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Abstract
The revolution in high throughput biology experiments producing genome-scale data has heightened the challenge of integrating functional genomics data. Data integration is essential for making reliable inferences from functional genomics data, as the datasets are neither error-free nor comprehensive. However, there are two major hurdles in data integration: heterogeneity and correlation of the data to be integrated. These problems can be circumvented by quantitative testing of all data in the same unified scoring scheme, and by using integration methods appropriate for handling correlated data. This chapter describes such a functional genomics data integration method designed to estimate the "functional coupling" between genes, applied to the baker's yeast Saccharomyces cerevisiae. The integrated dataset outperforms individual functional genomics datasets in both accuracy and coverage, leading to more reliable and comprehensive predictions of gene function. The approach is easily applied to multicellular organisms, including human.
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102
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Schwer B. A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release. Mol Cell 2008; 30:743-54. [PMID: 18570877 DOI: 10.1016/j.molcel.2008.05.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 04/16/2008] [Accepted: 05/02/2008] [Indexed: 12/16/2022]
Abstract
An essential step in pre-mRNA splicing is the release of the mRNA product from the spliceosome. The DEAH box RNA helicase Prp22 catalyzes mRNA release by remodeling contacts within the spliceosome that involve the U5 snRNP. Spliceosome disassembly requires a segment of more than 13 ribonucleotides downstream of the 3' splice site. I show here by site-specific crosslinking and RNase H protection that Prp22 interacts with the mRNA downstream of the exon-exon junction prior to mRNA release. The findings support a model for Prp22-catalyzed mRNA release from the spliceosome wherein a rearrangement that accompanies the second transesterification step deposits Prp22 on the mRNA downstream of the exon-exon junction. Bound to its target RNA, the 3'-->5' helicase acts to disrupt mRNA/U5 snRNP contacts, thereby liberating the mRNA from the spliceosome.
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Affiliation(s)
- Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
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103
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Stanek D, Pridalová-Hnilicová J, Novotný I, Huranová M, Blazíková M, Wen X, Sapra AK, Neugebauer KM. Spliceosomal small nuclear ribonucleoprotein particles repeatedly cycle through Cajal bodies. Mol Biol Cell 2008; 19:2534-43. [PMID: 18367544 DOI: 10.1091/mbc.e07-12-1259] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Cajal body (CB) is a nuclear structure closely associated with import and biogenesis of small nuclear ribonucleoprotein particles (snRNPs). Here, we tested whether CBs also contain mature snRNPs and whether CB integrity depends on the ongoing snRNP splicing cycle. Sm proteins tagged with photoactivatable and color-maturing variants of fluorescent proteins were used to monitor snRNP behavior in living cells over time; mature snRNPs accumulated in CBs, traveled from one CB to another, and they were not preferentially replaced by newly imported snRNPs. To test whether CB integrity depends on the snRNP splicing cycle, two human orthologues of yeast proteins involved in distinct steps in spliceosome disassembly after splicing, hPrp22 and hNtr1, were depleted by small interfering RNA treatment. Surprisingly, depletion of either protein led to the accumulation of U4/U6 snRNPs in CBs, suggesting that reassembly of the U4/U6.U5 tri-snRNP was delayed. Accordingly, a relative decrease in U5 snRNPs compared with U4/U6 snRNPs was observed in CBs, as well as in nuclear extracts of treated cells. Together, the data show that particular phases of the spliceosome cycle are compartmentalized in living cells, with reassembly of the tri-snRNP occurring in CBs.
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Affiliation(s)
- David Stanek
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic.
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104
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Friend K, Lovejoy AF, Steitz JA. U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation. Mol Cell 2008; 28:240-52. [PMID: 17964263 PMCID: PMC2149891 DOI: 10.1016/j.molcel.2007.09.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 08/08/2007] [Accepted: 09/14/2007] [Indexed: 11/17/2022]
Abstract
In metazoa, pre-mRNA 3' end formation occurs via two pathways: cleavage/polyadenylation for the majority of RNA polymerase II transcripts and U7-snRNP-dependent cleavage for replication-dependent histone pre-mRNAs. An RNA element derived from a replication-dependent histone gene affects multiple steps of pre-mRNA processing. Here, we demonstrate that a portion of this RNA element, present in the majority of histone mRNAs, stimulates U7-snRNP-dependent cleavage. Surprisingly, this element binds U2 snRNP, although it is derived from an intronless mRNA. Specifically, SF3b, a U2 and U12-snRNP component, contacts the RNA element both in vitro and in vivo in conjunction with hPrp43, a DEAH-box helicase. Tethering either U2 or U12 snRNP to histone pre-mRNA substrates stimulates U7-snRNP-dependent cleavage in vitro and in vivo. Finally, we show that U2 snRNP associates with histone pre-mRNAs in vivo. We conclude that U2 snRNP plays a nonsplicing role in histone mRNA maturation.
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Affiliation(s)
- Kyle Friend
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
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105
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Elles LMS, Uhlenbeck OC. Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype. Nucleic Acids Res 2007; 36:41-50. [PMID: 17986459 PMCID: PMC2248767 DOI: 10.1093/nar/gkm926] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Escherichia coli DEAD-box protein A (DbpA) is an ATP-dependent RNA helicase with specificity for 23S ribosomal RNA. Although DbpA has been extensively characterized biochemically, its biological function remains unknown. Previous work has shown that a DbpA deletion strain is viable with little or no effect on growth rate. In attempt to elucidate a phenotype for DbpA, point mutations were made at eleven conserved residues in the ATPase active site, which have exhibited dominant-negative phenotypes in other DExD/H proteins. Biochemical analysis of these DbpA mutants shows the expected decrease in RNA-dependent ATPase activity and helix unwinding activity. Only the least biochemically active mutation, R331A, produces small colony phenotype and a reduced growth rate. This dominant slow growth mutant will be valuable to determine the cellular function of DbpA.
