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-36223764

RESUMO

PURPOSE: We aimed to assess choroidal vascularity by diabetic retinopathy (DR) stage using the choroidal vascular density (CVD) obtained from swept-source optical coherence tomography en-face images. METHODS: This prospective, cross-sectional, multicenter study included patients from Niigata City General Hospital and Saiseikai Niigata Hospital between October 2016 and October 2017. Choroidal vascular density was obtained by binarizing swept-source optical coherence tomography en-face images of patients with diabetes and those with DR, patients without DR, and healthy age-matched volunteers. RESULTS: Patients were allocated to the healthy control (n = 28), no DR (n = 23), nonproliferative DR (NPDR) without diabetic macular edema (DME) (n = 50), NPDR + DME (n = 38), and proliferative DR (PDR) or any previous treatment with panretinal photocoagulation (n = 26) groups. Investigation of the choriocapillaris slab level indicated that the no DR group had significantly high CVD values ( P < 0.05), and the PDR groups had significantly low CVD values ( P < 0.01). Investigation of the large choroidal vessel level indicated that the NPDR + DME and PDR groups had significantly lower CVD values than the control group ( P < 0.05 and P < 0.01, respectively). CONCLUSION: We found that at the choriocapillaris slab level, the no DR group had a higher CVD and the NPDR with DME and PDR groups had a lower CVD than the control group. At the level of the large choroidal vessels, the NPDR with DME and PDR groups had a lower CVD than the control group. There were significant differences in choroidal vasculature found using CVD obtained from swept-source optical coherence tomography en-face images of patients with diabetes and DR.


Assuntos
Diabetes Mellitus , Retinopatia Diabética , Edema Macular , Humanos , Retinopatia Diabética/complicações , Retinopatia Diabética/diagnóstico , Tomografia de Coerência Óptica/métodos , Estudos Transversais , Estudos Prospectivos , Densidade Microvascular , Corioide/irrigação sanguínea
12.
J Phys Ther Sci ; 35(1): 70-74, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36628139

RESUMO

[Purpose] This study aimed to investigate the prevalence of frailty among community-dwelling elderly females, and to examine its relation to motor function and the main risk factors of frailty. [Participants and Methods] The participants were 67 community-dwelling elderly females, aged 76.2 ± 7.7 years. We performed measurements of physical parameters, motor functions (such as grip strength), timed up and go test (TUG), walking speed, and frailty (measured using the Kihon Checklist [KCL]). [Results] KCL scores were 31.3%, 31.3%, and 37.3% in the frailty, pre-frailty, and robust groups, respectively. The frailty group was older than the pre-frailty and robust groups. Additionally, the different groups showed significant differences in grip strength, TUG, and walking speed. The highest median KCL score was for depression, followed by physical function. As a results, frailty was evident even among health-conscious elderly people. [Conclusion] It is essential to identify frailty at an early stage and identify its preventive factors, in order to extend the healthy life expectancy of the local population.

13.
Biochemistry ; 61(21): 2417-2430, 2022 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-36227241

RESUMO

Fusicoccadiene synthase from the fungus Phomopsis amygdali (PaFS) is an assembly-line terpene synthase that catalyzes the first two steps in the biosynthesis of Fusiccocin A, a diterpene glycoside. The C-terminal prenyltransferase domain of PaFS catalyzes the condensation of one molecule of C5 dimethylallyl diphosphate and three molecules of C5 isopentenyl diphosphate to form C20 geranylgeranyl diphosphate, which then transits to the cyclase domain for cyclization to form fusicoccadiene. Previous structural studies of PaFS using electron microscopy (EM) revealed a central octameric prenyltransferase core with eight cyclase domains tethered in random distal positions through flexible 70-residue linkers. However, proximal prenyltransferase-cyclase configurations could be captured by covalent cross-linking and observed by cryo-EM and mass spectrometry. Here, we use cryo-EM to show that proximally configured prenyltransferase-cyclase complexes are observable even in the absence of covalent cross-linking; moreover, such complexes can involve multiple cyclase domains. A conserved basic patch on the prenyltransferase domain comprises the primary touchpoint with the cyclase domain. These results support a model for transient prenyltransferase-cyclase association in which the cyclase domains of PaFS are in facile equilibrium between proximal associated and random distal positions relative to the central prenyltransferase octamer. The results of biophysical measurements using small-angle X-ray scattering, analytical ultracentrifugation, dynamic light scattering, and size-exclusion chromatography in-line with multi-angle light scattering are consistent with this model. This model accordingly provides a framework for understanding substrate transit between the prenyltransferase and cyclase domains as well as the cooperativity observed for geranylgeranyl diphosphate cyclization.


