Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 351
Filtrar
1.
Cell ; 170(4): 701-713.e11, 2017 Aug 10.
Artículo en Inglés | MEDLINE | ID: mdl-28781166

RESUMEN

Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. The U2 snRNP-containing head domain is connected to the B complex main body via three main bridges. U4/U6.U5 tri-snRNP proteins, which are located in the main body, undergo significant rearrangements during tri-snRNP integration into the B complex. These include formation of a partially closed Prp8 conformation that creates, together with Dim1, a 5' splice site (ss) binding pocket, displacement of Sad1, and rearrangement of Brr2 such that it contacts its U4/U6 substrate and is poised for the subsequent spliceosome activation step. The molecular organization of several B-specific proteins suggests that they are involved in negatively regulating Brr2, positioning the U6/5'ss helix, and stabilizing the B complex structure. Our results indicate significant differences between the early activation phase of human and yeast spliceosomes.


Asunto(s)
Empalmosomas/química , Núcleo Celular/química , Microscopía por Crioelectrón , Células HeLa , Humanos , Modelos Moleculares , Proteínas de Unión al ARN/química , Ribonucleoproteínas Nucleares Pequeñas/química , Saccharomyces cerevisiae/química , Empalmosomas/ultraestructura
2.
Nature ; 630(8018): 1012-1019, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38778104

RESUMEN

Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron1. Alternatively, it can occur through an exon-defined pathway2-5, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex6,7. Exon definition promotes the splicing of upstream introns2,8,9 and plays a key part in alternative splicing regulation10-16. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.


Asunto(s)
Exones , Intrones , Empalme del ARN , Empalmosomas , Humanos , Empalme Alternativo , Microscopía por Crioelectrón , Exones/genética , Intrones/genética , Modelos Moleculares , Sitios de Empalme de ARN/genética , Empalme del ARN/genética , Empalmosomas/metabolismo , Empalmosomas/química , Empalmosomas/ultraestructura , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/ultraestructura
3.
Annu Rev Biochem ; 83: 697-725, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24635478

RESUMEN

Superfamily 2 helicase proteins are ubiquitous in RNA biology and have an extraordinarily broad set of functional roles. Central among these roles are the promotion of rearrangements of structured RNAs and the remodeling of ribonucleoprotein complexes (RNPs), allowing formation of native RNA structure or progression through a functional cycle of structures. Although all superfamily 2 helicases share a conserved helicase core, they are divided evolutionarily into several families, and it is principally proteins from three families, the DEAD-box, DEAH/RHA, and Ski2-like families, that function to manipulate structured RNAs and RNPs. Strikingly, there are emerging differences in the mechanisms of these proteins, both between families and within the largest family (DEAD-box), and these differences appear to be tuned to their RNA or RNP substrates and their specific roles. This review outlines basic mechanistic features of the three families and surveys individual proteins and the current understanding of their biological substrates and mechanisms.


Asunto(s)
G-Cuádruplex , Chaperonas Moleculares/química , ARN Helicasas/química , Empalmosomas/química , Empalme Alternativo , Catálisis , ADN Helicasas/química , Escherichia coli/metabolismo , Humanos , Intrones , Biosíntesis de Proteínas , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , ARN/química , Empalme del ARN , Ribonucleoproteínas Nucleares Pequeñas/química , Ribosomas/química , Saccharomyces cerevisiae/metabolismo
4.
Nucleic Acids Res ; 52(7): 4037-4052, 2024 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-38499487

RESUMEN

Here, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of U11/U12-65K, a known unique component of the U11/U12 di-snRNP. Both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with U11/U12-65K, which uses its N-terminal region to interact with U11 snRNP during intron recognition. Finally, while RBM41 knockout cells are viable, they show alterations in U12-type 3' splice site usage. Together, our results highlight the role of the 3'-terminal stem-loop of U12 snRNA as a dynamic binding platform for the U11/U12-65K and RBM41 proteins, which function at distinct stages of the assembly/disassembly cycle.