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Affiliation(s)
- Lisa M Sharpe Elles
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA
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106
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Goldfeder MB, Oliveira CC. Cwc24p, a novel Saccharomyces cerevisiae nuclear ring finger protein, affects pre-snoRNA U3 splicing. J Biol Chem 2007; 283:2644-53. [PMID: 17974558 DOI: 10.1074/jbc.m707885200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
U3 snoRNA is transcribed from two intron-containing genes in yeast, snR17A and snR17B. Although the assembly of the U3 snoRNP has not been precisely determined, at least some of the core box C/D proteins are known to bind pre-U3 co-transcriptionally, thereby affecting splicing and 3'-end processing of this snoRNA. We identified the interaction between the box C/D assembly factor Nop17p and Cwc24p, a novel yeast RING finger protein that had been previously isolated in a complex with the splicing factor Cef1p. Here we show that, consistent with the protein interaction data, Cwc24p localizes to the cell nucleus, and its depletion leads to the accumulation of both U3 pre-snoRNAs. U3 snoRNA is involved in the early cleavages of 35 S pre-rRNA, and the defective splicing of pre-U3 detected in cells depleted of Cwc24p causes the accumulation of the 35 S precursor rRNA. These results led us to the conclusion that Cwc24p is involved in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing.
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Affiliation(s)
- Mauricio B Goldfeder
- Department of Biochemistry, Chemistry Institute, University of São Paulo, 748 Av. Prof. Lineu Prestes, São Paulo, SP, Brazil
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107
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Tanaka N, Aronova A, Schwer B. Ntr1 activates the Prp43 helicase to trigger release of lariat-intron from the spliceosome. Genes Dev 2007; 21:2312-25. [PMID: 17875666 PMCID: PMC1973145 DOI: 10.1101/gad.1580507] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DEAD/H-box NTPases remodel the spliceosome at multiple steps during the pre-mRNA splicing cycle. The RNA-dependent NTPase Prp43 catalyzes dissociation of excised lariat-intron from the spliceosome, but it is unclear how Prp43 couples the energy of ATP hydrolysis to intron release. Here, we report that activation of Prp43's inherently feeble helicase activity by the splicing factor Ntr1 is required for lariat-intron release. Lethal Prp43 mutants T384A and T384V, which are active for ATP hydrolysis and fail to dissociate lariat-intron from spliceosomes, are refractory to stimulation of RNA unwinding by Ntr1. An N-terminal 120-amino-acid segment of Ntr1 suffices for binding to Prp43 and for stimulating its helicase activity. We identify missense mutations in Prp43 and Ntr1 that disrupt protein-protein interaction and impair Ntr1 enhancement of Prp43 RNA unwinding. Our results demonstrate for the first time that regulating the motor activity of a DEAH-box protein by an accessory factor is critical for mRNA splicing.
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Affiliation(s)
- Naoko Tanaka
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, USA
| | - Anna Aronova
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, USA
- Corresponding author.E-MAIL ; FAX (212) 746-8587
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108
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Tsai RT, Tseng CK, Lee PJ, Chen HC, Fu RH, Chang KJ, Yeh FL, Cheng SC. Dynamic interactions of Ntr1-Ntr2 with Prp43 and with U5 govern the recruitment of Prp43 to mediate spliceosome disassembly. Mol Cell Biol 2007; 27:8027-37. [PMID: 17893323 PMCID: PMC2169193 DOI: 10.1128/mcb.01213-07] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Saccharomyces cerevisiae splicing factors Ntr1 (also known as Spp382) and Ntr2 form a stable complex and can further associate with DExD/H-box RNA helicase Prp43 to form a functional complex, termed the NTR complex, which catalyzes spliceosome disassembly. We show that Prp43 interacts with Ntr1-Ntr2 in a dynamic manner. The Ntr1-Ntr2 complex can also bind to the spliceosome first, before recruiting Prp43 to catalyze disassembly. Binding of Ntr1-Ntr2 or Prp43 does not require ATP, but disassembly of the spliceosome requires hydrolysis of ATP. The NTR complex also dynamically interacts with U5 snRNP. Ntr2 interacts with U5 component Brr2 and is essential for both interactions of NTR with U5 and with the spliceosome. Ntr2 alone can also bind to U5 and to the spliceosome, suggesting a role of Ntr2 in mediating the binding of NTR to the spliceosome through its interaction with U5. Our results demonstrate that dynamic interactions of NTR with U5, through the interaction of Ntr2 with Brr2, and interactions of Ntr1 and Prp43 govern the recruitment of Prp43 to the spliceosome to mediate spliceosome disassembly.
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Affiliation(s)
- Rong-Tzong Tsai
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan, Republic of China
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109
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Chen YIG, Moore RE, Ge HY, Young MK, Lee TD, Stevens SW. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Nucleic Acids Res 2007; 35:3928-44. [PMID: 17537823 PMCID: PMC1919476 DOI: 10.1093/nar/gkm347] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Previous compositional studies of pre-mRNA processing complexes have been performed in vitro on synthetic pre-mRNAs containing a single intron. To provide a more comprehensive list of polypeptides associated with the pre-mRNA splicing apparatus, we have determined the composition of the bulk pre-mRNA processing machinery in living cells. We purified endogenous nuclear pre-mRNA processing complexes from human and chicken cells comprising the massive (>200S) supraspliceosomes (a.k.a. polyspliceosomes). As expected, RNA components include a heterogeneous mixture of pre-mRNAs and the five spliceosomal snRNAs. In addition to known pre-mRNA splicing factors, 5′ end binding factors, 3′ end processing factors, mRNA export factors, hnRNPs and other RNA binding proteins, the protein components identified by mass spectrometry include RNA adenosine deaminases and several novel factors. Intriguingly, our purified supraspliceosomes also contain a number of structural proteins, nucleoporins, chromatin remodeling factors and several novel proteins that were absent from splicing complexes assembled in vitro. These in vivo analyses bring the total number of factors associated with pre-mRNA to well over 300, and represent the most comprehensive analysis of the pre-mRNA processing machinery to date.
