scholarly journals Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells

2003 ◽  
Vol 373 (3) ◽  
pp. 775-783 ◽  
Author(s):  
Thomas SCHELL ◽  
Thomas KÖCHER ◽  
Matthias WILM ◽  
Bertrand SERAPHIN ◽  
Andreas E. KULOZIK ◽  
...  
Keyword(s):  
Cell Line ◽  
Mrna Decay ◽  
Translation Termination ◽  
Binding Protein ◽  
Size Exclusion ◽  
Exon Junction Complex ◽  
Affinity Tag ◽  
Exclusion Chromatography ◽  
Associated Proteins ◽  
Nonsense Mediated Mrna Decay

mRNAs harbouring premature translation-termination codons are usually degraded by the nonsense-mediated mRNA decay (NMD) pathway. Human up-frameshift protein 1 (Hupf1) is an NMD factor that is conserved between yeast and mammals. To isolate cellular complexes that are formed with Hupf1 and to explore the role of cellular proteins in NMD, we generated a HeLa cell line that stably expresses Hupf1 bearing a double-affinity tag (termed Hupf1-2tag). Hupf1-2tag is localized in the cytoplasm similar to the endogenous Hupf1 protein, and the Hupf1-2tag cell line is fully NMD-competent. Using affinity chromatography, Hupf1-2tag-associated proteins were isolated. MS and immunoblotting identified the NMD factors Hupf2 and Hupf3a/b as interaction partners of Hupf1. Size-exclusion chromatography indicates that the NMD factors Hupf1, Hupf2 and the large isoform of Hupf3a might exist in a stable, high-molecular-mass complex of approx. 1.3 MDa. Interestingly, the poly(A)-binding protein was also identified by MS to be associated specifically with Hupf1-2tag. In contrast with the interaction with Hupf2 and Hupf3a/b, the association of poly(A)-binding protein with Hupf1 is highly sensitive to treatment of the isolated complexes with RNase. Components of the exon–exon junction complex or the translational eukaryotic release factor (eRF) 3 were not identified in complexes associated with Hupf1-2tag. We discuss these findings in the context of current models of NMD.

scholarly journals The GTP-binding Release Factor eRF3 as a Key Mediator Coupling Translation Termination to mRNA Decay

2004 ◽  
Vol 279 (44) ◽  
pp. 45693-45700 ◽  
Author(s):  
Tetsuo Kobayashi ◽  
Yuji Funakoshi ◽  
Shin-ichi Hoshino ◽  
Toshiaki Katada
Keyword(s):  
Mrna Decay ◽  
Translation Termination ◽  
Binding Protein ◽  
Binding Activity ◽  
Release Factor ◽  
Guanine Nucleotide Binding Protein ◽  
Eukaryotic Translation ◽  
Gtp Binding ◽  
Nonsense Mediated Mrna Decay ◽  
Guanine Nucleotide Binding

GTP is essential for eukaryotic translation termination, where the release factor 3 (eRF3) complexed with eRF1 is involved as the guanine nucleotide-binding protein. In addition, eRF3 regulates the termination-coupled events, eRF3 interacts with poly(A)-binding protein (Pab1) and the surveillance factor Upf1 to mediate normal and nonsense-mediated mRNA decay. However, the roles of GTP binding to eRF3 in these processes remain largely unknown. Here, we showed in yeast that GTP is essentially required for the association of eRF3 with eRF1, but not with Pab1 and Upf1. A mutation in the GTP-binding motifs of eRF3 impairs the eRF1-binding ability without altering the Pab1- or Upf1-binding activity. Interestingly, the mutation causes not only a defect in translation termination but also delay of normal and nonsense-mediated mRNA decay, suggesting that GTP/eRF3-dependent termination exerts its influence on the subsequent mRNA degradation. The termination reaction itself is not sufficient, but eRF3 is essential for triggering mRNA decay. Thus, eRF3 is a key mediator that transduces termination signal to mRNA decay.

scholarly journals An intron proximal to a PTC enhances NMD in Saccharomyces cerevisiae

2017 ◽  
Author(s):  
Jikai Wen ◽  
Muyang He ◽  
Marija Petric ◽  
Laetitia Marzi ◽  
Jianming Wang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mammalian Cells ◽  
Mrna Decay ◽  
Translation Termination ◽  
Exon Junction Complex ◽  
Coding Region ◽  
Independent Mechanism ◽  
Nonsense Mediated Mrna Decay ◽  
Translation Termination Codon ◽  
Premature Translation Termination Codon

AbstractNonsense mediated mRNA decay (NMD) is regarded as the function of a specialized cytoplasmic translation-coupled mRNA decay pathway in eukaryotes, however, whether a premature translation termination codon (PTC) will lead to NMD often depends on splicing a downstream intron in the nucleus. Deposition of the exon junction complex (EJC) on mRNA is understood to mediate such splicing-dependent NMD in mammalian cells. The budding yeast, Saccharomyces cerevisiae, which has introns in only 5% of its genes, characteristically at the start of the coding region, and lacks proteins essential for EJC assembly, is not expected to undergo splicing-dependent NMD. However, we found that the presence of an intron near a PTC can also enhance NMD in this organism, regardless of whether it is downstream or upstream. These data provide evidence for a hitherto unsuspected EJC-independent mechanism linking translation and pre-mRNA in S. cerevisiae.

