Nuclear RNA Surveillance & Turnover

1. Nuclear RNA Surveillance & Turnover David Bedwell Post-Transcriptional Regulatory Mechanisms MIC759 Sept. 25, 2008

2. mRNA quality control • Multiple processing and localization steps are required for proper mRNA maturation following the synthesis of the primary transcript. • At a minimum, these include capping, splicing, 3´-end cleavage, polyadenylation, and nuclear export. • If each of these 5 processes are 90% efficient, only ~59% of mRNAs will be properly matured. • What happens to the improperly processed transcripts? • Do they get sent to the cytoplasm for protein synthesis anyway? • Do they get degraded before they can make potentially defective proteins?

3. Section I. Nuclear mRNA Turnover pathways

4. Nuclear mRNA surveillance occurs at checkpoints during maturation mRNA synthesis involves a series of processing steps to synthesize a mature transcript that is proofread in parallel by nuclear surveillance mechanisms at each step. The splicing and processing components as well as export factors are co-transcriptionally recruited to the nascent transcript, possibly by the transcription complex, and the correct mRNA forms the core of an export-competent mRNP that is eventually exported and expressed in the cytoplasm. Alternatively, aberrant synthesis or processing leads to retention of the defective transcript. These retained transcripts are usually subjected to exosome-mediated degradation.

5. 3´5´ turnover 5´3´ turnover decapping deadenylases Nuclear degradation activities in yeast Saguez et al., Curr Opin Cell Biol 17: 287-293 (2005)

6. Core Associated Subunits of the Eukaryotic and Archaeal Exosomes Vanacova & Stefl, EMBO Reports 8: 651-657 (2007)

7. Molecular architecture of exosomes archaeal exosome archaeal exosome with the cap formed by Rrp4 A model of an RNA substrate highlights a putative path of RNA into the exosome through the cleft that is specific to the human exosome Vanacova & Stefl, EMBO Reports 8: 651-657 (2007)

8. Schematic diagram of the exosome topologies and RNA threading • - The arrows indicate the confirmed or hypothetical (indicated by a question mark) pathways of an RNA substrate in various forms of the exosomes. • Yellow stars indicate catalytically active sites. • The predicted positions of the yeast hydrolytic exonucleases Rrp44 and Rrp6 are indicated. • Rrp, ribosomal RNA processing factor. Vanacova & Stefl, EMBO Reports 8: 651-657 (2007)

9. Roles of the TRAMP Complex in RNA Degradation • TRAMP complex: • Trf4p: poly(A) polymerase • Air2p: RNA binding protein • Mtr4p: ATP-dependant RNA helicase • Trf5p is highly related to Trf4p • Air1p is highly related to Air2p • - The TRAMP complex interacts with RNAs or RNP complexes, making them targets for degradation. For most substrates other than tRNAs, this will primarily be via protein:protein interactions. • The zinc finger domains of Air2p might be involved in substrate binding. The RNA is then polyadenylated by Trf4p. • Exosome recruitment and activation requires the intact TRAMP complex. The activated exosome then rapidly deadenylates the RNA and can penetrate into regions of stable structure. • Helicase activity of Mtr4p is important for dissociation or remodeling of stable RNP structures to allow passage of the exosome. LaCava et al., Cell 121: 713-724 (2005)

10. Exonucleolytic activity of the exosome is stimulated by accessory protein complexes in vitro and in vivo A) The Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex tags aberrant RNAs with short stretches of oligo(A)s, which initiates RNA digestion by the exosome. B) Mtr4 helicase of the TRAMP complex unwinds the structured parts of RNAs. The TRAMP complex associates with the Nrd1 complex that binds to short sequence elements on a subset of nuclear RNAs. The interaction between the specific RNA recognition mediated by the Nrd1 complex and the polyadenylation activity mediated by the TRAMP complex acts as the initiation step for RNA degradation by the exosome. C)The Nrd1 complex can stimulate exosome activity on RNAs with the Nrd1 complex-specific binding sites. This often leads to partial digestion of the RNA (trimming), but can also cause RNA degradation. D) The exosome destroys the leftovers of RNA processing, such as the products of endonucleolytic cleavage, apparently by itself. Air, arginine methyltransferase-interacting RING finger protein; Mtr, mRNA transport; Nrd, nuclear pre-mRNA down-regulation; Trf, topoisomerase one-related function. Vanacova & Stefl, EMBO Reports 8: 651-657 (2007)

