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1.
Nature ; 629(8011): 467-473, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38471529

RESUMEN

Prokaryotes have evolved intricate innate immune systems against phage infection1-7. Gabija is a highly widespread prokaryotic defence system that consists of two components, GajA and GajB8. GajA functions as a DNA endonuclease that is inactive in the presence of ATP9. Here, to explore how the Gabija system is activated for anti-phage defence, we report its cryo-electron microscopy structures in five states, including apo GajA, GajA in complex with DNA, GajA bound by ATP, apo GajA-GajB, and GajA-GajB in complex with ATP and Mg2+. GajA is a rhombus-shaped tetramer with its ATPase domain clustered at the centre and the topoisomerase-primase (Toprim) domain located peripherally. ATP binding at the ATPase domain stabilizes the insertion region within the ATPase domain, keeping the Toprim domain in a closed state. Upon ATP depletion by phages, the Toprim domain opens to bind and cleave the DNA substrate. GajB, which docks on GajA, is activated by the cleaved DNA, ultimately leading to prokaryotic cell death. Our study presents a mechanistic landscape of Gabija activation.


Asunto(s)
Bacillus cereus , Proteínas Bacterianas , Bacteriófagos , Microscopía por Crioelectrón , Inmunidad Innata , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/ultraestructura , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Apoproteínas/química , Apoproteínas/inmunología , Apoproteínas/metabolismo , Apoproteínas/ultraestructura , Proteínas Bacterianas/química , Proteínas Bacterianas/inmunología , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/ultraestructura , Bacteriófagos/inmunología , ADN/metabolismo , ADN/química , División del ADN , Magnesio/química , Magnesio/metabolismo , Modelos Moleculares , Unión Proteica , Dominios Proteicos , Viabilidad Microbiana , Bacillus cereus/química , Bacillus cereus/inmunología , Bacillus cereus/metabolismo , Bacillus cereus/ultraestructura , Estructura Cuaternaria de Proteína , ADN Primasa/química , ADN Primasa/metabolismo , ADN Primasa/ultraestructura , ADN-Topoisomerasas/química , ADN-Topoisomerasas/metabolismo , ADN-Topoisomerasas/ultraestructura
2.
Molecules ; 26(23)2021 Nov 25.
Artículo en Inglés | MEDLINE | ID: mdl-34885710

RESUMEN

Structural and biochemical studies elucidate that PAN may contribute to the host protein shutdown observed during influenza A infection. Thus, inhibition of the endonuclease activity of viral RdRP is an attractive approach for novel antiviral therapy. In order to envisage structurally diverse novel compounds with better efficacy as PAN endonuclease inhibitors, a ligand-based-pharmacophore model was developed using 3D-QSAR pharmacophore generation (HypoGen algorithm) methodology in Discovery Studio. As the training set, 25 compounds were taken to generate a significant pharmacophore model. The selected pharmacophore Hypo1 was further validated by 12 compounds in the test set and was used as a query model for further screening of 1916 compounds containing 71 HIV-1 integrase inhibitors, 37 antibacterial inhibitors, 131 antiviral inhibitors and other 1677 approved drugs by the FDA. Then, six compounds (Hit01-Hit06) with estimated activity values less than 10 µM were subjected to ADMET study and toxicity assessment. Only one potential inhibitory 'hit' molecule (Hit01, raltegravir's derivative) was further scrutinized by molecular docking analysis on the active site of PAN endonuclease (PDB ID: 6E6W). Hit01 was utilized for designing novel potential PAN endonuclease inhibitors through lead optimization, and then compounds were screened by pharmacophore Hypo1 and docking studies. Six raltegravir's derivatives with significant estimated activity values and docking scores were obtained. Further, these results certainly do not confirm or indicate the seven compounds (Hit01, Hit07, Hit08, Hit09, Hit10, Hit11 and Hit12) have antiviral activity, and extensive wet-laboratory experimentation is needed to transmute these compounds into clinical drugs.


Asunto(s)
Adenosina Trifosfatasas/química , Endonucleasas/química , Inhibidores Enzimáticos/química , Gripe Humana/enzimología , Adenosina Trifosfatasas/antagonistas & inhibidores , Adenosina Trifosfatasas/ultraestructura , Dominio Catalítico/efectos de los fármacos , Diseño de Fármacos/tendencias , Endonucleasas/antagonistas & inhibidores , Endonucleasas/ultraestructura , Humanos , Gripe Humana/tratamiento farmacológico , Gripe Humana/virología , Ligandos , Modelos Moleculares , Simulación del Acoplamiento Molecular , Relación Estructura-Actividad Cuantitativa
3.
Nat Commun ; 12(1): 6668, 2021 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-34795277

RESUMEN

Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoinflammatory disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more stably to synthetic Alu:Alu dsRNA. CryoEM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle- RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease.