scholarly journals Isolation of HDL by sequential flotation ultracentrifugation followed by size exclusion chromatography reveals size-based enrichment of HDL-associated proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jack Jingyuan Zheng ◽  
Joanne K. Agus ◽  
Brian V. Hong ◽  
Xinyu Tang ◽  
Christopher H. Rhodes ◽  
...  
Keyword(s):  
Structural Integrity ◽  
Polyacrylamide Gel Electrophoresis ◽  
Cholesterol Acyltransferase ◽  
Density Lipoprotein ◽  
Size Exclusion ◽  
High Yield ◽  
Phospholipid Transfer ◽  
Exclusion Chromatography ◽  
Associated Proteins ◽  
Alpha 1 Antitrypsin

AbstractHigh-density lipoprotein (HDL) particles have multiple beneficial and cardioprotective roles, yet our understanding of their full structural and functional repertoire is limited due to challenges in separating HDL particles from contaminating plasma proteins and other lipid-carrying particles that overlap HDL in size and/or density. Here we describe a method for isolating HDL particles using a combination of sequential flotation density ultracentrifugation and fast protein liquid chromatography with a size exclusion column. Purity was visualized by polyacrylamide gel electrophoresis and verified by proteomics, while size and structural integrity were confirmed by transmission electron microscopy. This HDL isolation method can be used to isolate a high yield of purified HDL from a low starting plasma volume for functional analyses. This method also enables investigators to select their specific HDL fraction of interest: from the least inclusive but highest purity HDL fraction eluting in the middle of the HDL peak, to pooling all of the fractions to capture the breadth of HDL particles in the original plasma sample. We show that certain proteins such as lecithin cholesterol acyltransferase (LCAT), phospholipid transfer protein (PLTP), and clusterin (CLUS) are enriched in large HDL particles whereas proteins such as alpha-2HS-glycoprotein (A2HSG), alpha-1 antitrypsin (A1AT), and vitamin D binding protein (VDBP) are enriched or found exclusively in small HDL particles.

scholarly journals A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay

2021 ◽  
Author(s):  
Sarah E. Fritz ◽  
Soumya Ranganathan ◽  
J. Robert Hogg
Keyword(s):  
Gene Expression ◽  
Mrna Decay ◽  
Gene Expression Regulation ◽  
Translation Termination ◽  
Translational Repression ◽  
The Core ◽  
Human Genes ◽  
Rna Quality Control ◽  
Nonsense Mediated Mrna Decay

AbstractThe nonsense-mediated mRNA decay (NMD) pathway monitors translation termination to degrade transcripts with premature stop codons and regulate thousands of human genes. Due to the major role of NMD in RNA quality control and gene expression regulation, it is important to understand how the pathway responds to changing cellular conditions. Here we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1LL, enables condition-dependent remodeling of NMD specificity. UPF1LL associates more stably with potential NMD target mRNAs than the major UPF1SL isoform, expanding the scope of NMD to include many transcripts normally immune to the pathway. Unexpectedly, the enhanced persistence of UPF1LL on mRNAs supports induction of NMD in response to rare translation termination events. Thus, while canonical NMD is abolished by translational repression, UPF1LL activity is enhanced, providing a mechanism to rapidly rewire NMD specificity in response to cellular stress.

scholarly journals Exon-Junction Complex Components Specify Distinct Routes of Nonsense-Mediated mRNA Decay with Differential Cofactor Requirements

2005 ◽  
Vol 20 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Niels H. Gehring ◽  
Joachim B. Kunz ◽  
Gabriele Neu-Yilik ◽  
Stephen Breit ◽  
Marcelo H. Viegas ◽  
...  
Keyword(s):  
Mrna Decay ◽  
Exon Junction Complex ◽  
Exon Junction ◽  
Nonsense Mediated Mrna Decay ◽  
Complex Components

Different molecular and messenger ribonucleic acid forms of insulin-like growth factor-binding protein-3 in the pregnant baboon (Papio anubis)

1995 ◽  
Vol 147 (3) ◽  
pp. 449-461 ◽  
Author(s):  
S E Gargosky ◽  
L C Giudice ◽  
R G Rosenfeld ◽  
A T Fazleabas
Keyword(s):  
Size Exclusion Chromatography ◽  
Binding Protein ◽  
Size Exclusion ◽  
Northern Analysis ◽  
Papio Anubis ◽  
Western Analysis ◽  
Explant Cultures ◽  
Exclusion Chromatography ◽  
In Pregnancy ◽  
Igfbp 3

