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1.
Nat Rev Mol Cell Biol ; 23(2): 93-106, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34594027

RESUMO

In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.


Assuntos
Eucariotos/genética , Regulação da Expressão Gênica , Poli A/metabolismo , RNA Mensageiro/metabolismo , Animais , Humanos , Biossíntese de Proteínas/genética , Estabilidade de RNA , RNA Mensageiro/genética
2.
Cell ; 176(5): 1014-1025.e12, 2019 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-30794773

RESUMO

Bioactive molecules can pass between microbiota and host to influence host cellular functions. However, general principles of interspecies communication have not been discovered. We show here in C. elegans that nitric oxide derived from resident bacteria promotes widespread S-nitrosylation of the host proteome. We further show that microbiota-dependent S-nitrosylation of C. elegans Argonaute protein (ALG-1)-at a site conserved and S-nitrosylated in mammalian Argonaute 2 (AGO2)-alters its function in controlling gene expression via microRNAs. By selectively eliminating nitric oxide generation by the microbiota or S-nitrosylation in ALG-1, we reveal unforeseen effects on host development. Thus, the microbiota can shape the post-translational landscape of the host proteome to regulate microRNA activity, gene expression, and host development. Our findings suggest a general mechanism by which the microbiota may control host cellular functions, as well as a new role for gasotransmitters.


Assuntos
Interações entre Hospedeiro e Microrganismos/genética , MicroRNAs/metabolismo , Óxido Nítrico/metabolismo , Animais , Proteínas Argonautas/genética , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Células HEK293 , Células HeLa , Humanos , MicroRNAs/fisiologia , Microbiota/genética , Óxido Nítrico/fisiologia , Processamento de Proteína Pós-Traducional/genética , Proteoma/genética , Proteoma/metabolismo , Proteômica/métodos , Proteínas de Ligação a RNA/genética
3.
Cell ; 167(1): 122-132.e9, 2016 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-27641505

RESUMO

A major determinant of mRNA half-life is the codon-dependent rate of translational elongation. How the processes of translational elongation and mRNA decay communicate is unclear. Here, we establish that the DEAD-box protein Dhh1p is a sensor of codon optimality that targets an mRNA for decay. First, we find mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a Dhh1p-dependent manner. Biochemical experiments show Dhh1p is preferentially associated with mRNAs with suboptimal codon choice. We find these effects on mRNA decay are sensitive to the number of slow-moving ribosomes on an mRNA. Moreover, we find Dhh1p overexpression leads to the accumulation of ribosomes specifically on mRNAs (and even codons) of low codon optimality. Lastly, Dhh1p physically interacts with ribosomes in vivo. Together, these data argue that Dhh1p is a sensor for ribosome speed, targeting an mRNA for repression and subsequent decay.


Assuntos
Códon/metabolismo , RNA Helicases DEAD-box/metabolismo , Biossíntese de Proteínas , Estabilidade de RNA , RNA Mensageiro/metabolismo , Ribossomos/metabolismo , Códon/genética , RNA Helicases DEAD-box/genética , Meia-Vida
4.
Nat Rev Mol Cell Biol ; 19(1): 20-30, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29018283

RESUMO

The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery. In this Review, we first discuss the evidence for codon-dependent effects on translation, beginning with the basic mechanisms through which translation perturbation can affect translation efficiency, protein folding and transcript stability. We then discuss how codon effects are leveraged by the cell to tailor the proteome to maintain homeostasis, execute specific gene expression programmes of growth or differentiation and optimize the efficiency of protein production.


Assuntos
Códon/genética , Biossíntese de Proteínas/genética , Proteínas/genética , Estabilidade de RNA/genética , RNA Mensageiro/genética , Animais , Homeostase/genética , Humanos , Dobramento de Proteína , Ribossomos/genética
5.
Cell ; 163(2): 292-300, 2015 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-26451481

RESUMO

Among the three phases of mRNA translation-initiation, elongation, and termination-initiation has traditionally been considered to be rate limiting and thus the focus of regulation. Emerging evidence, however, demonstrates that control of ribosome translocation (polypeptide elongation) can also be regulatory and indeed exerts a profound influence on development, neurologic disease, and cell stress. The correspondence of mRNA codon usage and the relative abundance of their cognate tRNAs is equally important for mediating the rate of polypeptide elongation. Here, we discuss recent results showing that ribosome pausing is a widely used mechanism for controlling translation and, as a result, biological transitions in health and disease.