Asunto(s)
ARN Helicasas DEAD-box , Factores de Empalme de ARN , ARN Nuclear Pequeño , Proteínas de Unión al ARN , Ribonucleoproteínas Nucleares Pequeñas , Empalmosomas , Empalmosomas/metabolismo , Empalmosomas/genética , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/genética , Ribonucleoproteínas Nucleares Pequeñas/química , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/química , Humanos , ARN Nuclear Pequeño/metabolismo , ARN Nuclear Pequeño/genética , ARN Nuclear Pequeño/química , ARN Helicasas DEAD-box/metabolismo , ARN Helicasas DEAD-box/genética , Empalme del ARN , Intrones/genética , Células HeLa , Unión Proteica , Cuerpos Enrollados/metabolismo , Células HEK293
5.
Nucleic Acids Res ; 50(2): 750-762, 2022 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-34935961

RESUMEN

P-TEFb modulates RNA polymerase II elongation through alternative interaction with negative and positive regulation factors. While inactive P-TEFbs are mainly sequestered in the 7SK snRNP complex in a chromatin-free state, most of its active forms are in complex with its recruitment factors, Brd4 and SEC, in a chromatin-associated state. Thus, switching from inactive 7SK snRNP to active P-TEFb (Brd4/P-TEFb or SEC/P-TEFb) is essential for global gene expression. Although it has been shown that cellular signaling stimulates the disruption of 7SK snRNP, releasing dephosphorylated and catalytically inactive P-TEFb, little is known about how the inactive released P-TEFb is reactivated. Here, we show that the Cdk9/CycT1 heterodimer released from 7SK snRNP is completely dissociated into monomers in response to stress. Brd4 or SEC then recruits monomerized Cdk9 and CycT1 to reassemble the core P-TEFb. Meanwhile, the binding of monomeric dephosphorylated Cdk9 to either Brd4 or SEC induces the autophosphorylation of T186 of Cdk9. Finally, the same mechanism is employed during nocodazole released entry into early G1 phase of cell cycle. Therefore, our studies demonstrate a novel mechanism by which Cdk9 and CycT1 monomers are reassembled on chromatin to form active P-TEFb by its interaction with Brd4 or SEC to regulate transcription.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Ciclina T/metabolismo , Quinasa 9 Dependiente de la Ciclina/metabolismo , Proteínas de Unión al ADN/metabolismo , Factor B de Elongación Transcripcional Positiva/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Factores de Transcripción/metabolismo , Factores de Elongación Transcripcional/metabolismo , Ciclo Celular , Línea Celular , Ciclina T/química , Quinasa 9 Dependiente de la Ciclina/química , Activación Enzimática , Humanos , Modelos Biológicos , Fosforilación , Unión Proteica , Multimerización de Proteína , Proteínas Recombinantes , Ribonucleoproteínas Nucleares Pequeñas/química , Estrés Fisiológico
6.
RNA ; 27(4): 496-512, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33483369

RESUMEN

Ribosomal RNA (rRNA) carries extensive 2'-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding, and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2'-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner. Extensive and partially conflicting structural information exists for the archaeal enzyme, while no structural data is available for the eukaryotic enzyme. The yeast Box C/D RNP consists of a guide RNA, the RNA-primary binding protein Snu13, the two scaffold proteins Nop56 and Nop58, and the enzymatic module Nop1. Here we present the high-resolution structure of the eukaryotic Box C/D methyltransferase Nop1 from Saccharomyces cerevisiae bound to the amino-terminal domain of Nop56. We discuss similarities and differences between the interaction modes of the two proteins in archaea and eukaryotes and demonstrate that eukaryotic Nop56 recruits the methyltransferase to the Box C/D RNP through a protein-protein interface that differs substantially from the archaeal orthologs. This study represents a first achievement in understanding the evolution of the structure and function of these proteins from archaea to eukaryotes.


