351
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Dybbs M, Ngai J, Kaplan JM. Using microarrays to facilitate positional cloning: identification of tomosyn as an inhibitor of neurosecretion. PLoS Genet 2005; 1:6-16. [PMID: 16103915 PMCID: PMC1183521 DOI: 10.1371/journal.pgen.0010002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Accepted: 02/01/2005] [Indexed: 12/03/2022] Open
Abstract
Forward genetic screens have been used as a powerful strategy to dissect complex biological pathways in many model systems. A significant limitation of this approach has been the time-consuming and costly process of positional cloning and molecular characterization of the mutations isolated in these screens. Here, the authors describe a strategy using microarray hybridizations to facilitate positional cloning. This method relies on the fact that premature stop codons (i.e., nonsense mutations) constitute a frequent class of mutations isolated in screens and that nonsense mutant messenger RNAs are efficiently degraded by the conserved nonsense-mediated decay pathway. They validate this strategy by identifying two previously uncharacterized mutations: (1) tom-1, a mutation found in a forward genetic screen for enhanced acetylcholine secretion in Caenorhabditis elegans, and (2) an apparently spontaneous mutation in the hif-1 transcription factor gene. They further demonstrate the broad applicability of this strategy using other known mutants in C. elegans,Arabidopsis, and mouse. Characterization of tom-1 mutants suggests that TOM-1, the C. elegans ortholog of mammalian tomosyn, functions as an endogenous inhibitor of neurotransmitter secretion. These results also suggest that microarray hybridizations have the potential to significantly reduce the time and effort required for positional cloning. Genetic screens are commonly used to figure out which genes are involved in a biological process. The first step in a genetic screen is to isolate mutant animals that are defective in the process being studied. The next step is to find which of the thousands of genes has the mutation that causes the observed defect. Positional cloning, the tried-and-true method for locating mutations, is slow and expensive. The authors propose using microarray hybridizations to speed the process. Their approach relies on the fact that a large fraction of the mutations found in screens are the results of premature stop codons, a particularly severe type of mutation. In cells, messages containing premature stop codons are rapidly destroyed by a protective pathway, called nonsense-mediated decay, thus making them directly detectable by microarray hybridization. The authors apply this strategy retrospectively to known mutants in Caenorhabditis elegans, Arabidopsis, and mouse. They identify two uncharacterized mutations in C. elegans, including one, tom-1, found in a forward genetic screen for enhancers of neurotransmission. Interestingly, their characterization of tom-1 mutants suggests that the highly conserved protein tomosyn inhibits neurotransmission in neurons. This study shows that microarray hybridizations will help reduce the time and effort required for positional cloning.
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Affiliation(s)
- Michael Dybbs
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular and Cell Biology, Functional Genomics Laboratory, Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - John Ngai
- Department of Molecular and Cell Biology, Functional Genomics Laboratory, Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- *To whom correspondence should be addressed. E-mail:
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352
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Garg V, Muth AN, Ransom JF, Schluterman MK, Barnes R, King IN, Grossfeld PD, Srivastava D. Mutations in NOTCH1 cause aortic valve disease. Nature 2005; 437:270-4. [PMID: 16025100 DOI: 10.1038/nature03940] [Citation(s) in RCA: 1001] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Accepted: 06/17/2005] [Indexed: 11/08/2022]
Abstract
Calcification of the aortic valve is the third leading cause of heart disease in adults. The incidence increases with age, and it is often associated with a bicuspid aortic valve present in 1-2% of the population. Despite the frequency, neither the mechanisms of valve calcification nor the developmental origin of a two, rather than three, leaflet aortic valve is known. Here, we show that mutations in the signalling and transcriptional regulator NOTCH1 cause a spectrum of developmental aortic valve anomalies and severe valve calcification in non-syndromic autosomal-dominant human pedigrees. Consistent with the valve calcification phenotype, Notch1 transcripts were most abundant in the developing aortic valve of mice, and Notch1 repressed the activity of Runx2, a central transcriptional regulator of osteoblast cell fate. The hairy-related family of transcriptional repressors (Hrt), which are activated by Notch1 signalling, physically interacted with Runx2 and repressed Runx2 transcriptional activity independent of histone deacetylase activity. These results suggest that NOTCH1 mutations cause an early developmental defect in the aortic valve and a later de-repression of calcium deposition that causes progressive aortic valve disease.
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Affiliation(s)
- Vidu Garg
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148, USA.
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353
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Wilson MA, Meaux S, Parker R, van Hoof A. Genetic interactions between [PSI+] and nonstop mRNA decay affect phenotypic variation. Proc Natl Acad Sci U S A 2005; 102:10244-9. [PMID: 16002465 PMCID: PMC1173365 DOI: 10.1073/pnas.0504557102] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Yeast strains can reversibly interconvert between [PSI+] and [psi-] states. The [PSI+] state is caused by a prion form of the translation termination factor eRF3. The [PSI+] state causes read-through at stop codons and can lead to phenotypic variation, although the molecular mechanisms causing those phenotypic changes remain unknown. We identify an interaction between [PSI+]-induced phenotypic variation and defects in nonstop mRNA decay. Nonstop mRNA decay is triggered when a ribosome reaches the 3' end of the transcript. In contrast, we observed little interaction between [PSI+]-induced phenotypic variation and defects in nonsense-mediated decay, which lead to suppression of premature stop codons. These results suggest that at least some of the phenotypic effects of [PSI+] may be due to read-through of "normal" stop codons, thereby producing extended proteins. Moreover, these observations suggest that nonstop mRNA decay may limit [PSI+]-induced phenotypic variation. Such a process would allow periodic sampling of the 3' UTR, which can diverge rapidly, for novel and beneficial protein extensions.
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Affiliation(s)
- Marenda A Wilson
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, 6431 Fannin Street, MSB 1.212, Houston, TX 77030, USA
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354
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Maranduba CMC, Friesema ECH, Kok F, Kester MHA, Jansen J, Sertié AL, Passos-Bueno MR, Visser TJ. Decreased cellular uptake and metabolism in Allan-Herndon-Dudley syndrome (AHDS) due to a novel mutation in the MCT8 thyroid hormone transporter. J Med Genet 2005; 43:457-60. [PMID: 15980113 PMCID: PMC2649011 DOI: 10.1136/jmg.2005.035840] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We report a novel 1 bp deletion (c.1834delC) in the MCT8 gene in a large Brazilian family with Allan-Herndon-Dudley syndrome (AHDS), an X linked condition characterised by severe mental retardation and neurological dysfunction. The c.1834delC segregates with the disease in this family and it was not present in 100 control chromosomes, further confirming its pathogenicity. This mutation causes a frameshift and the inclusion of 64 additional amino acids in the C-terminal region of the protein. Pathogenic mutations in the MCT8 gene, which encodes a thyroid hormone transporter, results in elevated serum triiodothyronine (T3) levels, which were confirmed in four affected males of this family, while normal levels were found among obligate carriers. Through in vitro functional assays, we showed that this mutation decreases cellular T3 uptake and intracellular T3 metabolism. Therefore, the severe neurological defects present in the patients are due not only to deficiency of intracellular T3, but also to altered metabolism of T3 in central neurones. In addition, the severe muscle hypoplasia observed in most AHDS patients may be a consequence of high serum T3 levels.
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355
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Abstract
Changes in protein conformation drive most biological processes, but none have seized the imagination of scientists and the public alike as have the self-replicating conformations of prions. Prions transmit lethal neurodegenerative diseases by means of the food chain. However, self-replicating protein conformations can also constitute molecular memories that transmit genetic information. Here, we showcase definitive evidence for the prion hypothesis and discuss examples in which prion-encoded heritable information has been harnessed during evolution to confer selective advantages. We then describe situations in which prion-enciphered events might have essential roles in long-term memory formation, transcriptional memory and genome-wide expression patterns.
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Affiliation(s)
- James Shorter
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
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356
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Chen N, Walsh MA, Liu Y, Parker R, Song H. Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J Mol Biol 2005; 347:707-18. [PMID: 15769464 DOI: 10.1016/j.jmb.2005.01.062] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 01/10/2005] [Accepted: 01/25/2005] [Indexed: 11/17/2022]
Abstract
Eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 3'-5' mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids. We report the structures of DcpS in ligand-free form and in a complex with m7GDP. apo-DcpS is a symmetric dimer, strikingly different from the asymmetric dimer observed in the structures of DcpS with bound cap analogues. In contrast, and similar to the m7GpppG-DcpS complex, DcpS with bound m7GDP is an asymmetric dimer in which the closed state appears to be the substrate-bound complex, whereas the open state mimics the product-bound complex. Comparisons of these structures revealed conformational changes of both the N-terminal swapped-dimeric domain and the cap-binding pocket upon cap binding. Moreover, Tyr273 in the cap-binding pocket displays remarkable conformational changes upon cap binding. Mutagenesis and biochemical analysis suggest that Tyr273 seems to play an important role in cap binding and product release. Examination of the crystallographic B-factors indicates that the N-terminal domain in apo-DcpS is inherently flexible, and in a dynamic state ready for substrate binding and product release.