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Affiliation(s)
- Yen-I G. Chen
- Graduate program in Microbiology, City of Hope Beckman Research Institute, Duarte, CA 91010, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University, Station #A4800, Austin, TX 78712 and Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
| | - Roger E. Moore
- Graduate program in Microbiology, City of Hope Beckman Research Institute, Duarte, CA 91010, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University, Station #A4800, Austin, TX 78712 and Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
| | - Helen Y. Ge
- Graduate program in Microbiology, City of Hope Beckman Research Institute, Duarte, CA 91010, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University, Station #A4800, Austin, TX 78712 and Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
| | - Mary K. Young
- Graduate program in Microbiology, City of Hope Beckman Research Institute, Duarte, CA 91010, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University, Station #A4800, Austin, TX 78712 and Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
| | - Terry D. Lee
- Graduate program in Microbiology, City of Hope Beckman Research Institute, Duarte, CA 91010, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University, Station #A4800, Austin, TX 78712 and Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
| | - Scott W. Stevens
- Graduate program in Microbiology, City of Hope Beckman Research Institute, Duarte, CA 91010, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University, Station #A4800, Austin, TX 78712 and Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
- *To whom correspondence should be addressed. +1-512-232-9303+1-512-232-3432
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110
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Lee I, Narayanaswamy R, Marcotte EM. 24 Bioinformatic Prediction of Yeast Gene Function. J Microbiol Methods 2007. [DOI: 10.1016/s0580-9517(06)36024-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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111
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Matlin AJ, Moore MJ. Spliceosome assembly and composition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:14-35. [PMID: 18380338 DOI: 10.1007/978-0-387-77374-2_2] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cells control alternative splicing by modulating assembly of the pre-mRNA splicing machinery at competing splice sites. Therefore, a working knowledge of spliceosome assembly is essential for understanding how alternative splice site choices are achieved. In this chapter, we review spliceosome assembly with particular emphasis on the known steps and factors subject to regulation during alternative splice site selection in mammalian cells. We also review recent advances regarding similarities and differences between the in vivo and in vitro assembly pathways, as well as proofreading mechanisms contributing to the fidelity of splice site selection.
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Affiliation(s)
- Arianne J Matlin
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
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112
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Small EC, Leggett SR, Winans AA, Staley JP. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol Cell 2006; 23:389-99. [PMID: 16885028 PMCID: PMC3777414 DOI: 10.1016/j.molcel.2006.05.043] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 05/30/2006] [Accepted: 05/31/2006] [Indexed: 11/26/2022]
Abstract
Binding of a pre-mRNA substrate triggers spliceosome activation, whereas the release of the mRNA product triggers spliceosome disassembly. The mechanisms that underlie the regulation of these rearrangements remain unclear. We find evidence that the GTPase Snu114p mediates the regulation of spliceosome activation and disassembly. Specifically, both unwinding of U4/U6, required for spliceosome activation, and disassembly of the postsplicing U2/U6.U5.intron complex are repressed by Snu114p bound to GDP and derepressed by Snu114p bound to GTP or nonhydrolyzable GTP analogs. Further, similar to U4/U6 unwinding, spliceosome disassembly requires the DExD/H box ATPase Brr2p. Together, our data define a common mechanism for regulating and executing spliceosome activation and disassembly. Although sequence similarity with EF-G suggests Snu114p functions as a molecular motor, our findings indicate that Snu114p functions as a classic regulatory G protein. We propose that Snu114p serves as a signal-dependent switch that transduces signals to Brr2p to control spliceosome dynamics.
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Affiliation(s)
- Eliza C. Small
- Department of Biochemistry and Molecular Biology, The University of Chicago Chicago, IL 60637
| | - Stephanie R. Leggett
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago, IL 60637
| | - Adrienne A. Winans
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago, IL 60637
| | - Jonathan P. Staley
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago, IL 60637
- Correspondence: 773-834-5886 (phone); 773-834-9064 (fax)
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113
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Boon KL, Auchynnikava T, Edwalds-Gilbert G, Barrass JD, Droop AP, Dez C, Beggs JD. Yeast ntr1/spp382 mediates prp43 function in postspliceosomes. Mol Cell Biol 2006; 26:6016-23. [PMID: 16880513 PMCID: PMC1592814 DOI: 10.1128/mcb.02347-05] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Ntr1 and Ntr2 proteins of Saccharomyces cerevisiae have been reported to interact with proteins involved in pre-mRNA splicing, but their roles in the splicing process are unknown. We show here that they associate with a postsplicing complex containing the excised intron and the spliceosomal U2, U5, and U6 snRNAs, supporting a link with a late stage in the pre-mRNA splicing process. Extract from cells that had been metabolically depleted of Ntr1 has low splicing activity and accumulates the excised intron. Also, the level of U4/U6 di-snRNP is increased but those of the free U5 and U6 snRNPs are decreased in Ntr1-depleted extract, and increased levels of U2 and decreased levels of U4 are found associated with the U5 snRNP protein Prp8. These results suggest a requirement for Ntr1 for turnover of the excised intron complex and recycling of snRNPs. Ntr1 interacts directly or indirectly with the intron release factor Prp43 and is required for its association with the excised intron. We propose that Ntr1 promotes release of excised introns from splicing complexes by acting as a spliceosome receptor or RNA-targeting factor for Prp43, possibly assisted by the Ntr2 protein.