Asunto(s)
Proteínas Arqueales/química , Proteínas Cromosómicas no Histona/química , Proteínas Nucleares/química , Pyrococcus furiosus/genética , Ribonucleoproteínas Nucleolares Pequeñas/química , Proteínas de Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Secuencia de Aminoácidos , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Sitios de Unión , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Cristalografía por Rayos X , Expresión Génica , Metilación , Modelos Moleculares , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Pyrococcus furiosus/metabolismo , ARN de Hongos/genética , ARN de Hongos/metabolismo , ARN Guía de Kinetoplastida/genética , ARN Guía de Kinetoplastida/metabolismo , ARN Ribosómico/genética , ARN Ribosómico/metabolismo , ARN Nucleolar Pequeño/genética , ARN Nucleolar Pequeño/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/genética , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Ribonucleoproteínas Nucleolares Pequeñas/genética , Ribonucleoproteínas Nucleolares Pequeñas/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Alineación de Secuencia , Homología Estructural de Proteína
7.
Acta Neuropathol ; 146(3): 477-498, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37369805

RESUMEN

GEMIN5 is essential for core assembly of small nuclear Ribonucleoproteins (snRNPs), the building blocks of spliceosome formation. Loss-of-function mutations in GEMIN5 lead to a neurodevelopmental syndrome among patients presenting with developmental delay, motor dysfunction, and cerebellar atrophy by perturbing SMN complex protein expression and assembly. Currently, molecular determinants of GEMIN5-mediated disease have yet to be explored. Here, we identified SMN as a genetic suppressor of GEMIN5-mediated neurodegeneration in vivo. We discovered that an increase in SMN expression by either SMN gene therapy replacement or the antisense oligonucleotide (ASO), Nusinersen, significantly upregulated the endogenous levels of GEMIN5 in mammalian cells and mutant GEMIN5-derived iPSC neurons. Further, we identified a strong functional association between the expression patterns of SMN and GEMIN5 in patient Spinal Muscular Atrophy (SMA)-derived motor neurons harboring loss-of-function mutations in the SMN gene. Interestingly, SMN binds to the C-terminus of GEMIN5 and requires the Tudor domain for GEMIN5 binding and expression regulation. Finally, we show that SMN upregulation ameliorates defective snRNP biogenesis and alternative splicing defects caused by loss of GEMIN5 in iPSC neurons and in vivo. Collectively, these studies indicate that SMN acts as a regulator of GEMIN5 expression and neuropathologies.


Asunto(s)
Atrofia Muscular Espinal , Proteínas de Unión al ARN , Humanos , Neuronas Motoras/metabolismo , Atrofia Muscular Espinal/genética , Atrofia Muscular Espinal/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/genética , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Proteínas de Unión al ARN/metabolismo , Proteínas del Complejo SMN/genética , Dominio Tudor
8.
Cell ; 135(3): 497-509, 2008 Oct 31.
Artículo en Inglés | MEDLINE | ID: mdl-18984161

RESUMEN

Spliceosomal small nuclear ribonucleoproteins (snRNPs) are essential components of the nuclear pre-mRNA processing machinery. A hallmark of these particles is a ring-shaped core domain generated by the binding of Sm proteins onto snRNA. PRMT5 and SMN complexes mediate the formation of the core domain in vivo. Here, we have elucidated the mechanism of this reaction by both biochemical and structural studies. We show that pICln, a component of the PRMT5 complex, induces the formation of an otherwise unstable higher-order Sm protein unit. In this state, the Sm proteins are kinetically trapped, preventing their association with snRNA. The SMN complex subsequently binds to these Sm protein units, dissociates pICln, and catalyzes ring closure on snRNA. Our data identify pICln as an assembly chaperone and the SMN complex as a catalyst of spliceosomal snRNP formation. The mode of action of this combined chaperone/catalyst system is reminiscent of the mechanism employed by DNA clamp loaders.


Asunto(s)
Proteína Metiltransferasas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Células HeLa , Humanos , Modelos Biológicos , Chaperonas Moleculares/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Proteína Metiltransferasas/metabolismo , Proteína-Arginina N-Metiltransferasas , ARN/metabolismo , Proteínas de Unión al ARN/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Proteína 1 para la Supervivencia de la Neurona Motora/metabolismo
9.
Nature ; 546(7660): 617-621, 2017 06 29.
Artículo en Inglés | MEDLINE | ID: mdl-28530653

RESUMEN

Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation.