Asunto(s)
Adenosina Trifosfato/metabolismo , Inflamación/metabolismo , Helicasa Inducida por Interferón IFIH1/metabolismo , Mutación Missense , ARN Bicatenario/metabolismo , ARN Viral/metabolismo , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Microscopía por Crioelectrón , Células HEK293 , Humanos , Inmunidad Innata/genética , Inflamación/genética , Helicasa Inducida por Interferón IFIH1/química , Helicasa Inducida por Interferón IFIH1/genética , Modelos Moleculares , Conformación de Ácido Nucleico , Unión Proteica , Conformación Proteica , ARN Bicatenario/química , ARN Bicatenario/genética , ARN Viral/genética
4.
Nature ; 599(7885): 497-502, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34759315

RESUMEN

Canonical CRISPR-Cas systems provide adaptive immunity against mobile genetic elements1. However, type I-F, I-B and V-K systems have been adopted by Tn7-like transposons to direct RNA-guided transposon insertion2-7. Type V-K CRISPR-associated transposons rely on the pseudonuclease Cas12k, the transposase TnsB, the AAA+ ATPase TnsC and the zinc-finger protein TniQ7, but the molecular mechanism of RNA-directed DNA transposition has remained elusive. Here we report cryo-electron microscopic structures of a Cas12k-guide RNA-target DNA complex and a DNA-bound, polymeric TnsC filament from the CRISPR-associated transposon system of the photosynthetic cyanobacterium Scytonema hofmanni. The Cas12k complex structure reveals an intricate guide RNA architecture and critical interactions mediating RNA-guided target DNA recognition. TnsC helical filament assembly is ATP-dependent and accompanied by structural remodelling of the bound DNA duplex. In vivo transposition assays corroborate key features of the structures, and biochemical experiments show that TniQ restricts TnsC polymerization, while TnsB interacts directly with TnsC filaments to trigger their disassembly upon ATP hydrolysis. Together, these results suggest that RNA-directed target selection by Cas12k primes TnsC polymerization and DNA remodelling, generating a recruitment platform for TnsB to catalyse site-specific transposon insertion. Insights from this work will inform the development of CRISPR-associated transposons as programmable site-specific gene insertion tools.


Asunto(s)
Sistemas CRISPR-Cas , Cianobacterias , Elementos Transponibles de ADN/genética , Edición Génica/métodos , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/ultraestructura , Biopolímeros , Proteínas Asociadas a CRISPR/metabolismo , Sistemas CRISPR-Cas/genética , Microscopía por Crioelectrón , Cianobacterias/enzimología , Cianobacterias/genética , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , ADN Bacteriano/ultraestructura , Modelos Moleculares , Mutagénesis Insercional , Polimerizacion , ARN/genética , ARN/metabolismo , Especificidad por Sustrato , Transposasas/metabolismo , Transposasas/ultraestructura , Dedos de Zinc
5.
J Mol Biol ; 432(24): 166693, 2020 12 04.
Artículo en Inglés | MEDLINE | ID: mdl-33122003

RESUMEN

Many Gram-negative bacterial pathogens use type III secretion systems (T3SS) to inject proteins into eukaryotic cells to subvert normal cellular functions. The T3SS apparatus (injectisome) shares a common architecture in all systems studied thus far, comprising three major components - the cytoplasmic sorting platform, envelope-spanning basal body and external needle with tip complex. The sorting platform consists of an ATPase (SctN) connected to "pods" (SctQ) having six-fold symmetry via radial spokes (SctL). These pods interface with the 24-fold symmetric SctD inner membrane ring (IR) via an adaptor protein (SctK). Here we report the first high-resolution structure of a SctK protein family member, PscK from Pseudomonas aeruginosa, as well as the structure of its interacting partner, the cytoplasmic domain of PscD (SctD). The cytoplasmic domain of PscD forms a forkhead-associated (FHA) fold, like that of its homologues from other T3SS. PscK, on the other hand, forms a helix-rich structure that does not resemble any known protein fold. Based on these structural findings, we present the first model for an interaction between proteins from the sorting platform and the IR. We also test the importance of the PscD residues predicted to mediate this electrostatic interaction using a two-hybrid analysis. The functional need for these residues in vivo was then confirmed by monitoring secretion of the effector ExoU. These structures will contribute to the development of atomic-resolution models of the entire sorting platform and to our understanding of the mechanistic interface between the sorting platform and the basal body of the injectisome.