Assuntos
Regulação da Expressão Gênica , Elongação Traducional da Cadeia Peptídica , Polirribossomos/metabolismo , Animais , Códon , Doença/genética , Humanos , Iniciação Traducional da Cadeia Peptídica , RNA Mensageiro/metabolismo , RNA de Transferência/metabolismo
6.
Cell ; 160(6): 1111-24, 2015 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-25768907

RESUMO

mRNA degradation represents a critical regulated step in gene expression. Although the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, whereas the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as a mechanism to finely tune levels of mRNAs and, ultimately, proteins.


Assuntos
Códon , RNA Fúngico/genética , RNA Fúngico/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Saccharomyces cerevisiae/metabolismo , Biossíntese de Proteínas , Estabilidade de RNA , RNA Fúngico/química , RNA Mensageiro/química
7.
Mol Cell ; 82(8): 1467-1476, 2022 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-35452615

RESUMO

Messenger RNA (mRNA) translation by the ribosome represents the final step of a complicated molecular dance from DNA to protein. Although classically considered a decipherer that translates a 64-word genetic code into a proteome of astonishing complexity, the ribosome can also shape the transcriptome by controlling mRNA stability. Recent work has discovered that the ribosome is an arbiter of the general mRNA degradation pathway, wherein the ribosome transit rate serves as a major determinant of transcript half-lives. Specifically, members of the degradation complex sense ribosome translocation rates as a function of ribosome elongation rates. Central to this notion is the concept of codon optimality: although all codons impact translation rates, some are deciphered quickly, whereas others cause ribosome hesitation as a consequence of relative cognate tRNA concentration. These transient pauses induce a unique ribosome conformational state that is probed by the deadenylase complex, thereby inducing an orchestrated set of events that enhance both poly(A) shortening and cap removal. Together, these data imply that the coding region of an mRNA not only encodes for protein content but also impacts protein levels through determining the transcript's fate.


Assuntos
Biossíntese de Proteínas , Estabilidade de RNA , Códon/genética , Códon/metabolismo , Proteínas/metabolismo , Estabilidade de RNA/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ribossomos/genética , Ribossomos/metabolismo
8.
Mol Cell ; 70(6): 1089-1100.e8, 2018 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-29932902

RESUMO

Translation and decay of eukaryotic mRNAs is controlled by shortening of the poly(A) tail and release of the poly(A)-binding protein Pab1/PABP. The Ccr4-Not complex contains two exonucleases-Ccr4 and Caf1/Pop2-that mediate mRNA deadenylation. Here, using a fully reconstituted biochemical system with proteins from the fission yeast Schizosaccharomyces pombe, we show that Pab1 interacts with Ccr4-Not, stimulates deadenylation, and differentiates the roles of the nuclease enzymes. Surprisingly, Pab1 release relies on Ccr4 activity. In agreement with this, in vivo experiments in budding yeast show that Ccr4 is a general deadenylase that acts on all mRNAs. In contrast, Caf1 only trims poly(A) not bound by Pab1. As a consequence, Caf1 is a specialized deadenylase required for the selective deadenylation of transcripts with lower rates of translation elongation and reduced Pab1 occupancy. These findings reveal a coupling between the rates of translation and deadenylation that is dependent on Pab1 and Ccr4-Not.