Assuntos
Alquil e Aril Transferases , Dimetilaliltranstransferase , Diterpenos , Diterpenos/química
14.
Proc Natl Acad Sci U S A ; 116(45): 22573-22582, 2019 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-31591205

RESUMO

After synthesis of a short nascent RNA, RNA polymerase II (pol II) dissociates general transcription factors (GTFs; TFIIA, TFIIB, TBP, TFIIE, TFIIF, and TFIIH) and escapes the promoter, but many of the mechanistic details of this process remain unclear. Here we developed an in vitro transcription system from the yeast Saccharomyces cerevisiae that allows conversion of the preinitiation complex (PIC) to bona fide initially transcribing complex (ITC), elongation complex (EC), and reinitiation complex (EC+ITC). By biochemically isolating postinitiation complexes stalled at different template positions, we have determined the timing of promoter escape and the composition of protein complexes associated with different lengths of RNA. Almost all of the postinitiation complexes retained the GTFs when pol II was stalled at position +27 relative to the transcription start site, whereas most complexes had completed promoter escape when stalled at +49. This indicates that GTFs remain associated with pol II much longer than previously expected. Nevertheless, the long-persisting transcription complex containing RNA and all of the GTFs is unstable and is susceptible to extensive backtracking of pol II. Addition of the capping enzyme and/or Spt4/5 significantly increased the frequency of promoter escape as well as assembly of a follow-on PIC at the promoter for reinitiation. These data indicate that elongation factors play an important role in promoter escape and that ejection of TFIIB from the RNA exit tunnel of pol II by the growing nascent RNA is not sufficient to complete promoter escape.


Assuntos
Regiões Promotoras Genéticas , RNA Polimerase II/metabolismo , Saccharomyces cerevisiae/genética , Transcrição Gênica , RNA Polimerase II/genética , RNA Fúngico/genética , RNA Fúngico/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Fatores de Elongação da Transcrição/genética , Fatores de Elongação da Transcrição/metabolismo
15.
Nature ; 525(7568): 274-7, 2015 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-26331540

RESUMO

Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.


Assuntos
RNA Polimerase II/química , RNA Polimerase II/metabolismo , Saccharomyces cerevisiae/enzimologia , Iniciação da Transcrição Genética , Pareamento de Bases/genética , DNA/genética , DNA/metabolismo , Pinças Ópticas , Regiões Promotoras Genéticas/genética , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , Saccharomyces cerevisiae/genética , Fator de Transcrição TFIIH/metabolismo
16.
Arch Virol ; 165(12): 2961-2966, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33037940

RESUMO

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL). We used microchip electrophoresis in combination with automatic image analysis to develop a novel high-throughput PCR-RFLP to type the gene sequences that encode BLV Tax 233. This method revealed that 233L-Tax is more prevalent than 233P-Tax in cattle in Japan. The proportion infected with BLV carrying the gene encoding 233L-Tax was significantly higher in Holstein cattle than in Japanese Black cattle. Holsteins infected with BLV encoding 233L-Tax had higher proviral loads than did Holsteins infected with BLV encoding 233P-Tax and Japanese Blacks infected with BLV encoding 233L-Tax or 233P-Tax. The novel method developed in this study will be a useful tool for identifying cattle harboring BLV with a higher risk of EBL and viral transmission.