11. Signals for Exosome Activation Houseley et al.Nature Reviews Molecular Cell Biology7, 529–539 (2006)

12. Polyadenylation is also involved in stable RNA degradation in bacteria Model for quality control of stable RNA synthesis in bacteria. Genes encoding normal (wt-tRNA) and defective (ts-tRNA) RNAs are transcribed with equal efficiency to generate tRNA precursors. However, whereas wt-tRNA precursor is rapidly converted to its mature form by the processing RNases, maturation of the defective precursor is greatly slowed. As a consequence, the defective tRNA precursor is first subject to polyadenylation by poly(A) polymerase, and is then degraded by PNPase and other RNases. Li et al., EMBO J 21: 1132-1138 (2002)

13. Section II. Nuclear surveillance occurs at various nuclear checkpoints and is coupled to transcription, mRNA processing and mRNA export

14. Simplified view of eukaryotic gene expression • Eukaryotic gene expression includes: • transcription • nuclear mRNP processing steps • 5´-end capping • splicing • mRNP assembly • 3´-end cleavage • polyadenylation • mRNP surveillance • RNA export • All of these steps are coupled or coordinated with transcription. • NMD, nonsense-mediated decay; NPC, nuclear pore complex; • RNAPII, RNA polymerase II. Aguilera, Curr Opin Cell Biol 17: 242-250 (2005)

15. Exosome Exosome Overview of nuclear mRNA surveillance Vasudevan and Peltz, Curr Opin Cell Biol 15: 332-337 (2003)

16. RNA Polymerase II • RNA polymerase II (also called RNAP II or Pol II) transcribes DNA to synthesize precursors of mRNAs and most snRNAs. • A 550 kDa complex of 12 subunits. A wide range of transcription factors are required for it to bind to its promoters and begin transcription. • The largest subunit of Pol II (Rpb1) has a domain at its C-terminus that is called the CTD. Phosphorylation of the CTD is an important regulation mechanism, as this allows the binding and release of many factors that influence not only the transcription process, but also mRNA maturation and export from the nucleus. In this way, the CTD provides a platform for various factors that load on the nascent mRNA chain during transcription. • The CTD consists of heptapeptide repeats (consensus: YSPTSPS) ranging from 26 in yeast and 52 in mammals, out of which serines and threonines get phosphorylated. • Patterns of phosphorylation on these repeats can change rapidly during transcription. The regulation of the phosphorylation pattern and the resulting differential association of factors plays a major role not only in the regulation of transcription, but also in the fate of mRNA transcripts.

17. Co-transcriptional recruitment of pre-mRNA processing factors at the 5´ end of a gene Capping enzymes (guanylyltransferase [GT] and 7-methyltransferase [MT]), cap binding complex (CBC), cleavage/ polyadenylation factors (C/P), and the RNA 5´3´ exonuclease, Rat1, are indicated. Processing factors interact with pol II elongation complex via the CTD (green line) and probably also via the nascent RNA (red line). Phosphorylation of Ser2 and Ser5 residues in the CTD heptad repeats are marked P2 and P5. Capping enzymes stimulate early steps in pol II transcription including promoter clearance denoted by the thick arrow. Following addition of the cap, MeGppp, GT is released from the elongation complex. Bentley, Curr Opin Cell Biol 17: 251-256 (2005)

18. Co-transcriptional splicing and cleavage/polyadenylation The spliceosome is recruited to intron RNA (black line) and probably also to the pol II elongation complex, at least in metazoans. Co-transcriptional splicing releases the intron (black lariat). Note that while spliceosome assembly probably occurs co-transcriptionally on most introns, excision of the intron can occur post-transcriptionally. More cleavage/polyadenylation factors (C/P) and Rat1 are detectable at the 3´ end than at the 5´ end of the gene. These factors interact with the nascent RNA at the poly(A) site, AAUAAA, to cleave and polyadenylate the transcript. The Rat1 exonuclease degrades RNA downstream of the cleavage site (scissors) and helps trigger termination of transcription. Bentley, Curr Opin Cell Biol 17: 251-256 (2005)

19. The “allosteric torpedo” model couples transcription termination with 3´-end cleavage • - Association of Rat1 and cleavage/polyadenylation factors exemplified by Pcf11 with the CTD Ser2 phosphorylated pol II elongation complex is shown at the poly(A) site (AAUAAA). • This interaction results in an allosteric change in pol II (designated by a change from green to red) that favors termination. (Blue Ps) Ser5-PO4; (red Ps) Ser2-PO4. • Nascent RNA downstream of the poly(A) cleavage site (blue line) is degraded by both Xrn1 and Rat1. This degradation could facilitate termination; however, it is not sufficient to cause termination. Luo et al., Genes & Development 20: 954-965 (2006)

20. THO Complex • THO was identified as a four protein complex containing proteins encoded by THO2 and HPR1, two genes previously identified by hyper-recombination mutations, and MFT1 and THP2. The null mutations of each of the four genes are viable and show defects intranscription elongation (resulting in 3´-truncated transcripts) and transcription-dependent hyper-recombination between direct repeats. • It was previously proposed that the THO complex has a functional role related to RNAP II transcription elongation. Whether this role is direct or indirect is not yet known. However, some studies suggest that THO might also have a role in RNA metabolism beyond transcription. • Recent studies have shown that THO and RNA export factors are functionally related. For example, multicopy Sub2p suppresses the transcriptional defect of hpr1 cells, and sub2, yra1, mex67 and mtr2 mutants show similar defective transcription and hyper-recombination phenotypes to THO mutants.