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Affiliation(s)
- Nan Chen
- Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673
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357
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Orban TI, Izaurralde E. Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA (NEW YORK, N.Y.) 2005; 11:459-69. [PMID: 15703439 PMCID: PMC1370735 DOI: 10.1261/rna.7231505] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Accepted: 12/20/2004] [Indexed: 05/21/2023]
Abstract
RNA interference (RNAi) is a conserved RNA silencing pathway that leads to sequence-specific mRNA decay in response to the presence of double-stranded RNA (dsRNA). Long dsRNA molecules are first processed by Dicer into 21-22-nucleotide small interfering RNAs (siRNAs). The siRNAs are incorporated into a multimeric RNA-induced silencing complex (RISC) that cleaves mRNAs at a site determined by complementarity with the siRNAs. Following this initial endonucleolytic cleavage, the mRNA is degraded by a mechanism that is not completely understood. We investigated the decay pathway of mRNAs targeted by RISC in Drosophila cells. We show that 5' mRNA fragments generated by RISC cleavage are rapidly degraded from their 3' ends by the exosome, whereas the 3' fragments are degraded from their 5' ends by XRN1. Exosome-mediated decay of the 5' fragments requires the Drosophila homologs of yeast Ski2p, Ski3p, and Ski8p, suggesting that their role as regulators of exosome activity is conserved. Our findings indicate that mRNAs targeted by siRNAs are degraded from the ends generated by RISC cleavage, without undergoing decapping or deadenylation.
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358
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Meyer S, Temme C, Wahle E. Messenger RNA turnover in eukaryotes: pathways and enzymes. Crit Rev Biochem Mol Biol 2005; 39:197-216. [PMID: 15596551 DOI: 10.1080/10409230490513991] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The control of mRNA degradation is an important component of the regulation of gene expression since the steady-state concentration of mRNA is determined both by the rates of synthesis and of decay. Two general pathways of mRNA decay have been described in eukaryotes. Both pathways share the exonucleolytic removal of the poly(A) tail (deadenylation) as the first step. In one pathway, deadenylation is followed by the hydrolysis of the cap and processive degradation of the mRNA body by a 5' exonuclease. In the second pathway, the mRNA body is degraded by a complex of 3' exonucleases before the remaining cap structure is hydrolyzed. This review discusses the proteins involved in the catalysis and control of both decay pathways.
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Affiliation(s)
- Sylke Meyer
- Institut für Biochemie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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359
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Inada T, Aiba H. Translation of aberrant mRNAs lacking a termination codon or with a shortened 3'-UTR is repressed after initiation in yeast. EMBO J 2005; 24:1584-95. [PMID: 15933721 PMCID: PMC1142571 DOI: 10.1038/sj.emboj.7600636] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Accepted: 03/03/2005] [Indexed: 11/09/2022] Open
Abstract
A novel mRNA surveillance for mRNA lacking a termination codon (nonstop mRNA) has been proposed in which Ski7p is thought to recognize stalled ribosomes at the 3' end of mRNA. Here we report our analysis of translation and decay of nonstop mRNAs in Saccharomyces cerevisiae. Although the reduction of nonstop mRNAs was only 4.5-fold, a level that is sufficient for residual protein synthesis, translation products of nonstop mRNAs were hardly detectable. We show that nonstop mRNAs were associated with polysomes, but not with Pab1p. We also show that ribosomes translating nonstop mRNA formed stable and heavy polysome complexes with mRNA. These data suggest that ribosome stalling at the 3' end of nonstop mRNA may block further rounds of translation, hence repressing protein synthesis. Furthermore, it was found that the 5' --> 3' decay pathway was accelerated for nonstop mRNA decay in the absence of Ski7p. We also found that translation of aberrant mRNAs with a shortened 3'-UTR was repressed, suggesting that an improper spatial distance between the termination codon and the 3' end of mRNA results in translation repression.
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Affiliation(s)
- Toshifumi Inada
- Department of Molecular Biology, Graduate School of Science, Nagoya University, Nagoya, Japan.
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360
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Scicchitano DA, Olesnicky EC, Dimitri A. Transcription and DNA adducts: what happens when the message gets cut off? DNA Repair (Amst) 2005; 3:1537-48. [PMID: 15474416 DOI: 10.1016/j.dnarep.2004.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 01/18/2023]
Abstract
DNA damage located within a gene's transcription unit can cause RNA polymerase to stall at the modified site, resulting in a truncated transcript, or progress past, producing full-length RNA. However, it is not immediately apparent why some lesions pose strong barriers to elongation while others do not. Studies using site-specifically damaged DNA templates have demonstrated that a wide range of lesions can impede the progress of elongating transcription complexes. The collected results of this work provide evidence for the idea that subtle structural elements can influence how an RNA polymerase behaves when it encounters a DNA adduct during elongation. These elements include: (1) the ability of the RNA polymerase active site to accommodate the damaged base; (2) the size and shape of the adduct, which includes the specific modified base; (3) the stereochemistry of the adduct; (4) the base incorporated into the growing transcript; and (5) the local DNA sequence.
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Affiliation(s)
- David A Scicchitano
- Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003, USA.
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361
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Roth KM, Wolf MK, Rossi M, Butler JS. The nuclear exosome contributes to autogenous control of NAB2 mRNA levels. Mol Cell Biol 2005; 25:1577-85. [PMID: 15713618 PMCID: PMC549385 DOI: 10.1128/mcb.25.5.1577-1585.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 11/15/2004] [Accepted: 12/01/2004] [Indexed: 11/20/2022] Open
Abstract
The RNA-processing exosome is a complex of riboexonucleases required for 3'-end formation of some noncoding RNAs and for the degradation of mRNAs in eukaryotes. The nuclear form of the exosome functions in an mRNA surveillance pathway that retains and degrades improperly processed precursor mRNAs within the nucleus. We report here that the nuclear exosome controls the level of NAB2 mRNA, encoding the nuclear poly(A)+-RNA-binding protein Nab2p. Mutations affecting the activity of the nuclear, but not the cytoplasmic, exosome cause an increase in the amount of NAB2 mRNA. Cis- and trans-acting mutations that inhibit degradation by the nuclear-exosome subunit Rrp6p result in elevated levels of NAB2 mRNA. Control of NAB2 mRNA levels occurs posttranscriptionally and requires a sequence of 26 consecutive adenosines (A26) in the NAB2 3' untranslated region, which represses NAB2 3'-end formation and sensitizes the transcript to degradation by Rrp6p. Analysis of NAB2 mRNA levels in a nab2-1 mutant and in the presence of excess Nab2p indicates that Nab2p activity negatively controls NAB2 mRNA levels in an A26- and Rrp6p-dependent manner. These findings suggest a novel regulatory circuit in which the nuclear exosome controls the level of NAB2 mRNA in response to changes in the activity of Nab2 protein.
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Affiliation(s)
- Kelly M Roth
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Box 672, 601 Elmwood Ave., Rochester, NY 14642, USA
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362
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Emtage L, Gu G, Hartwieg E, Chalfie M. Extracellular proteins organize the mechanosensory channel complex in C. elegans touch receptor neurons. Neuron 2005; 44:795-807. [PMID: 15572111 DOI: 10.1016/j.neuron.2004.11.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 08/02/2004] [Accepted: 10/16/2004] [Indexed: 10/26/2022]
Abstract
Specialized extracellular matrix (ECM) is associated with virtually every mechanosensory system studied. C. elegans touch receptor neurons have specialized ECM and attach to the surrounding epidermis. The mec-1 gene encodes an ECM protein with multiple EGF and Kunitz domains. MEC-1 is needed for the accumulation of the collagen MEC-5 and other ECM components, attachment, and, separately, for touch sensitivity. MEC-1 and MEC-5 bind to touch processes uniformly and in puncta. These puncta colocalize with and localize the mechanosensory channel complex in the touch neurons. In turn, the production of the MEC-1 and MEC-5 puncta appears to rely on interactions with the neighboring epidermal tissue. These and other observations lead us to propose that extracellular, but not cytoskeletal, tethering of the degenerin channel is needed for mechanosensory transduction. Additionally, our experiments demonstrate an important role of the ECM in organizing the placement of the channel complex.