Asunto(s)
Adenosina Trifosfatasas/ultraestructura , Proteínas Bacterianas/ultraestructura , Pseudomonas aeruginosa/ultraestructura , Sistemas de Secreción Tipo III/ultraestructura , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Cuerpos Basales/enzimología , Cuerpos Basales/ultraestructura , Citoplasma/química , Citoplasma/genética , Citoplasma/ultraestructura , Citosol/ultraestructura , Transporte de Proteínas/genética , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/patogenicidad , Sistemas de Secreción Tipo III/química , Sistemas de Secreción Tipo III/genética
6.
J Mol Biol ; 432(23): 6061-6074, 2020 11 20.
Artículo en Inglés | MEDLINE | ID: mdl-33058883

RESUMEN

The AAA-ATPase VCP/p97 cooperates with the SEP-domain adapters p37, UBXN2A and p47 in stripping inhibitor-3 (I3) from protein phosphatase-1 (PP1) for activation. In contrast to p97-mediated degradative processes, PP1 complex disassembly is ubiquitin-independent. It is therefore unclear how selective targeting is achieved. Using biochemical reconstitution and crosslink mass spectrometry, we show here that SEP-domain adapters use a multivalent substrate recognition strategy. An N-terminal sequence element predicted to form a helix, together with the SEP-domain, binds and engages the direct target I3 in the central pore of p97 for unfolding, while its partner PP1 is held by a linker between SHP box and UBX domain locked onto the peripheral N-domain of p97. Although the I3-binding element is functional in p47, p47 in vitro requires a transplant of the PP1-binding linker from p37 for activity stressing that both sites are essential to control specificity. Of note, unfolding is then governed by an inhibitory segment in the N-terminal region of p47, suggesting a regulatory function. Together, this study reveals how p97 adapters engage a protein complex for ubiquitin-independent disassembly while ensuring selectivity for one subunit.


Asunto(s)
Adenosina Trifosfatasas/química , Complejos Multiproteicos/química , Proteínas Nucleares/química , Conformación Proteica , Proteína Fosfatasa 1/química , Proteínas Adaptadoras Transductoras de Señales/química , Proteínas Adaptadoras Transductoras de Señales/genética , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Secuencia de Aminoácidos/genética , Dominio Catalítico/genética , Cristalografía por Rayos X , Humanos , Metaloendopeptidasas/química , Metaloendopeptidasas/genética , Complejos Multiproteicos/genética , Complejos Multiproteicos/ultraestructura , Proteínas Nucleares/genética , Proteínas Nucleares/ultraestructura , Unión Proteica/genética , Proteína Fosfatasa 1/genética , Proteína Fosfatasa 1/ultraestructura , Estructura Terciaria de Proteína , Subunidades de Proteína/química , Ubiquitina/genética , Ubiquitinas/química , Ubiquitinas/genética
7.
Lett Appl Microbiol ; 71(4): 413-419, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-32623751

RESUMEN

As a result of electron microscopic studies of morphogenesis in yeast Candida guilliermondii NP-4, the formation of new structures of volutin acidocalcisomes has been established within the cell cytoplasm. Under influence of X-irradiation, the changes in morphometric and electron-dense properties of yeast cells were identified: in yeast cytoplasm, the electron-dense volutin granules were increased up to 400 nm in size. After 24-h post-irradiation incubation of yeasts, the large volutin pellets are fragmented into smaller number particles in size up to 25-150 nm. The ATPase activity in yeast mitochondria was changed under X-irradiation. In latent phase of growth, ATPase activity was decreased 1·35-fold in comparison with non-irradiated yeasts. In logarithmic phase of growth, ATPase activity was three times higher than in latent phase, and in stationary phase of growth it has a value similar to the latent phase. Probably, the cells receive the necessary energy from alternative energy sources, such as volutin. Electron microscopy of volutin granule changes might serve as convenient method for evaluation of damages and repair processes in cells under influence of different environmental stress-factors.


Asunto(s)
Adenosina Trifosfatasas/metabolismo , Candida/efectos de la radiación , Candida/ultraestructura , Proteínas Fúngicas/metabolismo , Orgánulos/enzimología , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/ultraestructura , Adenosina Trifosfato/metabolismo , Candida/enzimología , Candida/genética , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Orgánulos/genética , Orgánulos/efectos de la radiación , Orgánulos/ultraestructura , Rayos X
8.
Nat Struct Mol Biol ; 27(8): 743-751, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32661420

RESUMEN

Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.