21. The TREX complex contains THO and 2 mRNA export factors • In yeast, the multi-subunit TREX complex plays a role in couplingtranscription to mRNA export. This complex contains the mRNA export factorsSub2p and Yra1p as well as the THO complex, which functions intranscription elongation. • Human TREX contains Aly/REF, UAP56, and the humancounterpart of the yeast THO complex. The human THO complex specifically associates with spliced mRNAand not with unspliced pre-mRNA. • Recent data indicatethat recruitment of the human TREX complex to spliced mRNA occursby a splicing-coupled mechanism rather than by the direct transcription-coupledmechanism that occurs in yeast. • Deletion mutants of THO components show defects intranscription elongation and have a hyper-recombination phenotype. The elongation defectsand hyper-recombination appear to be due to the presence ofRNA/DNA hybrids that form between the nascent RNA andthe DNA template. • Hyper-recombination and transcription defects are also observedwith mutations in Sub2 and Yra1, as well as with mutations inother proteins involved in mRNA export, including Sac3, Thp1,Mex67, Mtr2, and Nab2.

22. Co-transcriptional recruitment of mRNA export factors in yeast Stutz & Izaurralde, Trends in Cell Biol 13: 319-327 (2003) The THO complex in yeast is recruited co-transcriptionally to nascent mRNAs through interactions with factors implicated in transcription elongation. This leads to the recruitment of Sub2p and Yra1p (UAP56 and REF1/Aly in higher eukaryotes) forming the TREX complex. Properly assembled and processed mRNPs are released in the nucleoplasm and proceed to subsequent steps of mRNP export. Either delay or impairment of mRNP assembly and/or 3´-end processing results in the retention of the transcripts near or at the site of transcription (pale orange area), providing a window of opportunity for the exosome to act. It is currently unknown whether binding of Mex67p–Mtr2p (NXF1–p15 in higher eukaryotes) occurs in a co- or post-transcriptional manner. The association of Mex67p-Mtr2p may displace Sub2p just before NPC-translocation.

23. Non-exclusive models to explain low levels of 3´-truncated transcripts in TREX mutants Model 1: The exosomal model proposes that co-transcriptional surveillance by the nuclear exosome results in the retention and 3´5´ degradation of malformed mRNPs at or close to the site of transcription. In this view, transcripts are fully synthesized but unstable and degraded. Model 2: The transcriptional model claims that malformed mRNP complexes form stretches of DNA:RNA hybrids with the coding DNA strand. The DNA:RNA hybrids impair transcription elongation by creating an obstacle for the next elongating RNA polymerase. Both views propose that an important role of THO/TREX is to promote efficient mRNP assembly, preventing the formation of DNA:RNA hybrids during elongation and protecting the mRNP from degradation by the exosome. Vinciguerra & Stutz, Curr Opin Cell Biol 16: 285-292 (2004)

24. Section III. nuclear mRNA export receptors

25. mRNA export receptor mRNA export adaptors TREX Complex THO Complex The hodgepodge of factors that influence mRNA export Stutz & Izaurralde, Trends in Cell Biol 13: 319-327 (2003)

26. Factors involved in Nuclear Export of mRNA (Sub2p) (Mex67p) (Yra1p) (Mtr2p) (Corresponding yeast factors indicated in parentheses) Cullen, J. Cell Sci 116: 587 (2003)

27. The mRNA ‘relay race’ from the site of transcription to the delivery to ribosomes in the cytosol Sub2p/UAP56, Yra1p/Aly/REF and hnRNP proteins such as Npl3p associate co-transcriptionally with the mRNA (CBC is the cap-binding complex). In the case of intron-containing genes, the spliceosome also assembles on the pre-mRNA. In mammalian cells, Aly/REF and UAP56 are part of the exon-junction complex on the spliced mRNA (not shown). The Sub2p/UAP56 protein is replaced by the Mex67p–Mtr2p/TAP-p15 heterodimers, which mediate the interaction of the mRNP with components of the nuclear pore complex (NPC). The DEAD box protein Dbp5p is required for release of mRNP on the cytoplasmic side of the NPC. DEAD box-mediated ATPase activities important for mRNA export are indicated by stars. Linder & Stutz, Curr Biol 11: R961-963 (2001)