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Affiliation(s)
- Kum-Loong Boon
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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114
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Pandit S, Lynn B, Rymond BC. Inhibition of a spliceosome turnover pathway suppresses splicing defects. Proc Natl Acad Sci U S A 2006; 103:13700-5. [PMID: 16945917 PMCID: PMC1564266 DOI: 10.1073/pnas.0603188103] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Defects in assembly are suggested to signal the dissociation of faulty splicing complexes. A yeast genetic screen was performed to identify components of the putative discard pathway. Weak mutant alleles of SPP382 (also called NTR1) were found to suppress defects in two proteins required for spliceosome activation, Prp38p and Prp8p. Spp382p is shown necessary for cellular splicing, with premRNA and, for some alleles, excised intron, accumulating after inactivation. Like spp382-1, a mutant allele of AAR2 was identified in this suppressor screen. Like Spp382p, Aar2p has a reported role in spliceosome recycling and is found with Spp382p in a complex recovered with a mutant version of the spliceosomal core protein Prp8p. Possible insight into to the spp382 suppressor phenotype is provided by the observation that defective splicing complexes lacking the 5' exon cleavage intermediate are recovered by a tandem affinity purification-tagged Spp382 derivative. Stringent proteomic and two-hybrid analyses show that Spp382p also interacts with Cwc23p, a DNA J-like protein present in the spliceosome and copurified with the Prp43p DExD/H-box ATPase. Spp382p binds Prp43p and Prp43p requires Spp382p for intron release from the spliceosome. Consistent with a related function in the removal of defective complexes, three prp43 mutants are also shown to suppress splicing defects, with efficiencies inversely proportionate to the measured ATPase activities. These and related genetic data support the existence of a Spp382p-dependent turnover pathway acting on defective spliceosomes.
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Affiliation(s)
| | - Bert Lynn
- Chemistry, University of Kentucky, Lexington, KY 40506-0225
| | - Brian C. Rymond
- Departments of *Biology and
- To whom correspondence should be addressed. E-mail:
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115
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Linder P. Dead-box proteins: a family affair--active and passive players in RNP-remodeling. Nucleic Acids Res 2006; 34:4168-80. [PMID: 16936318 PMCID: PMC1616962 DOI: 10.1093/nar/gkl468] [Citation(s) in RCA: 341] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 11/23/2022] Open
Abstract
DEAD-box proteins are characterized by nine conserved motifs. According to these criteria, several hundreds of these proteins can be identified in databases. Many different DEAD-box proteins can be found in eukaryotes, whereas prokaryotes have small numbers of different DEAD-box proteins. DEAD-box proteins play important roles in RNA metabolism, and they are very specific and cannot mutually be replaced. In vitro, many DEAD-box proteins have been shown to have RNA-dependent ATPase and ATP-dependent RNA helicase activities. From the genetic and biochemical data obtained mainly in yeast, it has become clear that these proteins play important roles in remodeling RNP complexes in a temporally controlled fashion. Here, I shall give a general overview of the DEAD-box protein family.
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Affiliation(s)
- Patrick Linder
- Department of Microbiology and Molecular Medicine, CMU 1, rue Michel Servet, CH-1211 Genève 4, Switzerland.
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116
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Abstract
Synthesis of rRNA in eukaryotes involves the action of a large population of snoRNA-protein complexes (snoRNPs), which create modified nucleotides and participate in cleavage of pre-rRNA. The snoRNPs mediate these functions through direct base pairing, in many cases through long complementary sequences. This feature suggests that RNA helicases may be involved in the binding and release of snoRNPs from pre-rRNA. In this study, we determined that the DEAD box helicase Has1p, a nucleolar protein required for the production of 18S rRNA, copurifies with the snR30/U17 processing snoRNP but is also present with other snoRNPs. Blocking Has1p expression causes a substantial increase in snoRNPs associated with 60S-90S preribosomal RNP complexes, including the U3 and U14 processing snoRNPs and several modifying snoRNPs examined. Cosedimentation persisted even after deproteinization. This effect was not observed with depletion of two nonhelicase proteins, Esf1p and Dim2p, that are also required for 18S rRNA production. Point mutations in ATPase and helicase motifs of Has1p block U14 release from pre-rRNA. Surprisingly, depletion of Has1p causes a reduction in the level of free U6 snRNP. The results indicate that the Has1p helicase is required for snoRNA release from pre-rRNA and production of the U6 snRNP.
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Affiliation(s)
- Xue-Hai Liang
- Department of Biochemistry and Molecular Biology, Lederle Graduate Research Center, University of Massachusetts, Amherst, MA 01003, USA
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117
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Tanaka N, Schwer B. Mutations in PRP43 that uncouple RNA-dependent NTPase activity and pre-mRNA splicing function. Biochemistry 2006; 45:6510-21. [PMID: 16700561 PMCID: PMC2517181 DOI: 10.1021/bi052656g] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Saccharomyces cerevisiae Prp43 is a DEAH-box RNA-dependent ATPase that catalyzes the release of excised lariat intron from the mRNA spliceosome. Previous studies identified mutations in Prp43 motifs I, II, and VI that were lethal in vivo and ablated ATP hydrolysis in vitro. Such Prp43 mutants exerted dominant-negative growth phenotypes when expressed in wild type cells and blocked intron release in vitro when added to yeast splicing extracts. Here, we assessed the effects of alanine and conservative substitutions at conserved residues in motifs Ia ((146)TQPRRVAA(153)), IV ((307)LLFLTG(312)), and V ((376)TNIAETSLT(384)) and thereby identified Arg150 (motif Ia), Phe309 (motif IV), Thr376, Leu383, and Thr384 (motif V) as being important for Prp43 function in vivo. Motif V mutations T376V, T384A, and T384V were lethal and dominant negative in vivo, and the mutant proteins inhibited lariat release in vitro. The T384A and T384V proteins were proficient for ATP hydrolysis, suggesting that ATPase activity is necessary, but not sufficient, for Prp43 function. We report that Prp43 hydrolyzes all common NTPs and dNTPs and unwinds short 5'/3' tailed RNA/DNA duplexes in an ATP-dependent fashion. Optimal ATP hydrolysis requires an RNA cofactor of >or=20 nt. Prp43 is largely indifferent to mutations in its C-terminal segment, which is conserved in the DEAH-box splicing factors Prp2, Prp16, and Prp22.