Asunto(s)
Proteínas Portadoras/química , Proteínas Cromosómicas no Histona/química , Proteínas Nucleares/química , Proteínas de Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/química , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Adenosina Trifosfato/metabolismo , Proteínas Portadoras/metabolismo , Proteínas Portadoras/ultraestructura , Proteínas de Ciclo Celular , Proteínas Cromosómicas no Histona/metabolismo , Proteínas Cromosómicas no Histona/ultraestructura , Microscopía por Crioelectrón , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/ultraestructura , Modelos Moleculares , Complejos Multiproteicos/química , Complejos Multiproteicos/metabolismo , Complejos Multiproteicos/ultraestructura , Proteínas Nucleares/metabolismo , Proteínas Nucleares/ultraestructura , Conformación Proteica , Pliegue de Proteína , Multimerización de Proteína , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/ultraestructura
9.
Nucleic Acids Res ; 48(12): 6980-6995, 2020 07 09.
Artículo en Inglés | MEDLINE | ID: mdl-32453425

RESUMEN

DNA unwinding in eukaryotic replication is performed by the Cdc45-MCM-GINS (CMG) helicase. Although the CMG architecture has been elucidated, its mechanism of DNA unwinding and replisome interactions remain poorly understood. Here we report the cryoEM structure at 3.3 Å of human CMG bound to fork DNA and the ATP-analogue ATPγS. Eleven nucleotides of single-stranded (ss) DNA are bound within the C-tier of MCM2-7 AAA+ ATPase domains. All MCM subunits contact DNA, from MCM2 at the 5'-end to MCM5 at the 3'-end of the DNA spiral, but only MCM6, 4, 7 and 3 make a full set of interactions. DNA binding correlates with nucleotide occupancy: five MCM subunits are bound to either ATPγS or ADP, whereas the apo MCM2-5 interface remains open. We further report the cryoEM structure of human CMG bound to the replisome hub AND-1 (CMGA). The AND-1 trimer uses one ß-propeller domain of its trimerisation region to dock onto the side of the helicase assembly formed by Cdc45 and GINS. In the resulting CMGA architecture, the AND-1 trimer is closely positioned to the fork DNA while its CIP (Ctf4-interacting peptide)-binding helical domains remain available to recruit partner proteins.


Asunto(s)
Proteínas de Ciclo Celular/ultraestructura , ADN/ultraestructura , Proteínas de Mantenimiento de Minicromosoma/ultraestructura , Complejos Multiproteicos/ultraestructura , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/ultraestructura , Adenosina Trifosfato/análogos & derivados , Adenosina Trifosfato/química , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/genética , Microscopía por Crioelectrón , Cristalografía por Rayos X , ADN Helicasas/química , ADN Helicasas/genética , ADN Helicasas/ultraestructura , Replicación del ADN/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/ultraestructura , Humanos , Proteínas de Mantenimiento de Minicromosoma/química , Proteínas de Mantenimiento de Minicromosoma/genética , Modelos Moleculares , Complejos Multiproteicos/química , Complejos Multiproteicos/genética , Conformación de Ácido Nucleico , Conformación Proteica
10.
Biomolecules ; 10(4)2020 04 17.
Artículo en Inglés | MEDLINE | ID: mdl-32316569

RESUMEN

Magnesium transporter A (MgtA) is an active transporter responsible for importing magnesium ions into the cytoplasm of prokaryotic cells. This study focuses on the peptide corresponding to the intrinsically disordered N-terminal region of MgtA, referred to as KEIF. Primary-structure and bioinformatic analyses were performed, followed by studies of the undisturbed single chain using a combination of techniques including small-angle X-ray scattering, circular dichroism spectroscopy, and atomistic molecular-dynamics simulations. Moreover, interactions with large unilamellar vesicles were investigated by using dynamic light scattering, laser Doppler velocimetry, cryogenic transmission electron microscopy, and circular dichroism spectroscopy. KEIF was confirmed to be intrinsically disordered in aqueous solution, although extended and containing little ß -structure and possibly PPII structure. An increase of helical content was observed in organic solvent, and a similar effect was also seen in aqueous solution containing anionic vesicles. Interactions of cationic KEIF with anionic vesicles led to the hypothesis that KEIF adsorbs to the vesicle surface through electrostatic and entropic driving forces. Considering this, there is a possibility that the biological role of KEIF is to anchor MgtA in the cell membrane, although further investigation is needed to confirm this hypothesis.