28. Depletion of Drosophila cells of NXF1 by double stranded RNA inhibition causes nuclear mRNA accumulation. Mex67p and NXF1 are essential for export of bulk mRNA Shifting the mex67ts strain to the restrictive temperature (37°C) causes nuclear mRNA accumulation. In both experiments, poly(A) mRNA was visualized by in situ hybridization with a fluorescently-labeled oligo-dT probe Stutz & Izaurralde, Trends in Cell Biol 13: 319-327 (2003)

29. Non-mRNA Export from the Nucleus VA RNA represents Micro RNAs PHAX = Phosphorylated Adaptor for RNA Export Cullen, J. Cell Sci 116: 587 (2003)

30. The Ran-GTP gradient governs the directionality of some forms of nucleocytoplasmic transport • - The Ran-GTP gradient governs the directionality of nucleocytoplasmic transport mediated by members of the karyopherin family of nuclear transport factors. • The key role played by the GTP-bound form of Ran in mediating cargo binding and release by karyopherins functioning in nuclear import (importins) or nuclear export (exportins) is illustrated. • Imp, importin; Exp, exportin. • NOTE: the Ran system is not involved in mRNA export using the NXF (TAP) export receptors. Ran-GAP located in cytoplasm Ran-GEF located in nucleus Cullen, J. Cell Sci 116: 587 (2003)

31. The NPC mediates bidirectional nucleocytoplasmic trafficking Receptor-mediated transport involves sequential steps. A transport receptor recognizes a signal-bearing cargo and forms a receptor-cargo complex (1). The receptor-cargo complex then docks onthe near side of the NPC (2) before engaging in sequential, stochastic, low-affinity interactions withFG-Nups during translocation (3). At the far side of the NPC, the receptor-cargo complex isdisassembled (4) to deliver the cargo. For Kapimport, complex disassembly is initiated by nuclearbinding of RanGTP to the receptor. For Kapnuclear export, RanGTP in the export receptor-cargocomplex is hydrolyzed to RanGDP by the Ran GTPase activating protein (RanGAP), resulting incomplex disassembly. The Ran guanine nucleotide exchange factor (RanGEF) is localized to thenucleus and generates high RanGTP concentrations, and RanGDP is imported into the nucleus byNtf2 (not shown). Terry et al., Science 318: 1412-1416 (2007)

32. Nucleocytoplasmic transport is regulated at the level of the NPC, transport receptors, andindividual cargos The pyramid shows the hierarchy of levels used to regulate nucleocytoplasmictransport, with control at higher levels (right side) having broader impacts on trafficking. Eachlevel is controlled by multiple mechanisms. Terry et al., Science 318: 1412-1416 (2007)

33. Section IV. A nuclear surveillance checkpoint is also present at the nuclear pore

34. A quality control checkpoint at the nuclear pore is mediated by Mlp proteins Mlp proteins (Mlp1 and Mlp2) may play a general role in mRNP surveillance by preferentially interacting with properly packaged mRNP complexes, preventing mRNPs that lack essential signals from reaching the central channel of the NPC. The Mlp proteins are not essential for viability.

35. Mlp proteins form a selective filter at the entrance of the nuclear pore complex The perinuclear Mlp1p protein contributes to mRNP surveillance by retaining unspliced transcripts within the nucleus, possibly via recognition of a component associated with the 5´ splice site. Vinciguerra & Stutz, Curr Opin Cell Biol 16: 285-292 (2004)

36. Nab2p mediates the Mlp checkpoint at the entrance of the nuclear pore complex Nab2p, a shuttling mRNA binding protein involved in polyA tail length regulation, directly interacts with Mlp proteins. Nab2p may be important for the docking of mRNPs to the Mlp barrier, perhaps by signaling proper 3´ end formation. Vinciguerra & Stutz, Curr Opin Cell Biol 16: 285-292 (2004)

37. Mlp proteins establish a link between mRNA synthesis and export • - In wild type cells, the mRNA-binding proteins Yra1p and Nab2p are essential for mRNP docking to the Mlp export gate at the nuclear periphery. • mRNP complexes produced in the GFP-yra1-8 mutant strain are retained by the Mlp selective filter and mRNP stalling negatively feeds back on mRNA synthesis. • Loss of Mlp1p or Mlp2p alleviates the negative effect on mRNA synthesis and allows a fraction of transcripts to reach the cytoplasm. Vinciguerra et al., EMBO J 24: 813-823 (2005)

38. General Model of RNA Quality Control Doma & Parker, Cell 131: 660-667 (2007)

39. Kinetic Proofreading Models of RNA Quality Control Doma & Parker, Cell 131: 660-667 (2007)

40. Summary Of Nuclear Quality Control Doma & Parker., Cell 131: 660-667 (2007)