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Affiliation(s)
- Lesley Emtage
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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363
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Tian B, Hu J, Zhang H, Lutz CS. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005; 33:201-12. [PMID: 15647503 PMCID: PMC546146 DOI: 10.1093/nar/gki158] [Citation(s) in RCA: 707] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
mRNA polyadenylation is a critical cellular process in eukaryotes. It involves 3′ end cleavage of nascent mRNAs and addition of the poly(A) tail, which plays important roles in many aspects of the cellular metabolism of mRNA. The process is controlled by various cis-acting elements surrounding the cleavage site, and their binding factors. In this study, we surveyed genome regions containing cleavage sites [herein called poly(A) sites], for 13 942 human and 11 155 mouse genes. We found that a great proportion of human and mouse genes have alternative polyadenylation (∼54 and 32%, respectively). The conservation of alternative polyadenylation type or polyadenylation configuration between human and mouse orthologs is statistically significant, indicating that alternative polyadenylation is widely employed by these two species to produce alternative gene transcripts. Genes belonging to several functional groups, indicated by their Gene Ontology annotations, are biased with respect to polyadenylation configuration. Many poly(A) sites harbor multiple cleavage sites (51.25% human and 46.97% mouse sites), leading to heterogeneous 3′ end formation for transcripts. This implies that the cleavage process of polyadenylation is largely imprecise. Different types of poly(A) sites, with regard to their relative locations in a gene, are found to have distinct nucleotide composition in surrounding genomic regions. This large-scale study provides important insights into the mechanism of polyadenylation in mammalian species and represents a genomic view of the regulation of gene expression by alternative polyadenylation.
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Affiliation(s)
- Bin Tian
- Department of Biochemistry and Molecular Biology, New Jersey Medical School UMDNJ, Newark, NJ 07101, USA.
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364
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Williams I, Richardson J, Starkey A, Stansfield I. Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2004; 32:6605-16. [PMID: 15602002 PMCID: PMC545446 DOI: 10.1093/nar/gkh1004] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Revised: 11/04/2004] [Accepted: 11/28/2004] [Indexed: 11/13/2022] Open
Abstract
In-frame stop codons normally signal termination during mRNA translation, but they can be read as 'sense' (readthrough) depending on their context, comprising the 6 nt preceding and following the stop codon. To identify novel contexts directing readthrough, under-represented 5' and 3' stop codon contexts from Saccharomyces cerevisiae were identified by genome-wide survey in silico. In contrast with the nucleotide bias 3' of the stop codon, codon bias in the two codon positions 5' of the termination codon showed no correlation with known effects on stop codon readthrough. However, individually, poor 5' and 3' context elements were equally as effective in promoting stop codon readthrough in vivo, readthrough which in both cases responded identically to changes in release factor concentration. A novel method analysing specific nucleotide combinations in the 3' context region revealed positions +1,2,3,5 and +1,2,3,6 after the stop codon were most predictive of termination efficiency. Downstream of yeast open reading frames (ORFs), further in-frame stop codons were significantly over-represented at the +1, +2 and +3 codon positions after the ORF, acting to limit readthrough. Thus selection against stop codon readthrough is a dominant force acting on 3', but not on 5', nucleotides, with detectable selection on nucleotides as far downstream as +6 nucleotides. The approaches described can be employed to define potential readthrough contexts for any genome.
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Affiliation(s)
- I Williams
- School of Engineering and Physical Sciences, Fraser Noble Building, Kings College, Aberdeen AB24 3UE, UK
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365
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Forrester SG, Warfel PW, Pearce EJ. Tegumental expression of a novel type II receptor serine/threonine kinase (SmRK2) in Schistosoma mansoni. Mol Biochem Parasitol 2004; 136:149-56. [PMID: 15478794 DOI: 10.1016/j.molbiopara.2004.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The TGF-beta family of receptor serine/threonine kinases (RSTKs) is responsible for a diverse array of functions in metazoans. Here, we describe the isolation of SmRK2, a type II RSTK expressed in schistosomula and adult stages of Schistosoma mansoni. Based on amino acid sequence homology, SmRK2 is most closely related to the Activin type II receptor subset of RSTKs. SmRK2 appears to be expressed as three different transcripts: one encoding a full-length receptor with 5'- and 3'-untranslated regions (UTRs) (SmRK2), a second encoding a longer form containing no 3'-UTR and no stop codon (SmRK2a), and a third truncated variant (SmRK2b), which contains sequence encoding the first 53 amino acids of the N-terminal extracellular domain followed by an inserted 10 residue hydrophobic domain. Using an anti-peptide antibody raised against a partial extracellular domain sequence common to all three isoforms, SmRK2 was localized predominantly to the tegumental surface of the parasites. We hypothesize that SmRK2 is the receptor partner for the previously reported type I RSTK SmRK1 (or SmTbetaR1) and that together these proteins constitute a receptor system for receiving signals from the mammalian host.
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Affiliation(s)
- Sean G Forrester
- Department of Pathobiology, University of Pennsylvania, 202D Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
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366
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Ougland R, Zhang CM, Liiv A, Johansen RF, Seeberg E, Hou YM, Remme J, Falnes PØ. AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation. Mol Cell 2004; 16:107-16. [PMID: 15469826 DOI: 10.1016/j.molcel.2004.09.002] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 07/14/2004] [Accepted: 07/20/2004] [Indexed: 11/25/2022]
Abstract
Deleterious 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions are introduced into nucleic acids by methylating agents. It was recently demonstrated that the E. coli AlkB protein and a human homolog, hABH3, can demethylate these lesions both in DNA and RNA. To elucidate the biological significance of the RNA repair, we have tested whether such repair can rescue the function of chemically methylated RNA. We demonstrate that a methylation-induced block in translation of an mRNA can be readily relieved by treatment with AlkB and hABH3 prior to translation. Furthermore, we show that chemical methylation of tRNAPhe inhibits aminoacylation and translation, but that the inhibition can be reversed by AlkB and hABH3. AlkB-mediated repair of 1-meA in tRNA was also observed in E. coli in vivo. Our data demonstrate that AlkB proteins can mediate functional recovery of RNA exposed to methylation damage, supporting the notion that RNA repair is important.
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Affiliation(s)
- Rune Ougland
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet University Hospital, NO-0027 Oslo, Norway
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367
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Baker KE, Condon C. Under the Tucson sun: a meeting in the desert on mRNA decay. RNA (NEW YORK, N.Y.) 2004; 10:1680-1691. [PMID: 15496519 PMCID: PMC1370653 DOI: 10.1261/rna.7163104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Kristian E Baker
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, 1007 East Lowell Street, Room 403 Life Sciences South, Tucson, AZ 85745, USA.
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368
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Abstract
Eukaryotic mRNAs are primarily degraded by removal of the 3' poly(A) tail, followed either by cleavage of the 5' cap structure (decapping) and 5'->3' exonucleolytic digestion, or by 3' to 5' degradation. mRNA decapping represents a critical step in turnover because this permits the degradation of the mRNA and is a site of numerous control inputs. Recent analyses suggest decapping of an mRNA consists of four central and related events. These include removal, or inactivation, of the poly(A) tail as an inhibitor of decapping, exit from active translation, assembly of a decapping complex on the mRNA, and sequestration of the mRNA into discrete cytoplasmic foci where decapping can occur. Each of these steps is a demonstrated, or potential, site for the regulation of mRNA decay. We discuss the decapping process in the light of these central properties, which also suggest fundamental aspects of cytoplasmic mRNA physiology that connect decapping, translation, and storage of mRNA.
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Affiliation(s)
- Jeff Coller
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA.
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369
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Chang TC, Yamashita A, Chen CYA, Yamashita Y, Zhu W, Durdan S, Kahvejian A, Sonenberg N, Shyu AB. UNR, a new partner of poly(A)-binding protein, plays a key role in translationally coupled mRNA turnover mediated by the c-fos major coding-region determinant. Genes Dev 2004; 18:2010-23. [PMID: 15314026 PMCID: PMC514181 DOI: 10.1101/gad.1219104] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Messenger RNA decay mediated by the c-fos major protein coding-region determinant of instability (mCRD) is a useful system for studying translationally coupled mRNA turnover. Among the five mCRD-associated proteins identified previously, UNR was found to be an mCRD-binding protein and also a PABP-interacting protein. Interaction between UNR and PABP is necessary for the full destabilization function of the mCRD. By testing different classes of mammalian poly(A) nucleases, we identified CCR4 as a poly(A) nuclease involved in the mCRD-mediated rapid deadenylation in vivo and also associated with UNR. Blocking either translation initiation or elongation greatly impeded poly(A) shortening and mRNA decay mediated by the mCRD, demonstrating that the deadenylation step is coupled to ongoing translation of the message. These findings suggest a model in which the mCRD/UNR complex serves as a "landing/assembly" platform for formation of a deadenylation/decay mRNA-protein complex on an mCRD-containing transcript. The complex is dormant prior to translation. Accelerated deadenylation and decay of the transcript follows ribosome transit through the mCRD. This study provides new insights into a mechanism by which interplay between mRNA turnover and translation determines the lifespan of an mCRD-containing mRNA in the cytoplasm.
