RESUMO
RNA helicases are essential for virtually all cellular processes, however, their regulation is poorly understood. The activities of eight RNA helicases are required for pre-mRNA splicing. Amongst these, Brr2p is unusual in having two helicase modules, of which only the amino-terminal helicase domain appears to be catalytically active. Using genetic and biochemical approaches, we investigated interaction of the carboxy-terminal helicase module, in particular the carboxy-terminal Sec63-2 domain, with the splicing RNA helicase Prp16p. Combining mutations in BRR2 and PRP16 suppresses or enhances physical interaction and growth defects in an allele-specific manner, signifying functional interactions. Notably, we show that Brr2p Sec63-2 domain can modulate the ATPase activity of Prp16p in vitro by interfering with its ability to bind RNA. We therefore propose that the carboxy-terminal helicase module of Brr2p acquired a regulatory function that allows Brr2p to modulate the ATPase activity of Prp16p in the spliceosome by controlling access to its RNA substrate/cofactor.
Assuntos
Adenosina Trifosfatases/metabolismo , RNA Helicases/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Adenosina Trifosfatases/genética , Alelos , RNA Helicases DEAD-box/metabolismo , Temperatura Alta , Íntrons , Mutação , Estrutura Terciária de Proteína , RNA/metabolismo , RNA Helicases/química , RNA Helicases/genética , Splicing de RNA , Fatores de Processamento de RNA , Ribonucleoproteínas Nucleares Pequenas/química , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genéticaRESUMO
In eukaryotic cells, introns are spliced from pre-mRNAs by the spliceosome. Both the composition and the structure of the spliceosome are highly dynamic, and eight DExD/H RNA helicases play essential roles in controlling conformational rearrangements. There is evidence that the various helicases are functionally and physically connected with each other and with many other factors in the spliceosome. Understanding the dynamics of those interactions is essential to comprehend the mechanism and regulation of normal as well as of pathological splicing. This review focuses on recent advances in the characterization of the splicing helicases and their interactions, and highlights the deep integration of splicing helicases in global mRNP biogenesis pathways.
Assuntos
RNA Helicases/metabolismo , Splicing de RNA/fisiologia , RNA Helicases/genética , Precursores de RNA/genética , Precursores de RNA/metabolismo , Processamento Pós-Transcricional do RNA/fisiologia , Spliceossomos/química , Spliceossomos/metabolismoRESUMO
RNA helicases of the DEAD-box protein family have been shown to participate in every aspect of RNA metabolism. They are present in most organisms where they work as RNA helicases or RNPases. The properties of these enzymes in vivo remains poorly described, however some were extensively characterized in vitro, and the solved crystal structures of a few are now available. Taken together, this information gives insight into the regulation of ATP and RNA binding as well as in the ATPase and helicase activities. This review will focus on the description of the molecular characteristics of members of the DEAD-box protein family and on the enzymatic activities they possess.
Assuntos
RNA Helicases/genética , RNA Helicases/metabolismo , Difosfato de Adenosina/metabolismo , Adenosina Trifosfatases/metabolismo , Processamento Alternativo , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Sítios de Ligação , Sequência Conservada , Cristalografia por Raios X , Humanos , Modelos Biológicos , Modelos Moleculares , Dados de Sequência Molecular , Ligação Proteica , Conformação Proteica , Processamento de Proteína Pós-Traducional , Estrutura Terciária de Proteína , RNA Helicases/química , RNA Mensageiro/metabolismo , Homologia de Sequência de Aminoácidos , Transcrição GênicaRESUMO
Pre-mRNA splicing requires the activities of several ATPases from the DEAH-box, DEAD-box and Ski2-like helicase families to control conformational rearrangements within the spliceosome. Recent findings indicate that several spliceosomal helicases can act at multiple stages of the splicing reaction, and information on how those multiple actions are controlled are emerging. The recently solved crystal structure of the DEAH-box helicase Prp43 provides novel insights into the similarities and differences between the three helicase families. Here we discuss the potential family-specific mechanisms of spliceosomal RNA helicases and their regulation.