Asunto(s)
Microscopía por Crioelectrón , Saccharomyces cerevisiae , Empalmosomas/química , Empalmosomas/ultraestructura , Secuencia de Bases , Biocatálisis , Dominio Catalítico , Intrones/genética , Modelos Biológicos , Modelos Moleculares , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Unión Proteica , Dominios Proteicos , Estabilidad Proteica , ARN Helicasas/química , ARN Helicasas/metabolismo , ARN Helicasas/ultraestructura , Precursores del ARN/genética , Precursores del ARN/metabolismo , Precursores del ARN/ultraestructura , Sitios de Empalme de ARN/genética , Empalme del ARN , Factores de Empalme de ARN/química , Factores de Empalme de ARN/metabolismo , ARN Nuclear Pequeño/química , ARN Nuclear Pequeño/metabolismo , Ribonucleoproteína Nuclear Pequeña U2/química , Ribonucleoproteína Nuclear Pequeña U2/metabolismo , Ribonucleoproteína Nuclear Pequeña U4-U6/química , Ribonucleoproteína Nuclear Pequeña U4-U6/metabolismo , Ribonucleoproteína Nuclear Pequeña U5/química , Ribonucleoproteína Nuclear Pequeña U5/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/ultraestructura , Empalmosomas/metabolismo
10.
Nature ; 542(7641): 318-323, 2017 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-28076346

RESUMEN

Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.


Asunto(s)
Microscopía por Crioelectrón , Empalme del ARN , Empalmosomas/metabolismo , Empalmosomas/ultraestructura , Adenosina/metabolismo , Secuencia de Bases , Biocatálisis , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ciclo Celular/ultraestructura , ARN Helicasas DEAD-box/química , ARN Helicasas DEAD-box/metabolismo , ARN Helicasas DEAD-box/ultraestructura , Exones/genética , Humanos , Intrones/genética , Modelos Moleculares , Movimiento , Dominios Proteicos , Factores de Empalme de ARN/química , Factores de Empalme de ARN/metabolismo , Factores de Empalme de ARN/ultraestructura , Estabilidad del ARN , ARN Mensajero/química , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/ultraestructura , Ribonucleasa H/química , Ribonucleasa H/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/ultraestructura , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/enzimología , Empalmosomas/química
11.
Genes Dev ; 29(24): 2576-87, 2015 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-26637280

RESUMEN

The Brr2 helicase provides the key remodeling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein), and its activity has to be tightly regulated. Brr2 exhibits an unusual architecture, including an ∼ 500-residue N-terminal region, whose functions and molecular mechanisms are presently unknown, followed by a tandem array of structurally similar helicase units (cassettes), only the first of which is catalytically active. Here, we show by crystal structure analysis of full-length Brr2 in complex with a regulatory Jab1/MPN domain of the Prp8 protein and by cross-linking/mass spectrometry of isolated Brr2 that the Brr2 N-terminal region encompasses two folded domains and adjacent linear elements that clamp and interconnect the helicase cassettes. Stepwise N-terminal truncations led to yeast growth and splicing defects, reduced Brr2 association with U4/U6•U5 tri-snRNPs, and increased ATP-dependent disruption of the tri-snRNP, yielding U4/U6 di-snRNP and U5 snRNP. Trends in the RNA-binding, ATPase, and helicase activities of the Brr2 truncation variants are fully rationalized by the crystal structure, demonstrating that the N-terminal region autoinhibits Brr2 via substrate competition and conformational clamping. Our results reveal molecular mechanisms that prevent premature and unproductive tri-snRNP disruption and suggest novel principles of Brr2-dependent splicing regulation.