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Affiliation(s)
- Tsung-Cheng Chang
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston 77030, USA
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370
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Cheng Z, Liu Y, Wang C, Parker R, Song H. Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination. Protein Sci 2004; 13:2673-84. [PMID: 15340168 PMCID: PMC2001155 DOI: 10.1110/ps.04856504] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Ski8p is a WD-repeat protein with an essential role for the Ski complex assembly in an exosome-dependent 3'-to-5' mRNA decay. In addition, Ski8p is involved in meiotic recombination by interacting with Spo11p protein. We have determined the crystal structure of Ski8p from Saccharomyces cerevisiae at 2.2 A resolution. The structure reveals that Ski8p folds into a seven-bladed beta propeller. Mapping sequence conservation and hydrophobicities of amino acids on the molecular surface of Ski8p reveals a prominent site on the top surface of the beta propeller, which is most likely involved in mediating interactions of Ski8p with Ski3p and Spo11p. Mutagenesis combined with yeast two-hybrid and GST pull-down assays identified the top surface of the beta propeller as being required for Ski8p binding to Ski3p and Spo11p. The functional implications for Ski8p function in both mRNA decay and meiotic recombination are discussed.
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Affiliation(s)
- Zhihong Cheng
- Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
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371
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True HL, Berlin I, Lindquist SL. Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. Nature 2004; 431:184-7. [PMID: 15311209 DOI: 10.1038/nature02885] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Accepted: 07/23/2004] [Indexed: 11/08/2022]
Abstract
Phenotypic plasticity and the exposure of hidden genetic variation both affect the survival and evolution of new traits, but their contributing molecular mechanisms are largely unknown. A single factor, the yeast prion [PSI(+)], may exert a profound effect on both. [PSI(+)] is a conserved, protein-based genetic element that is formed by a change in the conformation and function of the translation termination factor Sup35p, and is transmitted from mother to progeny. Curing cells of [PSI(+)] alters their survival in different growth conditions and produces a spectrum of phenotypes in different genetic backgrounds. Here we show, by examining three plausible explanations for this phenotypic diversity, that all traits tested involved [PSI(+)]-mediated read-through of nonsense codons. Notably, the phenotypes analysed were genetically complex, and genetic re-assortment frequently converted [PSI(+)]-dependent phenotypes to stable traits that persisted in the absence of [PSI(+)]. Thus, [PSI(+)] provides a temporary survival advantage under diverse conditions, increasing the likelihood that new traits will become fixed by subsequent genetic change. As an epigenetic mechanism that globally affects the relationship between genotype and phenotype, [PSI(+)] expands the conceptual framework for phenotypic plasticity, provides a one-step mechanism for the acquisition of complex traits and affords a route to the genetic assimilation of initially transient epigenetic traits.
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Affiliation(s)
- Heather L True
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
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372
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Reverdatto SV, Dutko JA, Chekanova JA, Hamilton DA, Belostotsky DA. mRNA deadenylation by PARN is essential for embryogenesis in higher plants. RNA (NEW YORK, N.Y.) 2004; 10:1200-14. [PMID: 15247430 PMCID: PMC1370610 DOI: 10.1261/rna.7540204] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Deadenylation of mRNA is often the first and rate-limiting step in mRNA decay. PARN, a poly(A)-specific 3' --> 5' ribonuclease which is conserved in many eukaryotes, has been proposed to be primarily responsible for such a reaction, yet the importance of the PARN function at the whole-organism level has not been demonstrated in any species. Here, we show that mRNA deadenylation by PARN is essential for viability in higher plants (Arabidopsis thaliana). Yet, this essential requirement for the PARN function is not universal across the phylogenetic spectrum, because PARN is dispensable in Fungi (Schizosaccharomyces pombe), and can be at least severely downregulated without any obvious consequences in Metazoa (Caenorhabditis elegans). Development of the Arabidopsis embryos lacking PARN (AtPARN), as well as of those expressing an enzymatically inactive protein, was markedly retarded, and ultimately culminated in an arrest at the bent-cotyledon stage. Importantly, only some, rather than all, embryo-specific transcripts were hyperadenylated in the mutant embryos, suggesting that preferential deadenylation of a specific select subset of mRNAs, rather than a general deadenylation of the whole mRNA population, by AtPARN is indispensable for embryogenesis in Arabidopsis. These findings indicate a unique, nonredundant role of AtPARN among the multiple plant deadenylases.
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Affiliation(s)
- Sergei V Reverdatto
- Department of Biological Sciences, State University of New York at Albany, 12222, USA
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373
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Annilo T, Dean M. Degeneration of an ATP-binding cassette transporter gene, ABCC13, in different mammalian lineages. Genomics 2004; 84:34-46. [PMID: 15203202 DOI: 10.1016/j.ygeno.2004.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2003] [Accepted: 02/19/2004] [Indexed: 11/18/2022]
Abstract
The ABC transporter gene family has evolved by a gene "birth-and-death" process; however, the number of ABC pseudogenes in the human genome is surprisingly small. On chromosome 21q11.2, spanning 90 kb, is an ABC gene-like sequence (recently annotated as ABCC13) with the highest similarity to ABCC2. Here we show that while comparative analysis and in silico prediction methods indicate the presence of at least 28 exons, the major ABCC13 transcript in humans consists of only 6 exons with a total length of 1.1 kb. The open reading frame of this transcript is capable of encoding a polypeptide of only 274 amino acids, compared to the more than 1500 amino acids of related ABC transporters. The truncated ABCC13 transcript shows tissue-specific expression, highest in fetal liver, bone marrow, and colon. Since the last exon of the ABCC13 transcript contains an apparent frameshift, we sequenced the respective region from several primates and found that the frameshift is due to an 11-bp deletion that is shared between human, chimpanzee, and gorilla, but is not found in monkeys. In addition, the human ABCC13 gene contains two other frameshift indels in the exons that encode the second nucleotide-binding domain, indicating that ABCC13 is not capable of encoding a functional ABC protein. In an attempt to identify an intact ABCC13 ortholog, we have sequenced the full-length cDNA from rhesus macaque, which contains an open reading frame of 1296 amino acids, producing an apparently functional ABC transporter. Although the mouse and rat genomes contain long-range similarity in the locus where Abcc13 is expected to reside, most of the Abcc13 exons in rodents are degraded below the threshold of sequence homology searches or have been deleted completely.
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Affiliation(s)
- Tarmo Annilo
- Human Genetics Section, Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Building 560, Room 21-31, Frederick, MD 21702, USA.
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374
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Madrona AY, Wilson DK. The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure. Protein Sci 2004; 13:1557-65. [PMID: 15152089 PMCID: PMC2279974 DOI: 10.1110/ps.04704704] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Revised: 03/19/2004] [Accepted: 03/22/2004] [Indexed: 10/26/2022]
Abstract
Ski8p is a 44-kD protein that primarily functions in the regulation of exosome-mediated, 3'--> 5' degradation of damaged mRNA. It does so by forming a complex with two partner proteins, Ski2p and Ski3p, which complete a complex that is capable of recruiting and activating the exosome/Ski7p complex that functions in RNA degradation. Ski8p also functions in meiotic recombination in complex with Spo11 in yeast. It is one of the many hundreds of primarily eukaryotic proteins containing tandem copies of WD repeats (also known as WD40 or beta-transducin repeats), which are short ~40 amino acid motifs, often terminating in a Trp-Asp dipeptide. Genomic analyses have demonstrated that WD repeats are found in 1%-2% of proteins in a typical eukaryote, but are extremely rare in prokaryotes. Almost all structurally characterized WD-repeat proteins are composed of seven such repeats and fold into seven-bladed beta propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 A crystal structure unexpectedly exhibits a seven-bladed propeller fold with seven structurally authentic WD repeats. Structure-based sequence alignments show additional sequence diversity in the two undetected repeats. This demonstrates that many WD repeats have not yet been identified in sequences and also raises the possibility that the seven-bladed propeller may be the predominant fold for this family of proteins.
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Affiliation(s)
- A Yarrow Madrona
- Section of Molecular and Cellular Biology, 1 Shields Ave., University of California, Davis, CA 95616, USA
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375
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Xie HG, Wood AJJ, Kim RB, Stein CM, Wilkinson GR. Genetic variability in CYP3A5 and its possible consequences. Pharmacogenomics 2004; 5:243-72. [PMID: 15102541 DOI: 10.1517/phgs.5.3.243.29833] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cytochrome P450 3A (CYP3A) subfamily members are the most abundant and important drug-metabolizing enzymes in humans, and wide interindividual variability in CYP3A expression and function is present. CYP3A4 alone cannot fully explain the observed constitutive variability because its genetic variants are relatively uncommon and have limited functional significance, whereas CYP3A5 expression in humans is highly variable and may be contributory. However, it is difficult to delineate the relative contribution of CYP3A4 and CYP3A5, and to differentiate their effects on drug metabolism as their protein structure, function and substrates are so similar. By contrast, molecular biology methods provide the ability to identify CYP3A4 and CYP3A5 genotypes with certainty. This review collates currently available data on CYP3A5 polymorphisms, provides information on the population frequency of each genetic variant in major ethnic groups, and describes in vitro and in vivo studies that have attempted to identify genotype-phenotype associations.