Asunto(s)
Adenosina Trifosfatasas/química , Fenómenos Químicos , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Proteínas Intrínsecamente Desordenadas/química , Proteínas de Transporte de Membrana/química , Adenosina Trifosfatasas/ultraestructura , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Dicroismo Circular , Proteínas de Escherichia coli/ultraestructura , Proteínas Intrínsecamente Desordenadas/ultraestructura , Lípidos/química , Proteínas de Transporte de Membrana/ultraestructura , Simulación de Dinámica Molecular , Tamaño de la Partícula , Probabilidad , Estructura Secundaria de Proteína , Dispersión del Ángulo Pequeño , Liposomas Unilamelares/química , Difracción de Rayos X
11.
Nature ; 579(7799): 448-451, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32188943

RESUMEN

Chromatin-remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs)1,2. In the yeast Saccharomyces cerevisiae, the essential SWI/SNF complex RSC3 contains 16 subunits, including the ATP-dependent DNA translocase Sth14,5. RSC removes nucleosomes from promoter regions6,7 and positions the specialized +1 and -1 nucleosomes that flank NDRs8,9. Here we present the cryo-electron microscopy structure of RSC in complex with a nucleosome substrate. The structure reveals that RSC forms five protein modules and suggests key features of the remodelling mechanism. The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and actin-related protein (ARP) modules. The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements8,10,11 that influence RSC functionality12. The ATPase and arm modules sandwich the nucleosome disc with the Snf2 ATP-coupling (SnAC) domain and the finger helix, respectively. The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. The mobile ARP module may modulate translocase-nucleosome interactions to regulate RSC activity5. The RSC-nucleosome structure provides a basis for understanding NDR formation and the structure and function of human SWI/SNF complexes that are frequently mutated in cancer13.


Asunto(s)
Microscopía por Crioelectrón , Complejos Multiproteicos/química , Complejos Multiproteicos/ultraestructura , Nucleosomas/metabolismo , Nucleosomas/ultraestructura , Saccharomyces cerevisiae/química , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Secuencia de Aminoácidos , Animales , Transporte Biológico , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ciclo Celular/ultraestructura , Drosophila melanogaster , Humanos , Ratones , Modelos Moleculares , Complejos Multiproteicos/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Proteínas Nucleares/ultraestructura , Nucleosomas/química , Subunidades de Proteína/química , Subunidades de Proteína/metabolismo , Saccharomyces cerevisiae/ultraestructura , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/ultraestructura , Xenopus laevis
12.
mBio ; 11(1)2020 02 18.
Artículo en Inglés | MEDLINE | ID: mdl-32071271

RESUMEN

Type IV secretion systems (T4SSs) are sophisticated nanomachines used by many bacterial pathogens to translocate protein and DNA substrates across a host cell membrane. Although T4SSs have important roles in promoting bacterial infections, little is known about the biogenesis of the apparatus and the mechanism of substrate transfer. Here, high-throughput cryoelectron tomography (cryo-ET) was used to visualize Legionella pneumophila T4SSs (also known as Dot/Icm secretion machines) in both the whole-cell context and at the cell pole. These data revealed the distribution patterns of individual Dot/Icm machines in the bacterial cell and identified five distinct subassembled intermediates. High-resolution in situ structures of the Dot/Icm machine derived from subtomogram averaging revealed that docking of the cytoplasmic DotB (VirB11-related) ATPase complex onto the DotO (VirB4-related) ATPase complex promotes a conformational change in the secretion system that results in the opening of a channel in the bacterial inner membrane. A model is presented for how the Dot/Icm apparatus is assembled and for how this machine may initiate the transport of cytoplasmic substrates across the inner membrane.IMPORTANCE Many bacteria use type IV secretion systems (T4SSs) to translocate proteins and nucleic acids into target cells, which promotes DNA transfer and host infection. The Dot/Icm T4SS in Legionella pneumophila is a multiprotein nanomachine that is known to translocate over 300 different protein effectors into eukaryotic host cells. Here, advanced cryoelectron tomography and subtomogram analysis were used to visualize the Dot/Icm machine assembly and distribution in a single L. pneumophila cell. Extensive classification and averaging revealed five distinct intermediates of the Dot/Icm machine at high resolution. Comparative analysis of the Dot/Icm machine and subassemblies derived from wild-type cells and several mutants provided a structural basis for understanding mechanisms that underlie the assembly and activation of the Dot/Icm machine.