Assuntos
Regulação da Expressão Gênica , RNA Helicases/fisiologia , Spliceossomos/fisiologia , Adenosina Trifosfatases/química , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Adenosina Trifosfatases/fisiologia , Sequência de Aminoácidos , RNA Helicases DEAD-box/química , RNA Helicases DEAD-box/genética , RNA Helicases DEAD-box/metabolismo , RNA Helicases DEAD-box/fisiologia , Humanos , RNA Helicases/química , RNA Helicases/genética , RNA Helicases/metabolismo , Precursores de RNA/química , Precursores de RNA/genética , Precursores de RNA/metabolismo , Splicing de RNA , Spliceossomos/química , Spliceossomos/genética , Spliceossomos/metabolismoRESUMO
The DEAD-box family of putative RNA helicases is composed of ubiquitous proteins that are found in nearly all organisms and that are involved in virtually all processes involving RNA. They are characterized by two tandemly linked, RecA-like domains that contain 11 conserved motifs and highly variable amino- and carboxy-terminal flanking sequences. For this reason, they are often considered to be modular multi-domain proteins. We tested this by making extensive BLASTs and sequence alignments to elucidate the minimal functional unit in nature. We then used this information to construct chimeras and deletions of six essential yeast proteins that were assayed in vivo. We purified many of the different constructs and characterized their biochemical properties in vitro. We found that sequence elements can only be switched between closely related proteins and that the carboxy-terminal sequences are important for high ATPase and strand displacement activities and for high RNA binding affinity. The amino-terminal elements were often toxic when overexpressed in vivo, and they may play regulatory roles. Both the amino and the carboxyl regions have a high frequency of sequences that are predicted to be intrinsically disordered, indicating that the flanking regions do not form distinct modular domains but probably assume an ordered structure with ligand binding. Finally, the minimal functional unit of the DEAD-box core starts two amino acids before the isolated phenylalanine of the Q motif and extends to about 35 residues beyond motif VI. These experiments provide evidence for how a highly conserved structural domain can be adapted to different cellular needs.
Assuntos
RNA Helicases DEAD-box/química , Proteínas Mutantes Quiméricas/metabolismo , Saccharomyces cerevisiae/crescimento & desenvolvimento , Saccharomyces cerevisiae/genética , Deleção de Sequência , Adenosina Trifosfatases/metabolismo , Trifosfato de Adenosina/metabolismo , Motivos de Aminoácidos , Sequência Conservada , RNA Helicases DEAD-box/genética , RNA Helicases DEAD-box/metabolismo , Primers do DNA/química , Primers do DNA/genética , Técnicas In Vitro , Proteínas Mutantes Quiméricas/genética , Mutação/genética , Estrutura Terciária de Proteína , RNA Fúngico/genética , Saccharomyces cerevisiae/metabolismoRESUMO
We have identified a highly conserved phenylalanine in motif IV of the DEAD-box helicases that is important for their enzymatic activities. In vivo analyses of essential proteins in yeast showed that mutants of this residue had severe growth phenotypes. Most of the mutants also were temperature sensitive, which suggested that the mutations altered the conformational stability. Intragenic suppressors of the F405L mutation in yeast Ded1 mapped close to regions of the protein involved in ATP or RNA binding in DEAD-box crystal structures, which implicated a defect at this level. In vitro experiments showed that these mutations affected ATP binding and hydrolysis as well as strand displacement activity. However, the most pronounced effect was the loss of the ATP-dependent cooperative binding of the RNA substrates. Sequence analyses and an examination of the Protein Data Bank showed that the motif IV phenylalanine is conserved among superfamily 2 helicases. The phenylalanine appears to be an anchor that maintains the rigidity of the RecA-like domain. For DEAD-box proteins, the phenylalanine also aligns a highly conserved arginine of motif VI through van der Waals and cation-pi interactions, thereby helping to maintain the network of interactions that exist between the different motifs involved in ATP and RNA binding.
