A guard protein mediated quality control mechanism monitors 5’-capping of pre-mRNAs

Abstract Efficient gene expression requires properly matured mRNAs for functional transcript translation. Several factors including the guard proteins monitor maturation and act as nuclear retention factors for unprocessed pre-mRNAs. Here we show that the guard protein Npl3 monitors 5’-capping. In its absence, uncapped transcripts resist degradation, because the Rat1–Rai1 5’-end degradation factors are not efficiently recruited to these faulty transcripts. Importantly, in npl3Δ, these improperly capped transcripts escape this quality control checkpoint and leak into the cytoplasm. Our data suggest a model in which Npl3 associates with the Rai1 bound pre-mRNAs. In case the transcript was properly capped and is thus CBC (cap binding complex) bound, Rai1 dissociates from Npl3 allowing the export factor Mex67 to interact with this guard protein and support nuclear export. In case Npl3 does not detect proper capping through CBC attachment, Rai1 binding persists and Rat1 can join this 5’-complex to degrade the faulty transcript.

[1]  H. Krebber,et al.  Unraveling the stepwise maturation of the yeast telomerase including a Cse1 and Mtr10 mediated quality control checkpoint , 2021, Scientific Reports.

[2]  Bettina Neumann,et al.  Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay , 2021, RNA biology.

[3]  T. Lingner,et al.  Nuclear Pre-snRNA Export Is an Essential Quality Assurance Mechanism for Functional Spliceosomes. , 2019, Cell reports.

[4]  S. Bhaumik,et al.  Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export , 2019, Molecular and Cellular Biology.

[5]  M. Mofrad,et al.  Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system , 2018, Nucleus.

[6]  Michaela Müller-McNicoll,et al.  Nuclear retention of mRNAs - quality control, gene regulation and human disease. , 2017, Seminars in cell & developmental biology.

[7]  H. Krebber,et al.  Quick or quality? How mRNA escapes nuclear quality control during stress , 2017, RNA biology.

[8]  T. Lingner,et al.  mRNA quality control is bypassed for immediate export of stress-responsive transcripts , 2016, Nature.

[9]  P. Gleizes,et al.  Nucleocytoplasmic Transport of RNAs and RNA-Protein Complexes. , 2016, Journal of molecular biology.

[10]  A. Mosley,et al.  Rrp6: Integrated roles in nuclear RNA metabolism and transcription termination , 2016, Wiley interdisciplinary reviews. RNA.

[11]  L. Steinmetz,et al.  Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough , 2015, PLoS genetics.

[12]  T. Jensen,et al.  Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes , 2015, Nature Reviews Molecular Cell Biology.

[13]  L. Steinmetz,et al.  The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production. , 2015, Cell reports.

[14]  D. Meinel,et al.  Co‐transcriptional mRNP formation is coordinated within a molecular mRNP packaging station in S. cerevisiae , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[15]  Johannes Söding,et al.  Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. , 2014, Molecular cell.

[16]  N. Visa,et al.  Quality control of mRNP biogenesis: networking at the transcription site. , 2014, Seminars in cell & developmental biology.

[17]  A. Krainer,et al.  Emerging Functions of SRSF1, Splicing Factor and Oncoprotein, in RNA Metabolism and Cancer , 2014, Molecular Cancer Research.

[18]  L. Tong,et al.  Structure and Function of Pre-mRNA 5′-End Capping Quality Control and 3′-End Processing , 2014, Biochemistry.

[19]  Haijia Wu,et al.  Quality control of spliced mRNAs requires the shuttling SR proteins Gbp2 and Hrb1 , 2014, Nature Communications.

[20]  K. Neugebauer,et al.  Good cap/bad cap: how the cap-binding complex determines RNA fate , 2014, Nature Structural &Molecular Biology.

[21]  A. Babour,et al.  mRNA nuclear export in yeast. , 2013, Chemical reviews.

[22]  K. Sloan,et al.  Comparison of the yeast and human nuclear exosome complexes. , 2012, Biochemical Society transactions.