Asunto(s)
Adenosina Trifosfatasas/ultraestructura , Proteínas Bacterianas/ultraestructura , Microscopía por Crioelectrón/métodos , Tomografía con Microscopio Electrónico/métodos , Legionella pneumophila/metabolismo , Sistemas de Secreción Tipo IV/ultraestructura , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Legionella pneumophila/genética , Legionella pneumophila/ultraestructura , Modelos Moleculares , Conformación Proteica , Sistemas de Secreción Tipo IV/química , Sistemas de Secreción Tipo IV/metabolismo
13.
Mol Cell ; 78(2): 250-260.e5, 2020 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-32097603

RESUMEN

Structural maintenance of chromosomes (SMC) complexes organize chromosomes ubiquitously, thereby contributing to their faithful segregation. We demonstrate that under conditions of increased chromosome occupancy of the Escherichia coli SMC complex, MukBEF, the chromosome is organized as a series of loops around a thin (<130 nm) MukBEF axial core, whose length is ∼1,100 times shorter than the chromosomal DNA. The linear order of chromosomal loci is maintained in the axial cores, whose formation requires MukBEF ATP hydrolysis. Axial core structure in non-replicating chromosomes is predominantly linear (1 µm) but becomes circular (1.5 µm) in the absence of MatP because of its failure to displace MukBEF from the 800 kbp replication termination region (ter). Displacement of MukBEF from ter by MatP in wild-type cells directs MukBEF colocalization with the replication origin. We conclude that MukBEF individualizes and compacts the chromosome lengthwise, demonstrating a chromosome organization mechanism similar to condensin in mitotic chromosome formation.


Asunto(s)
Proteínas Cromosómicas no Histona/genética , Cromosomas Bacterianos/genética , Proteínas de Escherichia coli/genética , Proteínas Represoras/genética , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/ultraestructura , Adenosina Trifosfato/genética , Proteínas Cromosómicas no Histona/ultraestructura , Segregación Cromosómica/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/ultraestructura , Escherichia coli/genética , Proteínas de Escherichia coli/ultraestructura , Mitosis/genética , Complejos Multiproteicos/genética , Complejos Multiproteicos/ultraestructura , Origen de Réplica/genética , Proteínas Represoras/ultraestructura
14.
Genetics ; 214(3): 589-604, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31980450

RESUMEN

Ribosome biogenesis is tightly regulated through stress-sensing pathways that impact genome stability, aging and senescence. In Saccharomyces cerevisiae, ribosomal RNAs are transcribed from rDNA located on the right arm of chromosome XII. Numerous studies reveal that rDNA decondenses into a puff-like structure during interphase, and condenses into a tight loop-like structure during mitosis. Intriguingly, a novel and additional mechanism of increased mitotic rDNA compaction (termed hypercondensation) was recently discovered that occurs in response to temperature stress (hyperthermic-induced) and is rapidly reversible. Here, we report that neither changes in condensin binding or release of DNA during mitosis, nor mutation of factors that regulate cohesin binding and release, appear to play a critical role in hyperthermic-induced rDNA hypercondensation. A candidate genetic approach revealed that deletion of either HSP82 or HSC82 (Hsp90 encoding heat shock paralogs) result in significantly reduced hyperthermic-induced rDNA hypercondensation. Intriguingly, Hsp inhibitors do not impact rDNA hypercondensation. In combination, these findings suggest that Hsp90 either stabilizes client proteins, which are sensitive to very transient thermic challenges, or directly promotes rDNA hypercondensation during preanaphase. Our findings further reveal that the high mobility group protein Hmo1 is a negative regulator of mitotic rDNA condensation, distinct from its role in promoting premature condensation of rDNA during interphase upon nutrient starvation.


Asunto(s)
Proteínas de Ciclo Celular/genética , Proteínas Cromosómicas no Histona/genética , ADN Ribosómico/genética , Proteínas del Grupo de Alta Movilidad/genética , Ribosomas/genética , Proteínas de Saccharomyces cerevisiae/genética , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/ultraestructura , Proteínas de Ciclo Celular/ultraestructura , Proteínas Cromosómicas no Histona/ultraestructura , Cromosomas Fúngicos/genética , ADN Ribosómico/ultraestructura , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/ultraestructura , Proteínas HSP90 de Choque Térmico/genética , Proteínas del Grupo de Alta Movilidad/ultraestructura , Mitosis/genética , Complejos Multiproteicos/genética , Complejos Multiproteicos/ultraestructura , Conformación de Ácido Nucleico , Ribosomas/ultraestructura , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/ultraestructura , Proteínas de Saccharomyces cerevisiae/ultraestructura , Cohesinas
15.
Sci Rep ; 9(1): 18019, 2019 12 02.
Artículo en Inglés | MEDLINE | ID: mdl-31792243