Asunto(s)
Modelos Moleculares , ARN Helicasas/química , ARN Helicasas/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Empalmosomas/enzimología , Adenosina Trifosfatasas/metabolismo , Chaetomium/enzimología , Chaetomium/genética , Cristalización , Humanos , Unión Proteica , Pliegue de Proteína , Empalme de Proteína , Estructura Cuaternaria de Proteína , Estructura Terciaria de Proteína , ARN Helicasas/genética , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/metabolismo , Ribonucleoproteína Nuclear Pequeña U4-U6/química , Ribonucleoproteína Nuclear Pequeña U4-U6/metabolismo , Ribonucleoproteína Nuclear Pequeña U5/química , Ribonucleoproteína Nuclear Pequeña U5/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/genética , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crecimiento & desarrollo , Proteínas de Saccharomyces cerevisiae/genética , Empalmosomas/genética
12.
J Biol Chem ; 297(1): 100829, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34048711

RESUMEN

Brr2 is an essential Ski2-like RNA helicase that exhibits a unique structure among the spliceosomal helicases. Brr2 harbors a catalytically active N-terminal helicase cassette and a structurally similar but enzymatically inactive C-terminal helicase cassette connected by a linker region. Both cassettes contain a nucleotide-binding pocket, but it is unclear whether nucleotide binding in these two pockets is related. Here we use biophysical and computational methods to delineate the functional connectivity between the cassettes and determine whether occupancy of one nucleotide-binding site may influence nucleotide binding at the other cassette. Our results show that Brr2 exhibits high specificity for adenine nucleotides, with both cassettes binding ADP tighter than ATP. Adenine nucleotide affinity for the inactive C-terminal cassette is more than two orders of magnitude higher than that of the active N-terminal cassette, as determined by slow nucleotide release. Mutations at the intercassette surfaces and in the connecting linker diminish the affinity of adenine nucleotides for both cassettes. Moreover, we found that abrogation of nucleotide binding at the C-terminal cassette reduces nucleotide binding at the N-terminal cassette 70 Å away. Molecular dynamics simulations identified structural communication lines that likely mediate these long-range allosteric effects, predominantly across the intercassette interface. Together, our results reveal intricate networks of intramolecular interactions in the complex Brr2 RNA helicase, which fine-tune its nucleotide affinities and which could be exploited to regulate enzymatic activity during splicing.


Asunto(s)
Nucleótidos de Adenina/metabolismo , ARN Helicasas/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Adenosina Difosfato/metabolismo , Adenosina Trifosfato/análogos & derivados , Adenosina Trifosfato/metabolismo , Regulación Alostérica , Aminoácidos/metabolismo , Sitios de Unión , Humanos , Cinética , Simulación de Dinámica Molecular , Mutación/genética , Dominios Proteicos , Ribonucleoproteínas Nucleares Pequeñas/química , Especificidad por Sustrato
13.
Hum Mol Genet ; 29(6): 907-922, 2020 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-31985013

RESUMEN

Telomeres are nucleoprotein structures at the end of chromosomes. The telomerase complex, constituted of the catalytic subunit TERT, the RNA matrix hTR and several cofactors, including the H/ACA box ribonucleoproteins Dyskerin, NOP10, GAR1, NAF1 and NHP2, regulates telomere length. In humans, inherited defects in telomere length maintenance are responsible for a wide spectrum of clinical premature aging manifestations including pulmonary fibrosis (PF), dyskeratosis congenita (DC), bone marrow failure and predisposition to cancer. NHP2 mutations have been so far reported only in two patients with DC. Here, we report the first case of Høyeraal-Hreidarsson syndrome, the severe form of DC, caused by biallelic missense mutations in NHP2. Additionally, we identified three unrelated patients with PF carrying NHP2 heterozygous mutations. Strikingly, one of these patients acquired a somatic mutation in the promoter of TERT that likely conferred a selective advantage in a subset of blood cells. Finally, we demonstrate that a functional deficit of human NHP2 affects ribosomal RNA biogenesis. Together, our results broaden the functional consequences and clinical spectrum of NHP2 deficiency.