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Affiliation(s)
- Hong-Guang Xie
- Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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376
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Abstract
The degradation of eukaryotic mRNAs plays important roles in the modulation of gene expression, quality control of mRNA biogenesis and antiviral defenses. In the past five years, many of the enzymes involved in this process have been identified and mechanisms that modulate their activities have begun to be identified. In this review, we describe the enzymes of mRNA degradation and their properties. We highlight that there are a variety of enzymes with different specificities, suggesting that individual nucleases act on distinct subpopulations of transcripts within the cell. In several cases, translation factors that bind mRNA inhibit these nucleases. In addition, recent work has begun to identify distinct mRNP complexes that recruit the nucleases to transcripts through different mRNA-interacting proteins. These properties and complexes suggest multiple mechanisms by which mRNA degradation could be regulated.
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Affiliation(s)
- Roy Parker
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721-0106, USA.
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377
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Abstract
Understanding gene expression control requires defining the molecular and cellular basis of mRNA turnover. We have previously shown that the human decapping factors hDcp2 and hDcp1a are concentrated in specific cytoplasmic structures. Here, we show that hCcr4, hDcp1b, hLsm, and rck/p54 proteins related to 5'-3' mRNA decay also localize to these structures, whereas DcpS, which is involved in cap nucleotide catabolism, is nuclear. Functional analysis using fluorescence resonance energy transfer revealed that hDcp1a and hDcp2 interact in vivo in these structures that were shown to differ from the previously described stress granules. Our data indicate that these new structures are dynamic, as they disappear when mRNA breakdown is abolished by treatment with inhibitors. Accumulation of poly(A)(+) RNA in these structures, after RNAi-mediated inactivation of the Xrn1 exonuclease, demonstrates that they represent active mRNA decay sites. The occurrence of 5'-3' mRNA decay in specific subcellular locations in human cells suggests that the cytoplasm of eukaryotic cells may be more organized than previously anticipated.
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Affiliation(s)
- Nicolas Cougot
- Equipe labellisée La Ligue, Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Avenue de la Terrasse, 91198 Gif sur Yvette, France
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378
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Danckwardt S, Gehring NH, Neu-Yilik G, Hundsdoerfer P, Pforsich M, Frede U, Hentze MW, Kulozik AE. The prothrombin 3'end formation signal reveals a unique architecture that is sensitive to thrombophilic gain-of-function mutations. Blood 2004; 104:428-35. [PMID: 15059842 DOI: 10.1182/blood-2003-08-2894] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The functional analysis of the common prothrombin 20210 G>A(F2 20210(*)A) mutation has recently revealed gain of function of 3'end processing as a novel genetic mechanism predisposing to human disease. We now show that the physiologic G at the cleavage site at position 20210 is the functionally least efficient nucleotide to support 3'end processing but has evolved to be physiologically optimal. Furthermore, the F2 3'end processing signal is characterized by a weak downstream cleavage stimulating factor (CstF) binding site with a low uridine density, and the functional efficiency of F2 3'end processing can be enhanced by the introduction of additional uridine residues. The recently identified thrombosis-related mutation (F2 20221(*)T) within the CstF binding site up-regulates F2 3'end processing and prothrombin biosynthesis in vivo. F2 20221(*)T thus represents the first example of a likely pathologically relevant mutation of the putative CstF binding site in the 3'flanking sequence of a human gene. Finally, we show that the low-efficiency F2 cleavage and CstF binding sites are balanced by a stimulatory upstream uridine-rich element in the 3'UTR. The architecture of the F2 3'end processing signal is thus characterized by a delicate balance of positive and negative signals. This balance appears to be highly susceptible to being disturbed by clinically relevant gain-of-function mutations.
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Affiliation(s)
- Sven Danckwardt
- Molecular Medicine Partnership Unit, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany
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379
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Chrzanowska-Lightowlers ZMA, Temperley RJ, Smith PM, Seneca SH, Lightowlers RN. Functional polypeptides can be synthesized from human mitochondrial transcripts lacking termination codons. Biochem J 2004; 377:725-31. [PMID: 14585098 PMCID: PMC1223913 DOI: 10.1042/bj20031556] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 10/29/2003] [Accepted: 10/30/2003] [Indexed: 11/17/2022]
Abstract
The human mitochondrial genome (mtDNA) is a small, circular DNA duplex found in multi-copy in the mitochondrial matrix. It is almost fully transcribed from both strands to produce large polycistronic RNA units that are processed and matured. The 13 mtDNA-encoded polypeptides are translated from mt-mRNAs that have been matured by polyadenylation of their free 3'-termini. A patient with clinical features consistent with an mtDNA disorder was recently shown to carry a microdeletion, resulting in the loss of the termination codon for MTATP6 and in its juxtaposition with MTCO3. Cell lines from this patient exhibited low steady-state levels of RNA14, the bi-cistronic transcript encoding subunits 6 and 8 of the F(o)F(1)-ATP synthase, complex V, consistent with a decreased stability. Recent reports of 'non-stop' mRNA decay systems in the cytosol have failed to determine the fate of gene products derived from transcripts lacking termination codons, although enhanced decay clearly required the 'non-stop' transcripts to be translated. We wished to determine whether functional translation products could still be expressed from non-stop transcripts in the human mitochondrion. Although a minor defect in complex V assembly was noted in the patient-derived cell lines, the steady-state level of ATPase 6 was similar to controls, consistent with the pattern of de novo mitochondrial protein synthesis. Moreover, no significant difference in ATP synthase activity could be detected. We conclude that, in the absence of a functional termination codon, although mitochondrial transcripts are more rapidly degraded, they are also translated to generate stable polypeptides that are successfully integrated into functional enzyme complexes.
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380
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He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol Cell 2004; 12:1439-52. [PMID: 14690598 DOI: 10.1016/s1097-2765(03)00446-5] [Citation(s) in RCA: 289] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Transcripts regulated by the yeast nonsense-mediated and 5' to 3' mRNA decay pathways were identified by expression profiling of wild-type, upf1Delta, nmd2Delta, upf3Delta, dcp1Delta, and xrn1Delta cells. This analysis revealed that inactivation of Upf1p, Nmd2p, or Upf3p has identical effects on global RNA accumulation; inactivation of Dcp1p or Xrn1p exhibits both common and unique effects on global RNA accumulation but causes upregulation of only a small fraction of transcripts; and the majority of transcripts upregulated in upf/nmd strains are also upregulated to similar extents in dcp1Delta and xrn1Delta strains. Our results define the core transcripts regulated by NMD, identify several novel structural classes of NMD substrates, demonstrate that nonsense-containing mRNAs are primarily degraded by the 5' to 3' decay pathway even in the absence of functional NMD, and indicate that 3' to 5' decay, not 5' to 3' decay, may be the major mRNA decay activity in yeast cells.
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Affiliation(s)
- Feng He
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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381
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Brown KM, Gilmartin GM. A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im. Mol Cell 2004; 12:1467-76. [PMID: 14690600 DOI: 10.1016/s1097-2765(03)00453-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Human cleavage factor I(m) (CFI(m)) is a heterodimeric RNA binding protein complex that functions at an early step in the assembly of the pre-mRNA 3' processing complex. In this report we show that CFI(m) can stimulate both cleavage and poly(A) addition, and can act to suppress poly(A) site cleavage in a sequence-dependent manner. Elevated levels of CFI(m) suppressed cleavage at the primary poly(A) site of the pre-mRNA encoding the 68 kDa subunit of CFI(m). CFI(m)-mediated suppression of poly(A) site cleavage was dependent upon the presence of three copies of an RNA element initially identified by CFI(m)-SELEX. These data provide evidence for a mechanism for the regulation of poly(A) site selection by a basal pre-mRNA 3' processing factor.
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Affiliation(s)
- Kirk M Brown
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
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382
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Hayes CS, Sauer RT. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol Cell 2003; 12:903-11. [PMID: 14580341 DOI: 10.1016/s1097-2765(03)00385-x] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cells employ many mechanisms to ensure quality control during protein biosynthesis. Here, we show that, during the pausing of a bacterial ribosome, the mRNA being translated is cleaved at a site within or immediately adjacent to the A site codon. The extent of this A site mRNA cleavage is correlated with the extent of ribosome pausing as assayed by tmRNA-mediated tagging of the nascent polypeptide. Cleavage does not require tmRNA, the ribosomal alarmone (p)ppGpp, or bacterial toxins such as RelE which have been shown to stimulate a similar activity. Translation is required for cleavage, suggesting that the ribosome participates in the reaction in some fashion. When normal protein synthesis is compromised, A site mRNA cleavage and the tmRNA system provide a mechanism for reducing translational errors and the production of aberrant and potentially harmful polypeptides.