Assuntos
Exorribonucleases/metabolismo , Proteína I de Ligação a Poli(A)/metabolismo , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Citoplasma/metabolismo , Endonucleases/metabolismo , Exorribonucleases/genética , Poli A/metabolismo , Poliadenilação , Estabilidade de RNA , RNA Fúngico/genética , RNA Fúngico/metabolismo , RNA Mensageiro/genética , Proteínas de Ligação a RNA/genética , Ribonucleases/metabolismo , Schizosaccharomyces/enzimologia , Schizosaccharomyces/genética , Schizosaccharomyces/metabolismo , Proteínas de Schizosaccharomyces pombe/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcriptoma
9.
Nat Rev Mol Cell Biol ; 14(11): 699-712, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-24105322

RESUMO

The increased application of transcriptome-wide profiling approaches has led to an explosion in the number of documented long non-coding RNAs (lncRNAs). While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown. Early discoveries support a paradigm in which lncRNAs regulate transcription via chromatin modulation, but new functions are steadily emerging. Given the biochemical versatility of RNA, lncRNAs may be used for various tasks, including post-transcriptional regulation, organization of protein complexes, cell-cell signalling and allosteric regulation of proteins.


Assuntos
RNA Longo não Codificante/metabolismo , Animais , Variação Genética/genética , Variação Genética/fisiologia , Humanos , Modelos Biológicos , RNA Longo não Codificante/genética
10.
Mol Cell ; 59(5): 716-7, 2015 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-26340422

RESUMO

In an age of next-generation sequencing, the ability to purify RNA transcripts has become a critical issue. In this issue, Duffy et al. (2015) improve on a pre-existing technique of RNA labeling and purification by 4-thiouridine tagging. By increasing the efficiency of RNA capture, this method will enhance the ability to study RNA dynamics, especially for transcripts normally inefficiently captured by previous methods.


Assuntos
MicroRNAs/química , Humanos
11.
RNA ; 24(10): 1377-1389, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29997263

RESUMO

Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in eukaryotic cells. Previous work by us and others has shown that codon identity exerts a powerful influence on mRNA stability. In Saccharomyces cerevisiae, studies using a handful of reporter mRNAs show that optimal codons increase translation elongation rate, which in turn increases mRNA stability. However, a direct relationship between elongation rate and mRNA stability has not been established across the entire yeast transcriptome. In addition, there is evidence from work in higher eukaryotes that amino acid identity influences mRNA stability, raising the question as to whether the impact of translation elongation on mRNA decay is at the level of tRNA decoding, amino acid incorporation, or some combination of each. To address these questions, we performed ribosome profiling of wild-type yeast. In good agreement with other studies, our data showed faster codon-specific elongation over optimal codons and faster transcript-level elongation correlating with transcript optimality. At both the codon-level and transcript-level, faster elongation correlated with increased mRNA stability. These findings were reinforced by showing increased translation efficiency and kinetics for a panel of 11 HIS3 reporter mRNAs of increasing codon optimality. While we did observe that elongation measured by ribosome profiling is composed of both amino acid identity and synonymous codon effects, further analyses of these data establish that A-site tRNA decoding rather than other steps of translation elongation is driving mRNA decay in yeast.


Assuntos
Sítios de Ligação , Biossíntese de Proteínas/genética , RNA Mensageiro/genética , Ribossomos/metabolismo , Códon , Ligação Proteica , Processamento Pós-Transcricional do RNA , Estabilidade de RNA , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
12.
Mol Cell ; 45(3): 279-91, 2012 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-22226051

RESUMO

Decapping represents a critical control point in regulating expression of protein coding genes. Here, we demonstrate that decapping also modulates expression of long noncoding RNAs (lncRNAs). Specifically, levels of >100 lncRNAs in yeast are controlled by decapping and are degraded by a pathway that occurs independent of decapping regulators. We find many lncRNAs degraded by DCP2 are expressed proximal to inducible genes. Of these, we show several genes required for galactose utilization are associated with lncRNAs that have expression patterns inversely correlated with their mRNA counterpart. Moreover, decapping of these lncRNAs is critical for rapid and robust induction of GAL gene expression. Failure to destabilize a lncRNA known to exert repressive histone modifications results in perpetuation of a repressive chromatin state that contributes to reduced plasticity of gene activation. We propose that decapping and lncRNA degradation serve a vital role in transcriptional regulation specifically at inducible genes.


Assuntos
Exorribonucleases/genética , Regulação Fúngica da Expressão Gênica , Capuzes de RNA/metabolismo , Processamento Pós-Transcricional do RNA , RNA não Traduzido/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Endorribonucleases/genética , Endorribonucleases/metabolismo , Exorribonucleases/metabolismo , Técnicas de Inativação de Genes , Regiões Promotoras Genéticas , Capuzes de RNA/genética , Estabilidade de RNA , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA não Traduzido/genética , Saccharomyces cerevisiae/enzimologia , Proteínas de Saccharomyces cerevisiae/metabolismo , Análise de Sequência de RNA
13.
Trends Genet ; 32(11): 687-688, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27594172

RESUMO

Precise elimination of maternal mRNAs plays a critical role during the maternal-to-zygotic transition (MZT) to promote developmental processing. Two new studies demonstrate that, in eukaryotes, codon-mediated decay is a conserved mechanism to shape maternal mRNA stability by affecting deadenylation rate in a translation-dependent manner. These studies add to a growing body of literature suggesting that translational elongation rates are a major determinant of mRNA stability.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento/genética , Biossíntese de Proteínas , Estabilidade de RNA/genética , RNA Mensageiro/genética , Códon/genética , Eucariotos/genética , Humanos , Zigoto/crescimento & desenvolvimento
14.
RNA ; 22(5): 709-21, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26952104

RESUMO

Decay of mRNA is essential for the efficient regulation of gene expression. A major pathway of mRNA degradation is initiated by the shortening of the poly(A) tail via the CCR4/NOT deadenylase complex. Deadenylation is followed by removal of the 5' cap (i.e., decapping) and then 5' to 3' exonucleolytic decay of the message body. The highly conserved CCR4/NOT deadenylase complex consists of the exonucleases CCR4 and POP2/CAF1, as well as a group of four or five (depending on organism) accessory factors of unknown function, i.e., the NOT proteins. In this study, we find thatSaccharomyces cerevisiaeNot2p, Not3p, and Not5p (close paralogs of each other) are involved in promoting mRNA decapping. Furthermore, we find that Not3p and Not5p bind to the decapping activator protein Pat1p. Together, these data implicate the deadenylase complex in coordinating the downstream decapping reaction via Not2p, Not3p, and Not5p. This suggests that the coupling of deadenylation with decapping is, in part, a direct consequence of coordinated assembly of decay factors.


Assuntos
Capuzes de RNA , RNA Mensageiro/genética , Proteínas de Saccharomyces cerevisiae/fisiologia , Sequência de Aminoácidos , Western Blotting , Dados de Sequência Molecular , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Homologia de Sequência de Aminoácidos , Técnicas do Sistema de Duplo-Híbrido
15.
Mol Cell ; 40(3): 349-50, 2010 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-21070961

RESUMO

With most of the important players identified, the process of decapping is thought, for the most part, to be well understood. In this issue of Molecular Cell, Song et al. (2010) challenge this notion with the identification of a previously uncharacterized mRNA decapping enzyme.

16.
PLoS Biol ; 10(6): e1001342, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22719226

RESUMO

Translational control and messenger RNA (mRNA) decay represent important control points in the regulation of gene expression. In yeast, the major pathway for mRNA decay is initiated by deadenylation followed by decapping and 5'-3' exonucleolytic digestion of the mRNA. Proteins that activate decapping, such as the DEAD-box RNA helicase Dhh1, have been postulated to function by limiting translation initiation, thereby promoting a ribosome-free mRNA that is targeted for decapping. In contrast to this model, we show here that Dhh1 represses translation in vivo at a step subsequent to initiation. First, we establish that Dhh1 represses translation independent of initiation factors eIF4E and eIF3b. Second, we show association of Dhh1 on an mRNA leads to the accumulation of ribosomes on the transcript. Third, we demonstrate that endogenous Dhh1 accompanies slowly translocating polyribosomes. Lastly, Dhh1 activates decapping in response to impaired ribosome elongation. Together, these findings suggest that changes in ribosome transit rate represent a key event in the decapping and turnover of mRNA.