Asunto(s)
Disqueratosis Congénita/patología , Retardo del Crecimiento Fetal/patología , Discapacidad Intelectual/patología , Microcefalia/patología , Mutación , Proteínas Nucleares/deficiencia , Proteínas Nucleares/genética , Fibrosis Pulmonar/patología , ARN Ribosómico/biosíntesis , Ribonucleoproteínas Nucleares Pequeñas/deficiencia , Ribonucleoproteínas Nucleares Pequeñas/genética , Anciano , Secuencia de Aminoácidos , Disqueratosis Congénita/etiología , Femenino , Retardo del Crecimiento Fetal/etiología , Humanos , Recién Nacido , Discapacidad Intelectual/etiología , Masculino , Microcefalia/etiología , Persona de Mediana Edad , Proteínas Nucleares/química , Linaje , Regiones Promotoras Genéticas , Fibrosis Pulmonar/etiología , Ribonucleoproteínas Nucleares Pequeñas/química , Homología de Secuencia , Telomerasa/genética , Transcripción Genética
14.
Nature ; 530(7590): 298-302, 2016 Feb 18.
Artículo en Inglés | MEDLINE | ID: mdl-26829225

RESUMEN

U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Šresolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.


Asunto(s)
Microscopía por Crioelectrón , Ribonucleoproteínas Nucleares Pequeñas/ultraestructura , Proteínas de Saccharomyces cerevisiae/ultraestructura , Saccharomyces cerevisiae/ultraestructura , Emparejamiento Base , Dominio Catalítico , ADN Helicasas/metabolismo , Exones/genética , Guanosina Trifosfato/metabolismo , Enlace de Hidrógeno , Modelos Moleculares , Conformación de Ácido Nucleico , Sitios de Empalme de ARN , ARN Nuclear Pequeño/química , ARN Nuclear Pequeño/genética , ARN Nuclear Pequeño/metabolismo , Ribonucleoproteína Nuclear Pequeña U4-U6/química , Ribonucleoproteína Nuclear Pequeña U4-U6/metabolismo , Ribonucleoproteína Nuclear Pequeña U5/química , Ribonucleoproteína Nuclear Pequeña U5/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/genética , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crecimiento & desarrollo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Empalmosomas/metabolismo
15.
Nucleic Acids Res ; 48(2): 788-801, 2020 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-31799608

RESUMEN

In all organisms, a selected type of proteins accomplishes critical roles in cellular processes that govern gene expression. The multifunctional protein Gemin5 cooperates in translation control and ribosome binding, besides acting as the RNA-binding protein of the survival of motor neuron (SMN) complex. While these functions reside on distinct domains located at each end of the protein, the structure and function of the middle region remained unknown. Here, we solved the crystal structure of an extended tetratricopeptide (TPR)-like domain in human Gemin5 that self-assembles into a previously unknown canoe-shaped dimer. We further show that the dimerization module is functional in living cells driving the interaction between the viral-induced cleavage fragment p85 and the full-length Gemin5, which anchors splicing and translation members. Disruption of the dimerization surface by a point mutation in the TPR-like domain prevents this interaction and also abrogates translation enhancement induced by p85. The characterization of this unanticipated dimerization domain provides the structural basis for a role of the middle region of Gemin5 as a central hub for protein-protein interactions.


Asunto(s)
Biosíntesis de Proteínas , Proteínas de Unión al ARN/genética , Ribonucleoproteínas Nucleares Pequeñas/genética , Proteínas del Complejo SMN/genética , Humanos , Unión Proteica , Dominios y Motivos de Interacción de Proteínas/genética , Multimerización de Proteína/genética , Ribonucleoproteínas Nucleares Pequeñas/química , Proteínas del Complejo SMN/química
16.
Nucleic Acids Res ; 48(2): 895-911, 2020 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-31799625

RESUMEN

The assembly of snRNP cores, in which seven Sm proteins, D1/D2/F/E/G/D3/B, form a ring around the nonameric Sm site of snRNAs, is the early step of spliceosome formation and essential to eukaryotes. It is mediated by the PMRT5 and SMN complexes sequentially in vivo. SMN deficiency causes neurodegenerative disease spinal muscular atrophy (SMA). How the SMN complex assembles snRNP cores is largely unknown, especially how the SMN complex achieves high RNA assembly specificity and how it is released. Here we show, using crystallographic and biochemical approaches, that Gemin2 of the SMN complex enhances RNA specificity of SmD1/D2/F/E/G via a negative cooperativity between Gemin2 and RNA in binding SmD1/D2/F/E/G. Gemin2, independent of its N-tail, constrains the horseshoe-shaped SmD1/D2/F/E/G from outside in a physiologically relevant, narrow state, enabling high RNA specificity. Moreover, the assembly of RNAs inside widens SmD1/D2/F/E/G, causes the release of Gemin2/SMN allosterically and allows SmD3/B to join. The assembly of SmD3/B further facilitates the release of Gemin2/SMN. This is the first to show negative cooperativity in snRNP assembly, which provides insights into RNA selection and the SMN complex's release. These findings reveal a basic mechanism of snRNP core assembly and facilitate pathogenesis studies of SMA.