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Affiliation(s)
- Christopher S Hayes
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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383
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Seminara SB, Messager S, Chatzidaki EE, Thresher RR, Acierno JS, Shagoury JK, Bo-Abbas Y, Kuohung W, Schwinof KM, Hendrick AG, Zahn D, Dixon J, Kaiser UB, Slaugenhaupt SA, Gusella JF, O'Rahilly S, Carlton MBL, Crowley WF, Aparicio SAJR, Colledge WH. The GPR54 gene as a regulator of puberty. N Engl J Med 2003; 349:1614-27. [PMID: 14573733 DOI: 10.1056/nejmoa035322] [Citation(s) in RCA: 1754] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Puberty, a complex biologic process involving sexual development, accelerated linear growth, and adrenal maturation, is initiated when gonadotropin-releasing hormone begins to be secreted by the hypothalamus. We conducted studies in humans and mice to identify the genetic factors that determine the onset of puberty. METHODS We used complementary genetic approaches in humans and in mice. A consanguineous family with members who lacked pubertal development (idiopathic hypogonadotropic hypogonadism) was examined for mutations in a candidate gene, GPR54, which encodes a G protein-coupled receptor. Functional differences between wild-type and mutant GPR54 were examined in vitro. In parallel, a Gpr54-deficient mouse model was created and phenotyped. Responsiveness to exogenous gonadotropin-releasing hormone was assessed in both the humans and the mice. RESULTS Affected patients in the index pedigree were homozygous for an L148S mutation in GPR54, and an unrelated proband with idiopathic hypogonadotropic hypogonadism was determined to have two separate mutations, R331X and X399R. The in vitro transfection of COS-7 cells with mutant constructs demonstrated a significantly decreased accumulation of inositol phosphate. The patient carrying the compound heterozygous mutations (R331X and X399R) had attenuated secretion of endogenous gonadotropin-releasing hormone and a left-shifted dose-response curve for gonadotropin-releasing hormone as compared with six patients who had idiopathic hypogonadotropic hypogonadism without GPR54 mutations. The Gpr54-deficient mice had isolated hypogonadotropic hypogonadism (small testes in male mice and a delay in vaginal opening and an absence of follicular maturation in female mice), but they showed responsiveness to both exogenous gonadotropins and gonadotropin-releasing hormone and had normal levels of gonadotropin-releasing hormone in the hypothalamus. CONCLUSIONS Mutations in GPR54, a G protein-coupled receptor gene, cause autosomal recessive idiopathic hypogonadotropic hypogonadism in humans and mice, suggesting that this receptor is essential for normal gonadotropin-releasing hormone physiology and for puberty.
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Affiliation(s)
- Stephanie B Seminara
- Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
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384
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van Dijk E, Le Hir H, Séraphin B. DcpS can act in the 5'-3' mRNA decay pathway in addition to the 3'-5' pathway. Proc Natl Acad Sci U S A 2003; 100:12081-6. [PMID: 14523240 PMCID: PMC218716 DOI: 10.1073/pnas.1635192100] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3'-5' mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5'-3' pathway, the recently identified human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce m7GDP and 5'-phosphorylated mRNA. We investigated mRNA decay in human cell extracts by using a new assay for decapping. We observed that 5'-phosphorylated intermediates resulting from decapping appear after incubation of a substrate RNA in human cell extracts, indicating the presence of an active 5'-3' mRNA decay pathway. Surprisingly, however, the cognate m7GDP product was not detected, whereas abundant amounts of m7GMP were generated. Additional experiments revealed that m7GDP is, unexpectedly, efficiently converted to m7GMP in extracts from various organisms. The factor necessary and sufficient for this reaction was identified as DcpS in both yeast and human. m7GMP is thus a general, pathway-independent, by-product of eukaryotic mRNA decay. m7GDP breakdown should prevent misincorporation of methylated nucleotides in nucleic acids and could generate a unique indicator allowing the cell to monitor mRNA decay.
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Affiliation(s)
- Erwin van Dijk
- Equipe Labellisée La Ligue, Centre de Génétique Moléculaire, Unité Propre de Recherche 2167, Centre National de la Recherche Scientifique Associée à l'Université Paris VI, Avenue de la Terrasse, 91198 Gif sur Yvette, France
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385
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Phillips S, Butler JS. Contribution of domain structure to the RNA 3' end processing and degradation functions of the nuclear exosome subunit Rrp6p. RNA (NEW YORK, N.Y.) 2003; 9:1098-107. [PMID: 12923258 PMCID: PMC1370474 DOI: 10.1261/rna.5560903] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2003] [Accepted: 05/30/2003] [Indexed: 05/20/2023]
Abstract
The 3'-5' riboexonuclease Rrp6p, a nuclear component of the exosome, functions with other exosome components to produce the mature 3' ends of 5.8S rRNA, sno- and snRNAs, and to destroy improperly processed precursor (pre)-rRNAs and pre-mRNAs. Rrp6p is a member of the RNase D family of riboexonucleases and displays a high degree of homology with the active site of the deoxyriboexonuclease domain of Escherichia coli DNA polymerase I, the crystal structure of which indicates a two-metal ion mechanism for phosphodiester bond hydrolysis. Mutation of each of the conserved residues predicted to coordinate metal ions in the active site of Rrp6p abolished activity of the enzyme in vitro and in vivo. Complete loss of Rrp6p activity caused by the Y361F and Y361A mutations supports the critical role proposed for the phenolic hydroxyl of Tyr361 in the reaction mechanism. Rrp6p also contains an helicase RNase D C-terminal (HRDC) domain of unknown function that is similar to domains in the Werner's and Bloom's Syndrome proteins. A point mutation in this domain results in Rrp6p that localizes to the nucleus, but fails to efficiently process the 3' ends of 5.8S pre-rRNA and some pre-snoRNAs. In contrast, this mutant retains the ability to degrade rRNA processing intermediates and 3'-extended, poly(A)+ snoRNAs. These findings indicate the potential for independent control of the processing and degradation functions of Rrp6p.
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Affiliation(s)
- Seasson Phillips
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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386
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Gaudin C, Nonin-Lecomte S, Tisné C, Corvaisier S, Bordeau V, Dardel F, Felden B. The tRNA-like domains of E coli and A.aeolicus transfer-messenger RNA: structural and functional studies. J Mol Biol 2003; 331:457-71. [PMID: 12888352 DOI: 10.1016/s0022-2836(03)00760-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Transfer-messenger RNA (tmRNA, 10Sa RNA or ssrA) acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The understanding at molecular level of this ubiquitous quality control system in eubacteria requires structural information. Here, we describe the purification and structural analysis of a functional fragment of both Aquifex aeolicus and Escherichia coli tmRNA, recapitulating their tRNA-like domain, which were expressed in vivo from synthetic genes. Both recombinant RNA are correctly processed at both 5' and 3' ends and are produced in quantities suitable for structural analysis by NMR and/or X-ray crystallography. The sequence and solution structure of the tRNA-like domains were analysed by various methods including structural mapping with chemical and enzymatic probes and 2D NMR spectroscopy. The minimalist RNAs contain two post-transcriptional base modifications, 5-methyluridine and pseudouridine, as the full-length tmRNA. Both RNAs fold into three stems, a D-analogue, a T-loop and a GAAA tetra-loop. 2D NMR analysis of the imino proton resonances of both RNAs allowed the assignment of the three stems and of a number of tertiary interactions. It shows the existence of interactions between the TPsiC-loop and the D-analogue, exhibiting a number of similarities and also differences with the canonical tRNA fold, indicating that RNA tertiary interactions can be modulated according to the sequence and secondary structure contexts. Furthermore, the E.coli minimalist RNA is aminoacylatable with alanine with a catalytic efficiency an order of magnitude higher than that for full-length tmRNA.
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Affiliation(s)
- Cyril Gaudin
- Laboratoire de Biochimie Pharmaceutique UPRES JE2311, Faculté de Pharmacie, Université de Rennes I, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France
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387
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Abstract
A nuclear mRNA degradation (DRN) system was identified from analysis of mRNA turnover rates in nup116-Delta strains of Saccharomyces cerevisiae lacking the ability to export all RNAs, including poly(A) mRNAs, at the restrictive temperature. Northern blotting, in situ hybridization, and blocking transcription with thiolutin in nup116-delta strains revealed a rapid degradation of mRNAs in the nucleus that was suppressed by the rrp6-delta, rai1-delta, and cbc1-delta deletions, but not by the upf1-delta deletion, suggesting that DRN requires Rrp6p, a 3'-to-5' nuclear exonuclease, the Rat1p, a 5'-to-3' nuclear exonuclease, and Cbc1p, a component of CBC, the nuclear cap binding complex, which may direct the mRNAs to the site of degradation. We propose that certain normal mRNAs retained in the nucleus are degraded by the DRN system, similar to degradation of transcripts with 3' end formation defects in certain mutants.