[23]  F. Stutz,et al.  Keeping mRNPs in check during assembly and nuclear export , 2011, Nature Reviews Molecular Cell Biology.

[24]  L. Tong,et al.  Identification of a quality control mechanism for mRNA 5’-end capping , 2010, Nature.

[25]  J. Butler,et al.  TRAMP Complex Enhances RNA Degradation by the Nuclear Exosome Component Rrp6* , 2009, The Journal of Biological Chemistry.

[26]  L. Tong,et al.  Structure and function of the 5’→3’ exoribonuclease Rat1 and its activating partner Rai1 , 2009, Nature.

[27]  Nevan J Krogan,et al.  A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. , 2008, Molecular cell.

[28]  Sean R. Collins,et al.  A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. , 2008, Molecular cell.

[29]  Roy Parker,et al.  RNA Quality Control in Eukaryotes , 2007, Cell.

[30]  S. Buratowski,et al.  Npl3 is an antagonist of mRNA 3′ end formation by RNA polymerase II , 2005, The EMBO journal.

[31]  H. Krebber,et al.  Differential Export Requirements for Shuttling Serine/Arginine-type mRNA-binding Proteins* , 2004, Journal of Biological Chemistry.

[32]  Christine Guthrie,et al.  The Glc7p nuclear phosphatase promotes mRNA export by facilitating association of Mex67p with mRNA. , 2004, Molecular cell.

[33]  J. Steitz,et al.  SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. , 2003, Molecular cell.

[34]  H. Krebber,et al.  Identification of Gbp2 as a novel poly(A)+ RNA‐binding protein involved in the cytoplasmic delivery of messenger RNAs in yeast , 2003, EMBO reports.

[35]  A. Corbett,et al.  The C-terminal domain of myosin-like protein 1 (Mlp1p) is a docking site for heterogeneous nuclear ribonucleoproteins that are required for mRNA export , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[36]  M. Keogh,et al.  Divergent Subunit Interactions among Fungal mRNA 5′-Capping Machineries , 2002, Eukaryotic Cell.

[37]  P. Silver,et al.  Messenger RNAs are recruited for nuclear export during transcription. , 2001, Genes & development.

[38]  W. Gilbert,et al.  Phosphorylation by Sky1p promotes Npl3p shuttling and mRNA dissociation. , 2001, RNA.

[39]  P. Mitchell,et al.  Musing on the structural organization of the exosome complex , 2000, Nature Structural Biology.

[40]  P. Silver,et al.  7The Yeast mRNA-binding Protein Npl3p Interacts with the Cap-binding Complex* , 2000, The Journal of Biological Chemistry.

[41]  D. Tollervey,et al.  Mex67p Mediates Nuclear Export of a Variety of RNA Polymerase II Transcripts* , 2000, The Journal of Biological Chemistry.

[42]  S. Shuman,et al.  Structure-Function Analysis of Yeast mRNA Cap Methyltransferase and High-Copy Suppression of Conditional Mutants by AdoMet Synthase and the Ubiquitin Conjugating Enzyme Cdc 34 p , 2000 .

[43]  R. Vale,et al.  Circularization of mRNA by eukaryotic translation initiation factors. , 1998, Molecular cell.

[44]  E. Izaurralde,et al.  The role of the cap structure in RNA processing and nuclear export. , 1997, European journal of biochemistry.

[45]  S. Buratowski,et al.  Conditional mutants of the yeast mRNA capping enzyme show that the cap enhances, but is not required for, mRNA splicing. , 1996, RNA.

[46]  S. Shuman,et al.  Multicopy suppressors of temperature-sensitive mutations of yeast mRNA capping enzyme. , 1996, Gene expression.

[47]  A. Stevens,et al.  A 5'----3' exoribonuclease of Saccharomyces cerevisiae: size and novel substrate specificity. , 1987, Archives of biochemistry and biophysics.

[48]  A. Stevens,et al.  An exoribonuclease from Saccharomyces cerevisiae: effect of modifications of 5' end groups on the hydrolysis of substrates to 5' mononucleotides. , 1978, Biochemical and biophysical research communications.