RESUMEN

The ClpP protease is found in all kingdoms of life, from bacteria to humans. In general, this protease forms a homo-oligomeric complex composed of 14 identical subunits, which associates with its cognate ATPase in a symmetrical manner. Here we show that, in contrast to this general architecture, the Clp protease from Mycobacterium smegmatis (Msm) forms an asymmetric hetero-oligomeric complex ClpP1P2, which only associates with its cognate ATPase through the ClpP2 ring. Our structural and functional characterisation of this complex demonstrates that asymmetric docking of the ATPase component is controlled by both the composition of the ClpP1 hydrophobic pocket (Hp) and the presence of a unique C-terminal extension in ClpP1 that guards this Hp. Our structural analysis of MsmClpP1 also revealed openings in the side-walls of the inactive tetradecamer, which may represent sites for product egress.


Asunto(s)
Proteínas Bacterianas/ultraestructura , Endopeptidasa Clp/ultraestructura , Mycobacterium smegmatis/metabolismo , Multimerización de Proteína , Subunidades de Proteína/metabolismo , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Proteínas Bacterianas/metabolismo , Cristalografía por Rayos X , Endopeptidasa Clp/metabolismo , Simulación del Acoplamiento Molecular , Estructura Cuaternaria de Proteína , Proteolisis
16.
Nature ; 576(7786): 321-325, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31597161

RESUMEN

Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems1. A molecular understanding of the type VII secretion mechanism has been hampered owing to a lack of three-dimensional structures of the fully assembled secretion apparatus. Here we report the cryo-electron microscopy structure of a membrane-embedded core complex of the ESX-3/type VII secretion system from Mycobacterium smegmatis. The core of the ESX-3 secretion machine consists of four protein components-EccB3, EccC3, EccD3 and EccE3, in a 1:1:2:1 stoichiometry-which form two identical protomers. The EccC3 coupling protein comprises a flexible array of four ATPase domains, which are linked to the membrane through a stalk domain. The domain of unknown function (DUF) adjacent to the stalk is identified as an ATPase domain that is essential for secretion. EccB3 is predominantly periplasmatic, but a small segment crosses the membrane and contacts the stalk domain. This suggests that conformational changes in the stalk domain-triggered by substrate binding at the distal end of EccC3 and subsequent ATP hydrolysis in the DUF-could be coupled to substrate secretion to the periplasm. Our results reveal that the architecture of type VII secretion systems differs markedly from that of other known secretion machines2, and provide a structural understanding of these systems that will be useful for the design of antimicrobial strategies that target bacterial virulence.


Asunto(s)
Microscopía por Crioelectrón , Mycobacterium smegmatis/química , Sistemas de Secreción Tipo VII/química , Sistemas de Secreción Tipo VII/ultraestructura , Actinobacteria/química , Actinobacteria/enzimología , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/aislamiento & purificación , Adenosina Trifosfatasas/ultraestructura , Adenosina Trifosfato/metabolismo , Modelos Moleculares , Mycobacterium smegmatis/enzimología , Mycobacterium smegmatis/ultraestructura , Dominios Proteicos , Estructura Cuaternaria de Proteína , Subunidades de Proteína/química , Subunidades de Proteína/aislamiento & purificación , Relación Estructura-Actividad , Thermomonospora , Sistemas de Secreción Tipo VII/aislamiento & purificación
17.
Nucleic Acids Res ; 47(17): 9400-9409, 2019 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-31402386

RESUMEN

ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3. Density for other regions of ISWI is not observed, presumably due to disorder. Comparison with the structure of the free nucleosome reveals that although the histone core remains largely unchanged, remodeler binding causes perturbations in the nucleosomal DNA resulting in a bulge near the SHL2 site. Overall, the structure of the nucleotide-free ISWI-nucleosome complex is similar to the corresponding regions of the recently reported ADP bound ISWI-nucleosome structures, which are significantly different from that observed for the ADP-BeFx bound structure. Our findings are relevant to the initial step of ISWI binding to the nucleosome and provide additional insights into the nucleosome remodeling process driven by ISWI.