Abstract The ratio of the serum concentrations of insulin-like growth factors (IGF) to IGF-binding protein (IGFBP)-3 is highly correlated (Baxter & Martin 1986). During pregnancy in the baboon, this ratio is perturbed; serum IGFBP-3 concentrations increase 10-fold, yet IGF-I levels are unaltered and IGF-II is increased only 2-fold (Giudice et al. 1993). The aims of this study were to determine the molecular distribution of IGFBP-3 and to identify the tissue source and form(s) of IGFBP-3 during pregnancy in the baboon. Serum of non-pregnant and pregnant baboons, and conditioned media of decidua and placental explant cultures were characterized using neutral size-exclusion chromatography in combination with Western ligand blot, Western immunoblot, an IGFBP-3 radioimmunoassay (RIA) and an IGFBP-3 protease assay. Localization of immunoreactive IGFBP-3 was determined by immunocytochemistry, and expression of IGFBP-3 mRNA in the placental and decidual explants was examined by Northern blot analysis. RIA confirmed that immunoreactive IGFBP-3 is increased 10-fold in pregnancy serum compared with non-pregnancy serum. Size-exclusion chromatography combined with an IGFBP-3 RIA revealed that, unlike non-pregnancy serum where 70% of the immunoreactive IGFBP-3 elutes in the 150 kDa ternary complex, equal amounts of immunoreactive IGFBP-3 were measured in pregnancy serum in the ≤150 and 60 kDa IGFBP regions. Western analysis revealed that non-pregnancy serum contained predominantly a 45–40 kDa IGFBP-3 doublet and a 28 kDa immunoreactive form of IGFBP-3, while in pregnancy serum IGFBP-3 existed as a 45–40 kDa doublet, as well as 26–28 kDa and 18 kDa immunoreactive forms. These alternative forms of IGFBP-3 were not attributable to detectable IGFBP-3 protease activity. To identify the source of the increased serum levels of IGFBP-3 during pregnancy, we examined explant culture media of baboon decidua and placenta. Size-exclusion chromatography combined with RIA and Western analysis revealed that: (1) more immunoreactive IGFBP-3 was produced by decidual cultures than by placental explants, but less 45–40 kDa IGFBP-3 was present in decidua; (2) the immunoreactive forms of IGFBP-3 detected in decidua were similar to those found in maternal serum; (3) placental explants secreted only 45–40 kDa IGFBP-3 in culture. IGFBP-3 was immunohistochemically localized to the cells of placental villi, and to the perinuclear region of the decidual cells and staining for IGFBP-3 was more intense in the decidua than in the placenta. Northern analysis of the explant cultures revealed two IGFBP-3 mRNA transcripts of 2·4 and 1·7 kb in both decidua and placenta which may account for the different immunoreactive forms of IGFBP-3 detected in the baboon. However analysis of non-pregnancy liver also revealed two IGFBP-3 transcripts of 2·4 and 1·7 kb. These data suggest that the two transcripts are not solely pregnancy-associated and levels of protein may be the reason for detection of multiple immunoreactive IGFBP-3 fragments in pregnancy. Journal of Endocrinology (1995) 147, 449–461

scholarly journals Tpa1p Is Part of an mRNP Complex That Influences Translation Termination, mRNA Deadenylation, and mRNA Turnover in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (14) ◽  
pp. 5237-5248 ◽  
Author(s):  
Kim M. Keeling ◽  
Joe Salas-Marco ◽  
Lev Z. Osherovich ◽  
David M. Bedwell
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mrna Decay ◽  
Potential Role ◽  
Translation Termination ◽  
Tail Length ◽  
Fold Increase ◽  
Reading Frame ◽  
Yeast Strains ◽  
Messenger Ribonucleoprotein ◽  
Nonsense Mediated Mrna Decay

ABSTRACT In this report, we show that the Saccharomyces cerevisiae protein Tpa1p (for termination and polyadenylation) influences translation termination efficiency, mRNA poly(A) tail length, and mRNA stability. Tpa1p is encoded by the previously uncharacterized open reading frame YER049W. Yeast strains carrying a deletion of the TPA1 gene (tpa1Δ) exhibited increased readthrough of stop codons, and coimmunoprecipitation assays revealed that Tpa1p interacts with the translation termination factors eRF1 and eRF3. In addition, the tpa1Δ mutation led to a 1.5- to 2-fold increase in the half-lives of mRNAs degraded by the general 5′→3′ pathway or the 3′→5′ nonstop decay pathway. In contrast, this mutation did not have any affect on the nonsense-mediated mRNA decay pathway. Examination of mRNA poly(A) tail length revealed that poly(A) tails are longer than normal in a tpa1Δ strain. Consistent with a potential role in regulating poly(A) tail length, Tpa1p was also found to coimmunoprecipitate with the yeast poly(A) binding protein Pab1p. These results suggest that Tpa1p is a component of a messenger ribonucleoprotein complex bound to the 3′ untranslated region of mRNAs that affects translation termination, deadenylation, and mRNA decay.

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