Asunto(s)
Proteínas del Tejido Nervioso/química , Proteínas de Unión al ARN/química , ARN/química , Empalmosomas/química , Proteínas Nucleares snRNP/química , Cristalografía por Rayos X , Humanos , Atrofia Muscular Espinal/genética , Atrofia Muscular Espinal/patología , Proteínas del Tejido Nervioso/genética , Conformación Proteica , ARN/genética , Proteínas de Unión al ARN/genética , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/genética , Proteínas del Complejo SMN/química , Proteínas del Complejo SMN/genética , Empalmosomas/genética , Proteínas Nucleares snRNP/genética
17.
Proc Natl Acad Sci U S A ; 116(47): 23653-23661, 2019 11 19.
Artículo en Inglés | MEDLINE | ID: mdl-31694883

RESUMEN

The activation of innate immune receptors by pathogen-associated molecular patterns (PAMPs) is central to host defense against infections. On the other hand, these receptors are also activated by immunogenic damage-associated molecular patterns (DAMPs), typically released from dying cells, and the activation can evoke chronic inflammatory or autoimmune disorders. One of the best known receptors involved in the immune pathogenesis is Toll-like receptor 7 (TLR7), which recognizes RNA with single-stranded structure. However, the causative DAMP RNA(s) in the pathogenesis has yet to be identified. Here, we first developed a chemical compound, termed KN69, that suppresses autoimmunity in several established mouse models. A subsequent search for KN69-binding partners led to the identification of U11 small nuclear RNA (U11snRNA) as a candidate DAMP RNA involved in TLR7-induced autoimmunity. We then showed that U11snRNA robustly activated the TLR7 pathway in vitro and induced arthritis disease in vivo. We also found a correlation between high serum level of U11snRNA and autoimmune diseases in human subjects and established mouse models. Finally, by revealing the structural basis for U11snRNA's ability to activate TLR7, we developed more potent TLR7 agonists and TLR7 antagonists, which may offer new therapeutic approaches for autoimmunity or other immune-driven diseases. Thus, our study has revealed a hitherto unknown immune function of U11snRNA, providing insight into TLR7-mediated autoimmunity and its potential for further therapeutic applications.


Asunto(s)
Glicoproteínas de Membrana/agonistas , ARN Nuclear Pequeño/inmunología , Receptor Toll-Like 7/agonistas , Adulto , Alarminas/química , Animales , Artritis Reumatoide/sangre , Artritis Reumatoide/inmunología , Enfermedades Autoinmunes/sangre , Enfermedades Autoinmunes/inmunología , Secuencia de Bases , Línea Celular Tumoral , Modelos Animales de Enfermedad , Femenino , Humanos , Inmunosupresores/síntesis química , Inmunosupresores/farmacología , Lupus Eritematoso Sistémico/sangre , Lupus Eritematoso Sistémico/inmunología , Glicoproteínas de Membrana/deficiencia , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Ratones Endogámicos DBA , Persona de Mediana Edad , ARN/inmunología , ARN/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/inmunología , Análisis de Secuencia de ARN , Receptor Toll-Like 7/deficiencia , Adulto Joven
18.
J Biol Chem ; 295(7): 2097-2112, 2020 02 14.
Artículo en Inglés | MEDLINE | ID: mdl-31914407