Assuntos
Eletroforese em Microchip/instrumentação , Produtos do Gene tax/genética , Vírus da Leucemia Bovina/genética , Reação em Cadeia da Polimerase/métodos , Polimorfismo de Fragmento de Restrição , Animais , Bovinos , Leucose Enzoótica Bovina/virologia , Japão , Carga Viral
17.
Methods ; 159-160: 82-89, 2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30905750

RESUMO

Transcription initiation can be reconstituted from highly purified general transcription factors (GTFs), RNA polymerase II (pol II), and promoter DNA. However, earlier biochemical reconstitution systems had a serious technical limitation, namely very poor initiation efficiency. Due to the poor efficiency of the reaction and trace amounts of proteins involved in the pre-initiation complex (PIC) assembly, detection of transcription and PIC formation was only possible by the synthesis of a radiolabeled transcript and by immunoblotting for PIC components on templates. Here we describe a transcription system that is capable of initiating transcription with >90% efficiency of template usage using homogeneous, active yeast components including TFIIA, TFIIB, TBP, TFIIE, TFIIF, TFIIH, Sub1, and pol II. The abundant specifically assembled PICs on promoter DNA can be separated from free general transcription factors (GTFs) and pol II by density gradient sedimentation, irrespective of the length of promoter DNA. The system is robust, and can be modified to accommodate many other transcription factors, and the resulting complexes can be analyzed by SDS-PAGE followed by Coomassie Blue staining. This technical advance now paves the way to conduct definitive biochemical and structural studies of the complete process of pol II initiation from the PIC, through promoter escape, and finally to productive elongation.


Assuntos
Regiões Promotoras Genéticas , RNA Polimerase II/metabolismo , Fatores de Transcrição/metabolismo , Iniciação da Transcrição Genética , Complexos Multiproteicos , Proteínas de Saccharomyces cerevisiae/metabolismo , Fator de Transcrição TFIIA/metabolismo , Fator de Transcrição TFIIB/metabolismo , Fatores de Transcrição TFII/metabolismo , Leveduras/enzimologia , Leveduras/genética , Leveduras/metabolismo
18.
Proc Natl Acad Sci U S A ; 114(50): 13230-13235, 2017 12 12.
Artigo em Inglês | MEDLINE | ID: mdl-29180430

RESUMO

The DNA damage response is an essential process for the survival of living cells. In a subset of stress-responsive genes in humans, Elongin controls transcription in response to multiple stimuli, such as DNA damage, oxidative stress, and heat shock. Yeast Elongin (Ela1-Elc1), along with Def1, is known to facilitate ubiquitylation and degradation of RNA polymerase II (pol II) in response to multiple stimuli, yet transcription activity has not been examined. We have found that Def1 copurifies from yeast whole-cell extract with TFIIH, the largest general transcription factor required for transcription initiation and nucleotide excision repair. The addition of recombinant Def1 and Ela1-Elc1 enhanced transcription initiation in an in vitro reconstituted system including pol II, the general transcription factors, and TFIIS. Def1 also enhanced transcription restart from TFIIS-induced cleavage in a pol II transcribing complex. In the Δdef1 strain, heat shock genes were misregulated, indicating that Def1 is required for induction of some stress-responsive genes in yeast. Taken together, our results extend the understanding of the molecular mechanism of transcription regulation on cellular stress and reveal functional similarities to the mammalian system.