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Affiliation(s)
- Biswadip Das
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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388
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Takahashi S, Araki Y, Sakuno T, Katada T. Interaction between Ski7p and Upf1p is required for nonsense-mediated 3'-to-5' mRNA decay in yeast. EMBO J 2003; 22:3951-9. [PMID: 12881429 PMCID: PMC169047 DOI: 10.1093/emboj/cdg374] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2002] [Revised: 06/02/2003] [Accepted: 06/03/2003] [Indexed: 01/20/2023] Open
Abstract
Aberrant mRNAs containing premature termination codons (PTC-mRNAs) are degraded by a conserved surveillance system, referred to as the nonsense- mediated decay (NMD) pathway. Although NMD is reported to operate on the decapping and 5'-to-3' exonucleolytic decay of PTC-mRNAs without affecting deadenylation, a role for an opposite 3'-to-5' decay pathway remains largely unexplored. In this study, we have characterized the 3'-to-5' directed mRNA degradation in the yeast NMD pathway. PTC-mRNAs are stabilized in yeast cells lacking the components of 3'-to-5' mRNA-decay machinery. The 3'-to-5' directed degradation of PTC-mRNAs proceeds more rapidly than that of the PTC-free transcript, in a manner dependent on the cytoplasmic exosome and Upf proteins. Moreover, Upf1p, but not Upf2p, interacts physically with an N-terminal domain of Ski7p, although the interaction requires Upf2p. The efficiency of 3'-to-5' directed degradation of PTC-mRNAs is impaired by overexpression of Ski7p N-domain fragments that contain a sequence of the Upf1p-interaction region. These data suggest that the activation of 3'-to-5' directed NMD is mediated through the interaction between Upf1p and the Ski7p N domain.
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Affiliation(s)
- Shinya Takahashi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
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389
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Garg V, Kathiriya IS, Barnes R, Schluterman MK, King IN, Butler CA, Rothrock CR, Eapen RS, Hirayama-Yamada K, Joo K, Matsuoka R, Cohen JC, Srivastava D. GATA4 mutations cause human congenital heart defects and reveal an interaction with TBX5. Nature 2003; 424:443-7. [PMID: 12845333 DOI: 10.1038/nature01827] [Citation(s) in RCA: 862] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2003] [Accepted: 06/18/2003] [Indexed: 11/09/2022]
Abstract
Congenital heart defects (CHDs) are the most common developmental anomaly and are the leading non-infectious cause of mortality in newborns. Only one causative gene, NKX2-5, has been identified through genetic linkage analysis of pedigrees with non-syndromic CHDs. Here, we show that isolated cardiac septal defects in a large pedigree were linked to chromosome 8p22-23. A heterozygous G296S missense mutation of GATA4, a transcription factor essential for heart formation, was found in all available affected family members but not in any control individuals. This mutation resulted in diminished DNA-binding affinity and transcriptional activity of Gata4. Furthermore, the Gata4 mutation abrogated a physical interaction between Gata4 and TBX5, a T-box protein responsible for a subset of syndromic cardiac septal defects. Conversely, interaction of Gata4 and TBX5 was disrupted by specific human TBX5 missense mutations that cause similar cardiac septal defects. In a second family, we identified a frame-shift mutation of GATA4 (E359del) that was transcriptionally inactive and segregated with cardiac septal defects. These results implicate GATA4 as a genetic cause of human cardiac septal defects, perhaps through its interaction with TBX5.
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Affiliation(s)
- Vidu Garg
- Department of Pediatrics, University of Texas Southwestern Medical Center at Dallas, 6000 Harry Hines Boulevard, Rm. NA8.124, Dallas, Texas 75390-9148, USA.
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390
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Yasuda M, Shabbeer J, Osawa M, Desnick RJ. Fabry disease: novel alpha-galactosidase A 3'-terminal mutations result in multiple transcripts due to aberrant 3'-end formation. Am J Hum Genet 2003; 73:162-73. [PMID: 12796853 PMCID: PMC1180577 DOI: 10.1086/376608] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2003] [Accepted: 04/29/2003] [Indexed: 01/26/2023] Open
Abstract
Mutations in the gene that encodes the lysosomal exoglycohydrolase, alpha-galactosidase A (alpha-GalA), cause Fabry disease, an X-linked recessive inborn error of glycosphingolipid catabolism. Human alpha-GalA is one of the rare mammalian genes that has its polyadenylation signal in the coding sequence and lacks a 3' untranslated region (UTR). We identified two novel frameshift mutations, 1277delAA (del2) and 1284delACTT (del4), in unrelated men with classical Fabry disease. Both mutations occurred in the 3' terminus of the coding region and obliterated the termination codon, and del2 also altered the polyadenylation signal. To characterize these mutations, 3' rapid amplification of cDNA ends (RACE) and polymerase chain reactions (PCR) were performed, and the amplicons were subcloned and sequenced. Both mutations generated multiple transcripts with various lengths of 3' terminal sequences, some elongating approximately 1 kb. Mutant transcripts were classified as follows: type I transcripts had terminal in-frame thymidines that created termination codons when polyadenylated, type II had downstream termination codons within the elongated alpha-GalA sequence, and type III, the most abundant, lacked termination codons at their 3' ends. To determine if the type III transcripts were degraded by the recently described cytosolic messenger RNA degradation pathway for messages lacking termination codons, northern blot analysis was performed. However, the finding of similar levels of nuclear and cytoplasmic alpha-GalA mRNA in normal and patient lymphoblasts suggested that mRNA degradation did not result from either mutation. Expression of representative transcript types revealed differences in intracellular localization and/or protein stability and catalytic activity, with most mutant proteins being nonfunctional. Characterization of these 3' mutations identified a novel molecular mechanism causing classical Fabry disease.
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Affiliation(s)
- Makiko Yasuda
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
| | - Junaid Shabbeer
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
| | - Makiko Osawa
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
| | - Robert J. Desnick
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
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391
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Quesada V, Macknight R, Dean C, Simpson GG. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J 2003; 22:3142-52. [PMID: 12805228 PMCID: PMC162157 DOI: 10.1093/emboj/cdg305] [Citation(s) in RCA: 230] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The timing of the transition to flowering is critical for reproductive success in plants. Arabidopsis FCA encodes an RNA-binding protein that promotes flowering. FCA expression is regulated through alternative processing of its pre-mRNA. We demonstrate here that FCA negatively regulates its own expression by ultimately promoting cleavage and polyadenylation within intron 3. This causes the production of a truncated, inactive transcript at the expense of the full-length FCA mRNA, thus limiting the expression of active FCA protein. We show that this negative autoregulation is under developmental control and requires the FCA WW protein interaction domain. Removal of introns from FCA bypasses the autoregulation, and the resulting increased levels of FCA protein overcomes the repression of flowering normally conferred through the up-regulation of FLC by active FRI alleles. The negative autoregulation of FCA may therefore have evolved to limit FCA activity and hence control flowering time.
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Affiliation(s)
- Victor Quesada
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
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392
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Simpson GG, Dijkwel PP, Quesada V, Henderson I, Dean C. FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 2003; 113:777-87. [PMID: 12809608 DOI: 10.1016/s0092-8674(03)00425-2] [Citation(s) in RCA: 271] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.
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Affiliation(s)
- Gordon G Simpson
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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393
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Dannenberg H, De Krijger RR, van der Harst E, Abbou M, IJzendoorn Y, Komminoth P, Dinjens WNM. Von Hippel-Lindau gene alterations in sporadic benign and malignant pheochromocytomas. Int J Cancer 2003; 105:190-5. [PMID: 12673678 DOI: 10.1002/ijc.11060] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Von Hippel-Lindau (VHL) gene product has a wide spectrum of tissue-specific functions, and specific germline mutations are associated with clinical phenotypes in VHL disease. In particular, missense mutations are correlated with the susceptibility to pheochromocytomas. An association between VHL aberrations and prognosis has been suggested in renal clear cell carcinoma but has not been studied in pheochromocytomas. We studied the frequency and spectrum of VHL alterations in apparently sporadic pheochromocytomas in relation to the clinical behavior in 72 patients, including 48 patients with clinically benign and 24 patients with malignant pheochromocytomas. Single-strand conformation polymorphism (SSCP) analysis followed by DNA sequencing, loss of heterozygosity analysis of the VHL locus and immunohistochemistry for VHL protein expression were used to investigate somatic VHL gene alterations. In 2 patients, 1 with a malignant tumor, germline mutations were identified in the stop codon. Tumor-specific intragenic VHL mutations and accompanying loss of heterozygosity were identified in 2 (4.3%) of 47 sporadic benign pheochromocytomas compared to 4 (17.4%) of 23 malignant tumors (p = 0.064). Only one of these mutations has been previously described, in a renal clear cell carcinoma. Expression of the VHL protein was observed in all pheochromocytomas. No distinction in the nature of VHL alterations between benign and malignant pheochromocytomas and no correlation with histopathologic or clinical features was observed. We report novel VHL mutations in sporadic pheochromocytomas, which are slightly correlated with malignancy. VHL mutations may have some impact on the malignant transformation of pheochromocytomas.