RESUMEN

The RNA helicase bad response to refrigeration 2 homolog (BRR2) is required for the activation of the spliceosome before the first catalytic step of RNA splicing. BRR2 represents a distinct subgroup of Ski2-like nucleic acid helicases whose members comprise tandem helicase cassettes. Only the N-terminal cassette of BRR2 is an active ATPase and can unwind substrate RNAs. The C-terminal cassette represents a pseudoenzyme that can stimulate RNA-related activities of the N-terminal cassette. However, the molecular mechanisms by which the C-terminal cassette modulates the activities of the N-terminal unit remain elusive. Here, we show that N- and C-terminal cassettes adopt vastly different relative orientations in a crystal structure of BRR2 in complex with an activating domain of the spliceosomal Prp8 protein at 2.4 Å resolution compared with the crystal structure of BRR2 alone. Likewise, inspection of BRR2 structures within spliceosomal complexes revealed that the cassettes occupy different relative positions and engage in different intercassette contacts during different splicing stages. Engineered disulfide bridges that locked the cassettes in two different relative orientations had opposite effects on the RNA-unwinding activity of the N-terminal cassette, with one configuration enhancing and the other configuration inhibiting RNA unwinding compared with the unconstrained protein. Moreover, we found that differences in relative positioning of the cassettes strongly influence RNA-stimulated ATP hydrolysis by the N-terminal cassette. Our results indicate that the inactive C-terminal cassette of BRR2 can both positively and negatively affect the activity of the N-terminal helicase unit from a distance.


Asunto(s)
Empalme del ARN/genética , Proteínas de Unión al ARN/ultraestructura , Ribonucleoproteínas Nucleares Pequeñas/ultraestructura , Empalmosomas/genética , Adenosina Trifosfatasas/genética , Catálisis , Cristalografía por Rayos X , Humanos , Conformación Proteica , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/genética , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/genética , Empalmosomas/ultraestructura , Especificidad por Sustrato
19.
Nature ; 518(7538): 249-53, 2015 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-25470060

RESUMEN

DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.


Asunto(s)
ARN Helicasas DEAD-box/metabolismo , Genes de ARNr/genética , Procesamiento Postranscripcional del ARN , ARN Ribosómico/biosíntesis , ARN Ribosómico/metabolismo , Transcripción Genética , Cromatina/genética , Cromatina/metabolismo , Humanos , Factor B de Elongación Transcripcional Positiva/metabolismo , Unión Proteica , ARN Polimerasa I/metabolismo , ARN Polimerasa II/metabolismo , ARN Ribosómico/genética , ARN Nucleolar Pequeño/genética , ARN Nucleolar Pequeño/metabolismo , Proteínas de Unión al ARN/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/metabolismo
20.
Semin Cell Dev Biol ; 79: 92-102, 2018 07.
Artículo en Inglés | MEDLINE | ID: mdl-29037818

RESUMEN

Split gene architecture of most human genes requires removal of intervening sequences by mRNA splicing that occurs on large multiprotein complexes called spliceosomes. Mutations compromising several spliceosomal components have been recorded in degenerative syndromes and haematological neoplasia, thereby highlighting the importance of accurate splicing execution in homeostasis of assorted adult tissues. Moreover, insufficient splicing underlies defective development of craniofacial skeleton and upper extremities. This review summarizes recent advances in the understanding of splicing factor function deduced from cryo-EM structures. We combine these data with the characterization of splicing factors implicated in hereditary or somatic disorders, with a focus on potential functional consequences the mutations may elicit in spliceosome assembly and/or performance. Given aberrant splicing or perturbations in splicing efficiency substantially underpin disease pathogenesis, profound understanding of the mis-splicing principles may open new therapeutic vistas. In three major sections dedicated to retinal dystrophies, hereditary acrofacial syndromes, and haematological malignancies, we delineate the noticeable variety of conditions associated with dysfunctional splicing and accentuate recurrent patterns in splicing defects.


Asunto(s)
Enfermedad/genética , Precursores del ARN/genética , Empalme del ARN , Ribonucleoproteínas Nucleares Pequeñas/genética , Empalmosomas/genética , Animales , Microscopía por Crioelectrón , Humanos , Mutación , Conformación Proteica , Ribonucleoproteínas Nucleares Pequeñas/química , Ribonucleoproteínas Nucleares Pequeñas/ultraestructura
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA