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BBA - Gene Regulatory Mechanisms (v.1779, #9)
Nuclear quality control of RNA polymerase II ribonucleoproteins in yeast: Tilting the balance to shape the transcriptome by Tommaso Villa; Mathieu Rougemaille; Domenico Libri (pp. 524-531).
From the very first time they set foot in the nuclear landscape till the end of their life, RNAs are packaged in ribonucleoproteins (RNPs) and face numerous processing steps to achieve function. To avoid the catastrophic consequences of naturally occurring processing errors, cells employ numerous quality control strategies. Focusing on yeast as a model system, we will review here how nuclear mechanisms ensure the proper assembly and maturation of mRNPs for their release in the cytoplasm, and highlight how these mechanisms are exploited to shape the RNA polymerase II transcriptome.
Keywords: RNA quality control; RNA processing; RNA degradation; mRNP assembly; Transcriptome regulation
Take the “A” tail – quality control of ribosomal and transfer RNA by Kasper R. Andersen; Torben Heick Jensen; Ditlev E. Brodersen (pp. 532-537).
The overall fidelity of RNA biosynthesis and processing is very high. This goes for both mRNAs, which are turned over relatively quickly, and for stable RNAs, such as the components of the translational apparatus, the transfer and ribosomal RNAs. However, no enzymatic process is completely error-free, so to minimize the number of non-functional transcripts, the cell has degradation pathways in place to efficiently deal with those mistakes that inevitably occur. Though several “RNA surveillance” or “RNA quality control” systems have been described that are able to specifically eliminate misfolded and non-functional RNAs, we still do not understand neither what precise features define a faulty RNA, nor the molecular basis for recognition of such molecules. Nonetheless, our knowledge about the controlled degradation of both stable and labile RNAs is now converging into a unified picture that points to the poly(A) tail as a key discriminator of RNA quality in both bacteria and eukaryotes.
Keywords: RNA quality control; RNA surveillance; tRNA; rRNA; Exosome; TRAMP
Recognition and elimination of nonsense mRNA by Oliver Mühlemann; Andrea B. Eberle; Lukas Stalder; Rodolfo Zamudio Orozco (pp. 538-549).
Among the different cellular surveillance mechanisms in charge to prevent production of faulty gene products, nonsense-mediated mRNA decay (NMD) represents a translation-dependent posttranscriptional process that selectively recognizes and degrades mRNAs whose open reading frame (ORF) is truncated by a premature translation termination codon (PTC, also called “nonsense codon”). In doing so, NMD protects the cell from accumulating C-terminally truncated proteins with potentially deleterious functions. Transcriptome profiling of NMD-deficient yeast, Drosophila, and human cells revealed that 3–10% of all mRNA levels are regulated (directly or indirectly) by NMD, indicating an important role of NMD in gene regulation that extends beyond quality control [J. Rehwinkel, J. Raes, E. Izaurralde, Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors, Trends Biochem. Sci. 31 (2006) 639-646.]. In this review, we focus on recent results from different model organisms that indicate an evolutionarily conserved mechanism for PTC identification.
Keywords: mRNA surveillance; Nonsense-mediated mRNA decay; Premature translation; Termination; mRNA turnover; mRNA quality control
Diverse aberrancies target yeast mRNAs to cytoplasmic mRNA surveillance pathways by Marenda A. Wilson; Stacie Meaux; Ambro van Hoof (pp. 550-557).
Eukaryotic gene expression is a complex, multistep process that needs to be executed with high fidelity and two general methods help achieve the overall accuracy of this process. Maximizing accuracy in each step in gene expression increases the fraction of correct mRNAs made. Fidelity is further improved by mRNA surveillance mechanisms that degrade incorrect or aberrant mRNAs that are made when a step is not perfectly executed. Here, we review how cytoplasmic mRNA surveillance mechanisms selectively recognize and degrade a surprisingly wide variety of aberrant mRNAs that are exported from the nucleus into the cytoplasm.
Keywords: mRNA surveillance; mRNA decay; Nonstop mRNA decay; No go mRNA decay
Exosome-mediated quality control: Substrate recruitment and molecular activity by Alice Lebreton; Bertrand Séraphin (pp. 558-565).
The eukaryotic exosome is a multisubunit complex that is mainly responsible for 3′–5′ exonucleolytic degradation of RNAs, both in the nucleus and the cytoplasm. In this review we summarize the recent experiments that have provided information on the organisation, structure and activity of this large assembly. Interestingly, eukaryotic exosomes have been implicated in a large number of RNA degradation pathways including recently discovered RNA quality control mechanisms. A variety of cofactors have been shown to participate in substrate recruitment and/or assist exonucleolytic activities. Despite this avalanche of new results, further analyses will be required to improve our understanding of exosome regulation.
Keywords: Exosome; Helicase; RNA quality control; RNA degradation; 3′–5′ exoribonuclease; Structure–function analysis
Coping with cryptic and defective transcripts in plant mitochondria by Sarah Holec; Heike Lange; Jean Canaday; Dominique Gagliardi (pp. 566-573).
Plant mitochondria are particularly prone to the production of both defective and cryptic transcripts as a result of the complex organisation and mode of expression of their genome. Cryptic transcripts are generated from intergenic regions due to a relaxed control of transcription. Certain intergenic regions are transcribed at higher rates than genuine genes and therefore, cryptic transcripts are abundantly produced in plant mitochondria. In addition, primary transcripts from genuine genes must go through complex post-transcriptional processes such as C to U editing and cis or trans splicing of group II introns. These post-transcriptional processes are rather inefficient and as a result, defective transcripts are constantly produced in plant mitochondria. In this review, we will describe the nature of cryptic and defective transcripts as well as their fate in plant mitochondria. Although RNA surveillance is crucial to establishing the final transcriptome by degrading cryptic transcripts, plant mitochondria are able to tolerate a surprising high level of defective transcripts.
Keywords: Plant mitochondria; Polyadenylation; RNA degradation; PNPase
Quality control of bacterial mRNA decoding and decay by Jamie Richards; Thomas Sundermeier; Anton Svetlanov; A. Wali Karzai (pp. 574-582).
Studies in eukaryotes and prokaryotes have revealed that gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. Indeed, the expression level of a protein is strongly affected by the steady state level of its mRNA. RNA decay can, along with transcription, play an important role in regulating gene expression by fine-tuning the steady state level of a given transcript and affecting its subsequent decoding during translation. Alterations in mRNA stability can in turn have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have evolved unique post transcriptional control mechanisms to enact such adaptive responses through: 1) general mRNA decay, 2) differential mRNA degradation using small non-coding RNAs (sRNAs), and 3) selective mRNA degradation using the tmRNA quality control system. Here, we review our current understanding of these molecular mechanisms, gleaned primarily from studies of the model gram negative organism Escherichia coli, that regulate the stability and degradation of normal and defective transcripts.
Keywords: RNA quality control; SmpB; tmRNA; Trans; -translation; RNase R; RNA decay