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Affiliation(s)
| | - Beate Schwer
- corresponding author, Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, Tel: (212) 746-6518, Fax: (212) 746-8587,
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118
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Mayas RM, Maita H, Staley JP. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat Struct Mol Biol 2006; 13:482-90. [PMID: 16680161 PMCID: PMC3729281 DOI: 10.1038/nsmb1093] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 04/11/2006] [Indexed: 11/08/2022]
Abstract
To produce messenger RNA, the spliceosome excises introns from precursor (pre)-mRNA and splices the flanking exons. To establish fidelity, the spliceosome discriminates against aberrant introns, but current understanding of such fidelity mechanisms is limited. Here we show that an ATP-dependent activity represses formation of mRNA from aberrant intermediates having mutations in any of the intronic consensus sequences. This proofreading activity is disabled by mutations that impair the ATPase or RNA unwindase activity of Prp22p, a conserved spliceosomal DExD/H-box ATPase. Further, cold-sensitive prp22 mutants permit aberrant mRNA formation from a mutated 3' splice-site intermediate in vivo. We conclude that Prp22p generally represses splicing of aberrant intermediates, in addition to its known ATP-dependent role in promoting release of genuine mRNA. This dual function for Prp22p validates a general model in which fidelity can be enhanced by a DExD/H-box ATPase.
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Affiliation(s)
- Rabiah M Mayas
- Department of Biochemistry and Molecular Biology, The University of Chicago, Cummings Life Science Center 817, 920 E. 58th Street, Chicago, Illinois 60637, USA
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119
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Granneman S, Bernstein KA, Bleichert F, Baserga SJ. Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis. Mol Cell Biol 2006; 26:1183-94. [PMID: 16449634 PMCID: PMC1367182 DOI: 10.1128/mcb.26.4.1183-1194.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 17 putative RNA helicases required for pre-rRNA processing are predicted to play a crucial role in ribosome biogenesis by driving structural rearrangements within preribosomes. To better understand the function of these proteins, we have generated a battery of mutations in five putative RNA helicases involved in 18S rRNA synthesis and analyzed their effects on cell growth and pre-rRNA processing. Our results define functionally important residues within conserved motifs and demonstrate that lethal mutations in predicted ATP binding-hydrolysis motifs often confer a dominant negative phenotype in vivo when overexpressed in a wild-type background. We show that dominant negative mutants delay processing of the 35S pre-rRNA and cause accumulation of pre-rRNA species that normally have low steady-state levels. Our combined results establish that not all conserved domains function identically in each protein, suggesting that the RNA helicases may have distinct biochemical properties and diverse roles in ribosome biogenesis.
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Affiliation(s)
- Sander Granneman
- Molecular Biophysics & Biochemistry Department, Yale University School of Medicine, 333 Cedar St., SHM C-114, New Haven, CT 06520-8024, USA
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120
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Bernstein KA, Granneman S, Lee AV, Manickam S, Baserga SJ. Comprehensive mutational analysis of yeast DEXD/H box RNA helicases involved in large ribosomal subunit biogenesis. Mol Cell Biol 2006; 26:1195-208. [PMID: 16449635 PMCID: PMC1367183 DOI: 10.1128/mcb.26.4.1195-1208.2006] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DEXD/H box putative RNA helicases are required for pre-rRNA processing in Saccharomyces cerevisiae, although their exact roles and substrates are unknown. To characterize the significance of the conserved motifs for helicase function, a series of five mutations were created in each of the eight essential RNA helicases (Has1, Dbp6, Dbp10, Mak5, Mtr4, Drs1, Spb4, and Dbp9) involved in 60S ribosomal subunit biogenesis. Each mutant helicase was screened for the ability to confer dominant negative growth defects and for functional complementation. Different mutations showed different degrees of growth inhibition among the helicases, suggesting that the conserved regions do not function identically in vivo. Mutations in motif I and motif II (the DEXD/H box) often conferred dominant negative growth defects, indicating that these mutations do not interfere with substrate binding. In addition, mutations in the putative unwinding domains (motif III) demonstrated that conserved amino acids are often not essential for function. Northern analysis of steady-state RNA from strains expressing mutant helicases showed that the dominant negative mutations also altered pre-rRNA processing. Coimmunoprecipitation experiments indicated that some RNA helicases associated with each other. In addition, we found that yeasts disrupted in expression of the two nonessential RNA helicases, Dbp3 and Dbp7, grew worse than when either one alone was disrupted.
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Affiliation(s)
- Kara A Bernstein
- Molecular Biophysics & Biochemistry Department, Yale University School of Medicine, 333 Cedar St., SHM C-114, New Haven, CT 06520-8024, USA
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121
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Leeds NB, Small EC, Hiley SL, Hughes TR, Staley JP. The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis. Mol Cell Biol 2006; 26:513-22. [PMID: 16382143 PMCID: PMC1346897 DOI: 10.1128/mcb.26.2.513-522.2006] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biogenesis of the small and large ribosomal subunits requires modification, processing, and folding of pre-rRNA to yield mature rRNA. Here, we report that efficient biogenesis of both small- and large-subunit rRNAs requires the DEAH box ATPase Prp43p, a pre-mRNA splicing factor. By steady-state analysis, a cold-sensitive prp43 mutant accumulates 35S pre-rRNA and depletes 20S, 27S, and 7S pre-rRNAs, precursors to the small- and large-subunit rRNAs. By pulse-chase analysis, the prp43 mutant is defective in the formation of 20S and 27S pre-rRNAs and in the accumulation of 18S and 25S mature rRNAs. Wild-type Prp43p immunoprecipitates pre-rRNAs and mature rRNAs, indicating a direct role in ribosome biogenesis. The Prp43p-Q423N mutant immunoprecipitates 27SA2 pre-rRNA threefold more efficiently than the wild type, suggesting a critical role for Prp43p at the earliest stages of large-subunit biogenesis. Consistent with an early role for Prp43p in ribosome biogenesis, Prp43p immunoprecipitates the majority of snoRNAs; further, compared to the wild type, the prp43 mutant generally immunoprecipitates the snoRNAs more efficiently. In the prp43 mutant, the snoRNA snR64 fails to methylate residue C2337 in 27S pre-rRNA, suggesting a role in snoRNA function. We propose that Prp43p promotes recycling of snoRNAs and biogenesis factors during pre-rRNA processing, similar to its recycling role in pre-mRNA splicing. The dual function for Prp43p in the cell raises the possibility that ribosome biogenesis and pre-mRNA splicing may be coordinately regulated.