Assuntos
Proteínas Cromossômicas não Histona/metabolismo , RNA Polimerase II/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Fator de Transcrição TFIIH/metabolismo , Proteínas Cromossômicas não Histona/genética , Elonguina/genética , Elonguina/metabolismo , Ligação Proteica , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Estresse Fisiológico , Iniciação da Transcrição Genética
19.
J Shoulder Elbow Surg ; 28(1): 149-157, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30241983

RESUMO

BACKGROUND: Although past studies using video analysis indicated that the arm tackle and head-in-front shoulder tackle are possible risks for shoulder dislocation, the underlying mechanisms of tackling-related shoulder dislocation have not been sufficiently investigated. This study aimed to analyze the kinematic aspects of these tackling motions in 1-on-1 tackles in an experimental setting using a 3-dimensional motion-capture system. METHODS: A total of 65 one-on-one tackles were recorded using a marker-based, automatic, digitizing motion-capture system. A documented tackle was classified into 1 of 3 types, which was decided based on the first point of contact on the ball carrier and the head position at the time of impact: shoulder tackle (reference tackle), arm tackle, and head-in-front tackle. The orientations of the head, trunk, and shoulder at impact were calculated and statistically compared with each other. RESULTS: The distribution of tackles recorded in this study was as follows: 38 shoulder, 23 arm, and 4 head-in-front tackles. In comparison with the shoulder tackle as a reference, shoulder abduction on the side of impact was higher in both the arm and head-in-front tackles, while shoulder external rotation was lower in the head-in-front tackles. In the latter type of tackle, significant decreases in neck extension and ipsilateral neck rotation were also indicated. CONCLUSION: The kinematics in both the arm tackle and the head-in-front tackle is significantly different from that in the shoulder tackle and may represent a distinct risk factor for shoulder dislocation.


Assuntos
Fenômenos Biomecânicos/fisiologia , Simulação por Computador , Futebol Americano/lesões , Imageamento Tridimensional , Humanos , Masculino , Luxação do Ombro/fisiopatologia , Adulto Jovem
20.
BMC Vet Res ; 14(1): 419, 2018 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-30594182

RESUMO

BACKGROUND: Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL). The incidence of EBL in Japan is increasing annually; and the cases of EBL in cattle younger than 2 years old has been reported. Therefore, it is vital to find a method to control BLV infection, especially in young calves. In this study, to evaluate the protective ability of colostral antibodies against BLV infection, as well as the potential for BLV infection mediated by colostrum/milk, we investigated temporal fluctuations in the anti-BLV antibody titer and BLV proviral load (PVL) in colostrum/milk and peripheral blood of six infected dams during lactation. The association between PVL and antibody titer in colostrum and peripheral blood was then investigated using samples from a further twenty-seven cattle. Antibody concentrations were measured with a Syncytium-induction Inhibition Assay using colostral/milk whey and serum. PVL in peripheral blood and colostrum was measured by real-time PCR. RESULTS: Colostral antibodies showed high inhibitory activity until day 3 of lactation. The antibody titer and PVL in peripheral blood showed lesser changes than those in colostrum/milk throughout lactation. The colostral antibody titer was significantly higher than the serum antibody titer in all samples, whereas the colostrum PVL was significantly lower than the blood PVL. The blood PVL showed a significant correlation with serum antibody titer, colostrum PVL, and colostral antibody titer. However, there were no major correlations between the serum and colostral antibody titers. CONCLUSIONS: This is the first report investigating the temporal changes in colostral antibody titer in terms of inhibiting BLV infection in vitro. The results of antibody detection by Syncytium-induction Inhibition Assay suggested that the protective activity of the colostral antibodies against BLV infection would be conferred by anti-BLV gp51 antibody. The high antibody titer of colostral whey suggests that colostral whey could be a potential source of antibodies with a low risk of infection in neonatal calves.


Assuntos
Anticorpos Antivirais/imunologia , Doenças dos Bovinos/prevenção & controle , Colostro/imunologia , Animais , Anticorpos Antivirais/sangue , Bovinos , Doenças dos Bovinos/imunologia , Técnicas In Vitro , Vírus da Leucemia Bovina/imunologia
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