Asunto(s)
Adenosina Trifosfatasas/química , Proteínas de Unión al ADN/ultraestructura , Nucleosomas/ultraestructura , Factores de Transcripción/ultraestructura , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/ultraestructura , Animales , Chaetomium/genética , Chaetomium/ultraestructura , Cromatina/genética , Ensamble y Desensamble de Cromatina/genética , Microscopía por Crioelectrón , Proteínas de Unión al ADN/genética , Drosophila melanogaster/genética , Escherichia coli/genética , Histonas/química , Histonas/ultraestructura , Nucleosomas/genética , Unión Proteica/genética , Dominios Proteicos/genética , Saccharomyces cerevisiae/genética , Factores de Transcripción/genética
18.
Nat Struct Mol Biol ; 26(8): 671-678, 2019 08.
Artículo en Inglés | MEDLINE | ID: mdl-31285604

RESUMEN

The AAA+ ATPase spastin remodels microtubule arrays through severing and its mutation is the most common cause of hereditary spastic paraplegias (HSP). Polyglutamylation of the tubulin C-terminal tail recruits spastin to microtubules and modulates severing activity. Here, we present a ~3.2 Å resolution cryo-EM structure of the Drosophila melanogaster spastin hexamer with a polyglutamate peptide bound in its central pore. Two electropositive loops arranged in a double-helical staircase coordinate the substrate sidechains. The structure reveals how concurrent nucleotide and substrate binding organizes the conserved spastin pore loops into an ordered network that is allosterically coupled to oligomerization, and suggests how tubulin tail engagement activates spastin for microtubule disassembly. This allosteric coupling may apply generally in organizing AAA+ protein translocases into their active conformations. We show that this allosteric network is essential for severing and is a hotspot for HSP mutations.


Asunto(s)
Adenosina Trifosfatasas/ultraestructura , Proteínas de Drosophila/ultraestructura , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Regulación Alostérica , Animales , Microscopía por Crioelectrón , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Microtúbulos/metabolismo , Modelos Moleculares , Mutación , Ácido Poliglutámico/metabolismo , Polimerizacion , Unión Proteica , Conformación Proteica , Dominios Proteicos , Relación Estructura-Actividad , Especificidad por Sustrato , Tubulina (Proteína)/metabolismo
19.
J Biol Chem ; 294(37): 13822-13829, 2019 09 13.
Artículo en Inglés | MEDLINE | ID: mdl-31350339

RESUMEN

High-resolution structural analysis of flexible proteins is frequently challenging and requires the synergistic application of different experimental techniques. For these proteins, small-angle X-ray scattering (SAXS) allows for a quantitative assessment and modeling of potentially flexible and heterogeneous structural states. Here, we report SAXS characterization of the condensin HEAT-repeat subunit Ycg1Cnd3 in solution, complementing currently available high-resolution crystallographic models. We show that the free Ycg1 subunit is flexible in solution but becomes considerably more rigid when bound to its kleisin-binding partner protein Brn1Cnd2 The analysis of SAXS and dynamic and static multiangle light scattering data furthermore reveals that Ycg1 tends to oligomerize with increasing concentrations in the absence of Brn1. Based on these data, we present a model of the free Ycg1 protein constructed by normal mode analysis, as well as tentative models of Ycg1 dimers and tetramers. These models enable visualization of the conformational transitions that Ycg1 has to undergo to adopt a closed rigid shape and thereby create a DNA-binding surface in the condensin complex.


Asunto(s)
Adenosina Trifosfatasas/ultraestructura , Chaetomium/ultraestructura , Proteínas de Unión al ADN/ultraestructura , Complejos Multiproteicos/ultraestructura , Difracción de Rayos X/métodos , Adenosina Trifosfatasas/metabolismo , Chaetomium/metabolismo , Proteínas de Unión al ADN/metabolismo , Modelos Moleculares , Complejos Multiproteicos/metabolismo , Unión Proteica , Conformación Proteica , Dispersión del Ángulo Pequeño
20.
Elife ; 82019 06 18.
Artículo en Inglés | MEDLINE | ID: mdl-31210637

RESUMEN

The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.


Asunto(s)
Adenosina Trifosfatasas/ultraestructura , Proteínas Cromosómicas no Histona/ultraestructura , Nucleosomas/ultraestructura , Adenosina Trifosfatasas/metabolismo , Regulación Alostérica , Proteínas Cromosómicas no Histona/metabolismo , Microscopía por Crioelectrón , Histonas/ultraestructura , Humanos , Conformación Proteica , Multimerización de Proteína
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