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Affiliation(s)
- Nina B Leeds
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E. 58th St., Chicago, Illinois 60637, USA
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122
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Tsai RT, Fu RH, Yeh FL, Tseng CK, Lin YC, Huang YH, Cheng SC. Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev 2006; 19:2991-3003. [PMID: 16357217 PMCID: PMC1315403 DOI: 10.1101/gad.1377405] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Two novel yeast splicing factors required for spliceosome disassembly have been identified. Ntr1 and Ntr2 (NineTeen complex-Related proteins) were identified for their weak association with components of the Prp19-associated complex. Unlike other Prp19-associated components, these two proteins were primarily associated with the intron-containing spliceosome during the splicing reaction. Extracts depleted of Ntr1 or Ntr2 exhibited full splicing activity, but accumulated large amounts of lariat-intron in the spliceosome after splicing, indicating that the normal function of the Prp19-associated complex in spliceosome activation was not affected, but spliceosome disassembly was hindered. Immunoprecipitation analysis revealed that Ntr1 and Ntr2 formed a stable complex with DExD/H-box RNA helicase Prp43 in the splicing extract. Ntr1 interacted with Prp43 through the N-terminal G-patch domain, with Ntr2 through a middle region, and with itself through the carboxyl half of the protein. The affinity-purified Ntr1-Ntr2-Prp43 complex could catalyze disassembly of the spliceosome in an ATP-dependent manner, separating U2, U5, U6, NTC (NineTeen Complex), and lariat-intron. This is the first demonstration of physical disassembly of the spliceosome, catalyzed by a complex containing a DExD/H-box RNA helicase and two accessory factors, which might function in targeting the helicase to the correct substrate.
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Affiliation(s)
- Rong-Tzong Tsai
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan, Republic of China
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123
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Combs DJ, Nagel RJ, Ares M, Stevens SW. Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Mol Cell Biol 2006; 26:523-34. [PMID: 16382144 PMCID: PMC1346896 DOI: 10.1128/mcb.26.2.523-534.2006] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/13/2005] [Accepted: 10/17/2005] [Indexed: 11/20/2022] Open
Abstract
The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis.
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Affiliation(s)
- D Joshua Combs
- Program in Cellular and Molecular Biology, University of Texas at Austin, 1 University Station #A4800, 2500 Speedway 2.448, Austin, Texas 78712, USA
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124
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Lebaron S, Froment C, Fromont-Racine M, Rain JC, Monsarrat B, Caizergues-Ferrer M, Henry Y. The splicing ATPase prp43p is a component of multiple preribosomal particles. Mol Cell Biol 2005; 25:9269-82. [PMID: 16227579 PMCID: PMC1265834 DOI: 10.1128/mcb.25.21.9269-9282.2005] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prp43p is a putative helicase of the DEAH family which is required for the release of the lariat intron from the spliceosome. Prp43p could also play a role in ribosome synthesis, since it accumulates in the nucleolus. Consistent with this hypothesis, we find that depletion of Prp43p leads to accumulation of 35S pre-rRNA and strongly reduces levels of all downstream pre-rRNA processing intermediates. As a result, the steady-state levels of mature rRNAs are greatly diminished following Prp43p depletion. We present data arguing that such effects are unlikely to be solely due to splicing defects. Moreover, we demonstrate by a combination of a comprehensive two-hybrid screen, tandem-affinity purification followed by mass spectrometry, and Northern analyses that Prp43p is associated with 90S, pre-60S, and pre-40S ribosomal particles. Prp43p seems preferentially associated with Pfa1p, a novel specific component of pre-40S ribosomal particles. In addition, Prp43p interacts with components of the RNA polymerase I (Pol I) transcription machinery and with mature 18S and 25S rRNAs. Hence, Prp43p might be delivered to nascent 90S ribosomal particles during pre-rRNA transcription and remain associated with preribosomal particles until their final maturation steps in the cytoplasm. Our data also suggest that the ATPase activity of Prp43p is required for early steps of pre-rRNA processing and normal accumulation of mature rRNAs.
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Affiliation(s)
- Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099 CNRS-Université Paul Sabatier, IFR109, 118 route de Narbonne, 31062 Toulouse cedex 09, France
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125
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Khalid MF, Damha MJ, Shuman S, Schwer B. Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase. Nucleic Acids Res 2005; 33:6349-60. [PMID: 16275784 PMCID: PMC1278944 DOI: 10.1093/nar/gki934] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 10/12/2005] [Accepted: 10/12/2005] [Indexed: 11/17/2022] Open
Abstract
Saccharomyces cerevisiae Dbr1 is a 405-amino acid RNA debranching enzyme that cleaves the 2'-5' phosphodiester bonds of the lariat introns formed during pre-mRNA splicing. Debranching appears to be a rate-limiting step for the turnover of intronic RNA, insofar as the steady-state levels of lariat introns are greatly increased in a Deltadbr1 strain. To gain insight to the requirements for yeast Dbr1 function, we performed a mutational analysis of 28 amino acids that are conserved in Dbr1 homologs from other organisms. We identified 13 residues (His13, Asp40, Arg45, Asp49, Tyr68, Tyr69, Asn85, His86, Glu87, His179, Asp180, His231 and His233) at which alanine substitutions resulted in lariat intron accumulation in vivo. Conservative replacements at these positions were introduced to illuminate structure-activity relationships. Residues important for Dbr1 function include putative counterparts of the amino acids that comprise the active site of the metallophosphoesterase superfamily, exemplified by the DNA phosphodiesterase Mre11. Using natural lariat RNAs and synthetic branched RNAs as substrates, we found that mutation of Asp40, Asn85, His86, His179, His231 or His233 to alanine abolishes or greatly diminishes debranching activity in vitro. Dbr1 sediments as a monomer and requires manganese as the metal cofactor for debranching.