Assuntos
RNA Helicases DEAD-box/química , RNA Helicases DEAD-box/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Trifosfato de Adenosina/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Arginina/química , Sequência de Bases , Sequência Conservada , RNA Helicases DEAD-box/genética , Cinética , Modelos Moleculares , Mutagênese Sítio-Dirigida , Fenótipo , Fenilalanina/química , RNA Fúngico/genética , RNA Fúngico/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Supressão GenéticaRESUMO
DEAD-box proteins are the most common RNA helicases, and they are associated with virtually all processes involving RNA. They have nine conserved motifs that are required for ATP and RNA binding, and for linking phosphoanhydride cleavage of ATP with helicase activity. The Q motif is the most recently identified conserved element, and it occurs approximately 17 amino acids upstream of motif I. There is a highly conserved, but isolated, aromatic group approximately 17 amino acids upstream of the Q motif. These two elements are involved in adenine recognition and in ATPase activity of DEAD-box proteins. We made extensive analyses of the Q motif and upstream aromatic residue in the yeast translation-initiation factor Ded1. We made site-specific mutations and tested them for viability in yeast. Moreover, we purified various mutant proteins and obtained the Michaelis-Menten parameters for the ATPase activities. We also measured RNA affinities and strand-displacement activities. We find that the Q motif not only regulates ATP binding and hydrolysis but also regulates the affinity of the protein for RNA substrates and ultimately the helicase activity.
Assuntos
Proteínas Fúngicas/metabolismo , RNA Helicases/química , RNA Helicases/metabolismo , RNA Fúngico/metabolismo , Adenina/química , Adenina/metabolismo , Adenosina Trifosfatases/metabolismo , Trifosfato de Adenosina/metabolismo , Alanina/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Substituição de Aminoácidos , Aminoácidos Aromáticos/química , Sequência Consenso , Ensaio de Desvio de Mobilidade Eletroforética , Escherichia coli/genética , Fator de Iniciação 4A em Eucariotos/genética , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Teste de Complementação Genética , Glicina/química , Cinética , Leucina/metabolismo , Dados de Sequência Molecular , Estrutura Secundária de Proteína , RNA Helicases/genética , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismoRESUMO
Pre-mRNA splicing requires the function of a number of RNA-dependent ATPases/helicases, yet no three-dimensional structure of any spliceosomal ATPases/helicases is known. The highly conserved DECD-box protein UAP56/Sub2 is an essential splicing factor that is also important for mRNA export. The expected ATPase/helicase activity appears to be essential for the UAP56/Sub2 functions. Here, we show that purified human UAP56 is an active RNA-dependent ATPase, and we also report the crystal structures of UAP56 alone and in complex with ADP, as well as a DECD to DEAD mutant. The structures reveal a unique spatial arrangement of the two conserved helicase domains, and ADP-binding induces significant conformational changes of key residues in the ATP-binding pocket. Our structural analyses suggest a specific protein-RNA displacement model of UAP56/Sub2. The detailed structural information provides important mechanistic insights into the splicing function of UAP56/Sub2. The structures also will be useful for the analysis of other spliceosomal DExD-box ATPases/helicases.
Assuntos
RNA Helicases/química , RNA Helicases/metabolismo , Difosfato de Adenosina/metabolismo , Adenosina Trifosfatases/química , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Trifosfato de Adenosina/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Sítios de Ligação , Cristalografia por Raios X , RNA Helicases DEAD-box , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Mutação/genética , Conformação Proteica , RNA/metabolismo , RNA Helicases/genética , Alinhamento de SequênciaRESUMO
SF1 and SF2 helicases have structurally conserved cores containing seven to eight distinctive motifs and variable amino- and carboxyl-terminal flanking sequences. We have discovered a motif upstream of motif I that is unique to and characteristic of the DEAD box family of RNA helicases. It consists of a 9 amino acid sequence containing an invariant glutamine. A conserved phenylalanine occurs 17 aa further upstream. Sequence alignments, site-specific mutagenesis, and ATPase assays show that this motif and the upstream phenylalanine are highly conserved, that they are essential for viability in the yeast Saccharomyces cerevisiae, and that they control ATP binding and hydrolysis in the yeast translation-initiation factor eIF4A. These results are consistent with computer studies of the solved crystal structures.