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Affiliation(s)
- Hilde Dannenberg
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam, The Netherlands
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394
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Mitchell P, Tollervey D. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation. Mol Cell 2003; 11:1405-13. [PMID: 12769863 DOI: 10.1016/s1097-2765(03)00190-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Eukaryotic mRNAs containing premature termination codons are subjected to accelerated turnover, known as nonsense-mediated decay (NMD). Recognition of translation termination events as premature requires a surveillance complex, which includes the RNA helicase Upf1p. In Saccharomyces cerevisiae, NMD provokes rapid decapping followed by 5'-->3' exonucleolytic decay. Here we report an alternative, decapping-independent NMD pathway involving deadenylation and subsequent 3'-->5' exonucleolytic decay. Accelerated turnover via this pathway required Upf1p and was blocked by the translation inhibitor cycloheximide. Degradation of the deadenylated mRNA required the Rrp4p and Ski7p components of the cytoplasmic exosome complex, as well as the putative RNA helicase Ski2p. We conclude that recognition of NMD substrates by the Upf surveillance complex can target mRNAs to rapid deadenylation and exosome-mediated degradation.
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Affiliation(s)
- Philip Mitchell
- Wellcome Trust Centre for Cell Biology, Institute for Cell and Molecular Biology, King's Buildings, University of Edinburgh, EH9 3JR, United Kingdom.
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395
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Yamamoto Y, Sunohara T, Jojima K, Inada T, Aiba H. SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs. RNA (NEW YORK, N.Y.) 2003; 9:408-18. [PMID: 12649493 PMCID: PMC1370408 DOI: 10.1261/rna.2174803] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2002] [Accepted: 12/16/2002] [Indexed: 05/22/2023]
Abstract
An important unsolved question regarding the bacterial SsrA system is the fate of target mRNAs replaced by SsrA RNA during trans-translation. The aim of the present study is to address the potential role of SsrA system in mRNA quality control, focusing on truncated mRNAs that are expected to arise from 3'-to-5' exonucleolytic attack. We found that significant amounts of truncated mRNAs and polypeptides were produced from genes lacking a rho-independent terminator in SsrA-deficient cells. These truncated mRNAs, hence truncated polypeptides, were no longer observed in the presence of SsrA RNA. The data indicate that the SsrA system facilitates degradation of "nonstop" mRNAs by presumably removing the stalled ribosomes. Furthermore, analysis of affinity-purified proteins indicated that truncated polypeptides could be produced even from a gene with an intact rho-independent terminator, although less efficiently, implying that C-terminally truncated proteins and 3'-truncated mRNA may be produced from virtually all protein-coding genes. We conclude that the SsrA system not only promotes the degradation of incomplete polypeptides but also minimizes the synthesis of incomplete polypeptides by facilitating the degradation of truncated mRNAs that are produced in cells.
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Affiliation(s)
- Yasufumi Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
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396
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Hagmaier K, Jennings S, Buse J, Weber F, Kochs G. Novel gene product of Thogoto virus segment 6 codes for an interferon antagonist. J Virol 2003; 77:2747-52. [PMID: 12552016 PMCID: PMC141086 DOI: 10.1128/jvi.77.4.2747-2752.2003] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2002] [Accepted: 11/19/2002] [Indexed: 11/20/2022] Open
Abstract
Thogoto virus (THOV) is a tick-transmitted orthomyxovirus with a genome of six negative-stranded RNA segments. The sixth segment encodes two different transcripts: a spliced transcript that is translated into the matrix protein (M) and an unspliced transcript. Here, we report that the unspliced transcript encodes an elongated form of M named ML. A THOV isolate deficient in ML expression was an efficient interferon inducer, whereas ML-expressing wild-type strains were poor interferon inducers. These results were confirmed with recombinant THOVs rescued from cDNAs. Expression of ML efficiently suppressed activation of the beta interferon promoter by double-stranded RNA. These results indicate that ML is an accessory protein that functions as a potent interferon antagonist by blocking transcriptional activation of alpha/beta interferons.
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Affiliation(s)
- Kathrin Hagmaier
- Abteilung Virologie, Institut für Medizinische Mikrobiologie und Hygiene, Universität Freiburg, D-79008 Freiburg, Germany
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397
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Abstract
Trans-translation is a process found in all bacteria, which contributes to the release of ribosomes that are stalled through a variety of causes, for example when the 3' end of a truncated mRNA lacking a stop codon is reached or at internal clusters of rare codons. Trans-translation requires tmRNA. Trans-translation is not essential for cell viability under laboratory conditions, but recently it has been shown that it can contribute to cell viability in the presence of protein synthesis inhibitors. In this minireview, we consider the connection between trans-translation and antibiotics and the potential of using trans-translation as a therapeutic target.
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Affiliation(s)
- Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Centro de Investigaciones Científicas Isla de la Cartuja, Avda Américo Vespucio s/n, E-41092, Seville, Spain.
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398
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van Dijk E, Cougot N, Meyer S, Babajko S, Wahle E, Séraphin B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J 2002; 21:6915-24. [PMID: 12486012 PMCID: PMC139098 DOI: 10.1093/emboj/cdf678] [Citation(s) in RCA: 365] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2002] [Revised: 10/23/2002] [Accepted: 10/25/2002] [Indexed: 02/04/2023] Open
Abstract
We have cloned cDNAs for the human homologues of the yeast Dcp1 and Dcp2 factors involved in the major (5'-3') and NMD mRNA decay pathways. While yeast Dcp1 has been reported to be the decapping enzyme, we show that recombinant human Dcp2 (hDcp2) is enzymatically active. Dcp2 activity appears evolutionarily conserved. Mutational and biochemical analyses indicate that the hDcp2 MutT/Nudix domain mediates this activity. hDcp2 generates m7GDP and 5'-phosphorylated mRNAs that are 5'-3' exonuclease substrates. Corresponding decay intermediates are present in human cells showing the relevance of this activity. hDcp1 and hDcp2 co-localize in cell cytoplasm, consistent with a role in mRNA decay. Interestingly, these two proteins show a non-uniform distribution, accumulating in specific foci.
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Affiliation(s)
| | | | - Sylke Meyer
- Équipe labelisée La Ligue, Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France and
Institut für Biochemie, Universitaet Halle-Wittenberg, D-06099 Halle, Germany Corresponding author e-mail:
| | | | - Elmar Wahle
- Équipe labelisée La Ligue, Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France and
Institut für Biochemie, Universitaet Halle-Wittenberg, D-06099 Halle, Germany Corresponding author e-mail:
| | - Bertrand Séraphin
- Équipe labelisée La Ligue, Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France and
Institut für Biochemie, Universitaet Halle-Wittenberg, D-06099 Halle, Germany Corresponding author e-mail:
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399
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Lykke-Andersen J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol 2002; 22:8114-21. [PMID: 12417715 PMCID: PMC134073 DOI: 10.1128/mcb.22.23.8114-8121.2002] [Citation(s) in RCA: 296] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2002] [Revised: 08/19/2002] [Accepted: 09/10/2002] [Indexed: 12/31/2022] Open
Abstract
Decapping is a key step in general and regulated mRNA decay. In Saccharomyces cerevisiae it constitutes a rate-limiting step in the nonsense-mediated decay pathway that rids cells of mRNAs containing premature termination codons. Here two human decapping enzymes are identified, hDcp1a and hDcp2, as well as a homolog of hDcp1a, termed hDcp1b. Transiently expressed hDcp1a and hDcp2 proteins localize primarily to the cytoplasm and form a complex in human cell extracts. hDcp1a and hDcp2 copurify with decapping activity, an activity sensitive to mutation of critical hDcp residues. Importantly, coimmunoprecipitation assays demonstrate that hDcp1a and hDcp2 interact with the nonsense-mediated decay factor hUpf1, both in the presence and in the absence of the other hUpf proteins, hUpf2, hUpf3a, and hUpf3b. These data suggest that a human decapping complex may be recruited to mRNAs containing premature termination codons by the hUpf proteins.
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Affiliation(s)
- Jens Lykke-Andersen
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.
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400
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Riley DE, Krieger JN. Diverse eukaryotic transcripts suggest short tandem repeats have cellular functions. Biochem Biophys Res Commun 2002; 298:581-6. [PMID: 12408991 DOI: 10.1016/s0006-291x(02)02509-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Previously thought "junk" DNA, short tandem repeats consisting of (GATA)n, or its compliment, were found in varied metazoan eukaryotic genomes but were rare in yeast and bacterial genomes. The (GATA)n sequence was found in cDNAs encoding mRNAs with known functions. At least 16 of 18 such transcripts encode membrane-associated proteins including: plasma membranes, synapses, mitochondrial membranes, nuclear envelopes, and brush border membranes. Flanking sequences were diverse but (GATA)n sequences clustered around 500 bases from stop codons. The (GATA)n sequences occurred in both orientations and showed constrained polymorphism. In sets of splice variants with and without (GAUA)n, the STR containing transcripts were the most abundant. These observations suggest that (GATA)n sequences probably function. In many cases, the function may be to encode post-transcriptional signals for mRNAs encoding membrane-associated proteins.
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Affiliation(s)
- Donald E Riley
- Department of Urology, University of Washington, Seattle, WA 98195, USA.
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