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Affiliation(s)
- M. Fahad Khalid
- Department of Microbiology and Immunology, Weill Medical College of Cornell UniversityNew York, NY 10021 USA
- Department of Chemistry, McGill UniversityMontreal, Quebec, Canada
- Molecular Biology Program, Sloan-Kettering InstituteNew York, NY 10021 USA
| | - Masad J. Damha
- Department of Chemistry, McGill UniversityMontreal, Quebec, Canada
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering InstituteNew York, NY 10021 USA
| | - Beate Schwer
- To whom correspondence should be addressed. Tel: +1 212 746 6518; Fax: +1 212 746 8587;
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126
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Alli Z, Nam EH, Beimnet K, Abdelhaleem M. The activation-induced expression of DHX32 in Jurkat T cells is specific and involves calcium and nuclear factor of activated T cells. Cell Immunol 2005; 237:141-6. [PMID: 16414036 DOI: 10.1016/j.cellimm.2005.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 12/12/2005] [Accepted: 12/13/2005] [Indexed: 11/20/2022]
Abstract
In this report, we studied DHX32 expression in human Jurkat T cells. Co-stimulation of CD3 and CD28 resulted in upregulation of DHX32. No significant changes in the expression of the closely related RNA helicases were seen. Ionomycin treatment alone was sufficient to upregulate the expression of DHX32 mRNA isoform transcribed from the proximal promoter. We cloned DHX32 proximal promoter and identified a 218bp fragment containing two potential binding sites for the transcription factor nuclear factor of activated T cells (NF-AT). Mutation of core sequence of NF-AT resulted in reduced transcriptional activity, with more reduction observed in the second NF-AT site. Electrophoretic mobility shift assay results were consistent with a specific binding of NF-AT from ionomycin stimulated nuclear extract of Jurkat cells to oligonucleotide probes from DHX32 proximal promoter. These results suggest that the DHX32 expression is modulated in Jurkat T cells via a pathway that involves NF-AT.
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Affiliation(s)
- Zaman Alli
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
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127
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Liang XH, Liu Q, Liu L, Tschudi C, Michaeli S. Analysis of spliceosomal complexes in Trypanosoma brucei and silencing of two splicing factors Prp31 and Prp43. Mol Biochem Parasitol 2005; 145:29-39. [PMID: 16219373 DOI: 10.1016/j.molbiopara.2005.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 09/06/2005] [Indexed: 11/21/2022]
Abstract
In trypanosomatids all mRNAs undergo trans-splicing, whereas cis-splicing is restricted to a few transcripts. Trans-splicing is mechanistically similar to cis-splicing, however, little is known about the trans-splicing machinery and its underlying mechanism. In this study, we examined the involvement of splicing factors in cis- and trans-splicing by RNA interference (RNAi). Two factors (Prp31 and Prp43) were found to be essential for both pathways, suggesting that splicing factors are shared by these two reactions. We identified a 45S complex carrying pre-mRNA and all the U-snRNAs, including U1 and the SL RNA, suggesting that a single spliceosomal complex may potentially conduct both trans- and cis-splicing.
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Affiliation(s)
- Xue-hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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128
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Villa T, Guthrie C. The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev 2005; 19:1894-904. [PMID: 16103217 PMCID: PMC1186189 DOI: 10.1101/gad.1336305] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Prp16p is a DEAH-box ATPase that transiently associates with the spliceosome to promote the structural transition required for the second chemical step. Yeast strains carrying the cold-sensitive allele prp16-302 stall the release of Prp16p at low temperatures, yet splice precursors with aberrant branchpoints at increased frequency. To identify new factors involved in the regulation of splicing fidelity, we sought suppressors of the prp16-302 growth phenotype. Deletion of the nonessential ISY1 gene (1) improves growth of prp16-302 strains, (2) alleviates stalling, and (3) restores fidelity of branchpoint usage to wild-type levels. Isy1p is a subunit of the NineTeen Complex containing Prp19p, an essential E3 ubiquitin ligase homolog required for splicing. Notably, Deltaisy1 PRP16 strains display reduced fidelity of 3'-splice site selection. Consistent with a recent two-state model of the spliceosome, our genetic and biochemical results suggest that Isy1p acts together with U6 snRNA to promote a spliceosomal conformation favorable for first-step chemistry. We propose that deletion of ISY1 favors the premature release of Prp16p, thus promoting second-step chemistry of precursors with inappropriate 3'-splice sites.
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Affiliation(s)
- Tommaso Villa
- Department of Biochemistry and Biophysics, University of California, San Francisco, 94143-2200, USA
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129
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Brenner TJ, Guthrie C. Genetic analysis reveals a role for the C terminus of the Saccharomyces cerevisiae GTPase Snu114 during spliceosome activation. Genetics 2005; 170:1063-80. [PMID: 15911574 PMCID: PMC1451163 DOI: 10.1534/genetics.105.042044] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Snu114 is the only GTPase required for mRNA splicing. As a homolog of elongation factor G, it contains three domains (III-V) predicted to undergo a large rearrangement following GTP hydrolysis. To assess the functional importance of the domains of Snu114, we used random mutagenesis to create conditionally lethal alleles. We identified three main classes: (1) mutations that are predicted to affect GTP binding and hydrolysis, (2) mutations that are clustered in 10- to 20-amino-acid stretches in each of domains III-V, and (3) mutations that result in deletion of up to 70 amino acids from the C terminus. Representative mutations from each of these classes blocked the first step of splicing in vivo and in vitro. The growth defects caused by most alleles were synthetically exacerbated by mutations in PRP8, a U5 snRNP protein that physically interacts with Snu114, as well as in genes involved in snRNP biogenesis, including SAD1 and BRR1. The allele snu114-60, which truncates the C terminus, was synthetically lethal with factors required for activation of the spliceosome, including the DExD/H-box ATPases BRR2 and PRP28. We propose that GTP hydrolysis results in a rearrangement between Prp8 and the C terminus of Snu114 that leads to release of U1 and U4, thus activating the spliceosome for catalysis.