Assuntos
RNA Helicases DEAD-box/metabolismo , Ribossomos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , RNA Helicases DEAD-box/genética , Fator de Iniciação 3 em Eucariotos/genética , Fator de Iniciação 3 em Eucariotos/metabolismo , Fator de Iniciação 4E em Eucariotos/genética , Fator de Iniciação 4E em Eucariotos/metabolismo , Biossíntese de Proteínas , Capuzes de RNA/metabolismo , Estabilidade de RNA/genética , Estabilidade de RNA/fisiologia , RNA Mensageiro/metabolismo , Saccharomyces cerevisiae/enzimologia , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética
17.
Nature ; 461(7261): 225-9, 2009 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-19701183

RESUMO

The rates of RNA decay and transcription determine the steady-state levels of all messenger RNA and both can be subject to regulation. Although the details of transcriptional regulation are becoming increasingly understood, the mechanism(s) controlling mRNA decay remain unclear. In yeast, a major pathway of mRNA decay begins with deadenylation followed by decapping and 5'-3' exonuclease digestion. Importantly, it is hypothesized that ribosomes must be removed from mRNA before transcripts are destroyed. Contrary to this prediction, here we show that decay takes place while mRNAs are associated with actively translating ribosomes. The data indicate that dissociation of ribosomes from mRNA is not a prerequisite for decay and we suggest that the 5'-3' polarity of mRNA degradation has evolved to ensure that the last translocating ribosome can complete translation.


Assuntos
Biossíntese de Proteínas , Estabilidade de RNA , RNA Fúngico/metabolismo , RNA Mensageiro/metabolismo , Saccharomyces cerevisiae/genética , Poli A/metabolismo , Poliadenilação , Polirribossomos/metabolismo , Capuzes de RNA/metabolismo , RNA Fúngico/genética , RNA Mensageiro/genética
18.
Biochim Biophys Acta ; 1829(8): 817-23, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23528737

RESUMO

Translational control is a vital aspect of gene expression. Message specific translational repressors have been known for decades. Recent evidence, however, suggests that a general machinery exists that dampens the translational capacity of the majority of mRNAs. This activity has been best ascribed to a conserved family of RNA helicases called the DHH1/RCKp54 family. The function of these helicases is to promote translational silencing. By transitioning mRNA into quiescence, DHH1/RCKp54 helicases promote either mRNA destruction or storage. In this review we describe the known roles of these helicases and propose a mechanistic model to explain their mode of action. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.


Assuntos
RNA Helicases DEAD-box/genética , RNA Helicases DEAD-box/metabolismo , Interferência de RNA , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Animais , RNA Helicases DEAD-box/química , Humanos , RNA Mensageiro/química
20.
Nat Rev Drug Discov ; 23(2): 108-125, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-38049504

RESUMO

Transfer RNAs (tRNAs) have a crucial role in protein synthesis, and in recent years, their therapeutic potential for the treatment of genetic diseases - primarily those associated with a mutation altering mRNA translation - has gained significant attention. Engineering tRNAs to readthrough nonsense mutation-associated premature termination of mRNA translation can restore protein synthesis and function. In addition, supplementation of natural tRNAs can counteract effects of missense mutations in proteins crucial for tRNA biogenesis and function in translation. This Review will present advances in the development of tRNA therapeutics with high activity and safety in vivo and discuss different formulation approaches for single or chronic treatment modalities. The field of tRNA therapeutics is still in its early stages, and a series of challenges related to tRNA efficacy and stability in vivo, delivery systems with tissue-specific tropism, and safe and efficient manufacturing need to be addressed.


Assuntos
Códon sem Sentido , RNA de Transferência , Humanos , Mutação , RNA de Transferência/genética , RNA de Transferência/metabolismo , Biossíntese de Proteínas
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