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Affiliation(s)
| | - Christine Guthrie
- Corresponding author: Department of Biochemistry and Biophysics, 600 16th St., Genentech Hall, San Francisco, CA 94143-2200. E-mail:
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130
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Abstract
Pre-messenger RNA (pre-mRNA) splicing is a central step in gene expression. Lying between transcription and protein synthesis, pre-mRNA splicing removes sequences (introns) that would otherwise disrupt the coding potential of intron-containing transcripts. This process takes place in the nucleus, catalyzed by a large RNA-protein complex called the spliceosome. Prp8p, one of the largest and most highly conserved of nuclear proteins, occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there. Recently, Prp8p has also come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa.Prp8 is unique, having no obvious homology to other proteins; however, using bioinformatical analysis we reveal the presence of a conserved RNA recognition motif (RRM), an MPN/JAB domain and a putative nuclear localization signal (NLS). Here, we review biochemical and genetical data, mostly related to the human and yeast proteins, that describe Prp8's central role within the spliceosome and its molecular interactions during spliceosome formation, as splicing proceeds, and in post-splicing complexes.
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Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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131
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Rocak S, Emery B, Tanner NK, Linder P. Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs. Nucleic Acids Res 2005; 33:999-1009. [PMID: 15718299 PMCID: PMC549409 DOI: 10.1093/nar/gki244] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The yeast DEAD-box protein Has1p is required for the maturation of 18S rRNA, the biogenesis of 40S r-subunits and for the processing of 27S pre-rRNAs during 60S r-subunit biogenesis. We purified recombinant Has1p and characterized its biochemical activities. We show that Has1p is an RNA-dependent ATPase in vitro and that it is able to unwind RNA/DNA duplexes in an ATP-dependent manner. We also report a mutational analysis of the conserved residues in motif I (86AKTGSGKT93), motif III (228SAT230) and motif VI (375HRVGRTARG383). The in vivo lethal K92A substitution in motif I abolishes ATPase activity in vitro. The mutations S228A and T230A partially dissociate ATPase and helicase activities, and they have cold-sensitive and lethal growth phenotypes, respectively. The H375E substitution in motif VI significantly decreased helicase but not ATPase activity and was lethal in vivo. These results suggest that both ATPase and unwinding activities are required in vivo. Has1p possesses a Walker A-like motif downstream of motif VI (383GTKGKGKS390). K389A substitution in this motif significantly increases the Has1p activity in vitro, which indicates it potentially plays a role as a negative regulator. Finally, rRNAs and poly(A) RNA serve as the best stimulators of the ATPase activity of Has1p among the tested RNAs.
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Affiliation(s)
| | | | | | - Patrick Linder
- To whom correspondence should be addressed. Tel: +41 22 379 54 84; Fax: +41 22 379 55 02;
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132
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Silverman EJ, Maeda A, Wei J, Smith P, Beggs JD, Lin RJ. Interaction between a G-patch protein and a spliceosomal DEXD/H-box ATPase that is critical for splicing. Mol Cell Biol 2005; 24:10101-10. [PMID: 15542821 PMCID: PMC529041 DOI: 10.1128/mcb.24.23.10101-10110.2004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Prp2 is an RNA-dependent ATPase that activates the spliceosome before the first transesterification reaction of pre-mRNA splicing. Prp2 has extensive homology throughout the helicase domain characteristic of DEXD/H-box helicases and a conserved carboxyl-terminal domain also found in the spliceosomal helicases Prp16, Prp22, and Prp43. Despite the extensive homology shared by these helicases, each has a distinct, sequential role in splicing; thus, uncovering the determinants of specificity becomes crucial to the understanding of Prp2 and the other DEAH-splicing helicases. Mutations in an 11-mer near the C-terminal end of Prp2 eliminate its spliceosome binding and splicing activity. Here we show that a helicase-associated protein interacts with this domain and that this interaction contributes to the splicing process. First, a genome-wide yeast two-hybrid screen using Prp2 as bait identified Spp2, which contained a motif with glycine residues found in a number of RNA binding proteins. SPP2 was originally isolated as a genetic suppressor of a prp2 mutant. In a reciprocal screen, Spp2 specifically pulled out the C-terminal half of Prp2. Mutations in the Prp2 C-terminal 11-mer that disrupted function or spliceosome binding also disrupted Spp2 interaction. A screen of randomly mutagenized SPP2 clones identified an Spp2 protein with a mutation in the G patch that could restore interaction with Prp2 and enhanced splicing in a prp2 mutant strain. The study identifies a potential mechanism for Prp2 specificity mediated through a unique interaction with Spp2 and elucidates a role for a helicase-associated protein in the binding of a DEXD/H-box protein to the spliceosome.
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Affiliation(s)
- Edward J Silverman
- City of Hope Graduate School of Biological Sciences, Duarte, CA 91010, USA
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133
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Abstract
A conceptual framework for integrating diverse functional genomics data was developed by reinterpreting experiments to provide numerical likelihoods that genes are functionally linked. This allows direct comparison and integration of different classes of data. The resulting probabilistic gene network estimates the functional coupling between genes. Within this framework, we reconstructed an extensive, high-quality functional gene network for Saccharomyces cerevisiae, consisting of 4681 (approximately 81%) of the known yeast genes linked by approximately 34,000 probabilistic linkages comparable in accuracy to small-scale interaction assays. The integrated linkages distinguish true from false-positive interactions in earlier data sets; new interactions emerge from genes' network contexts, as shown for genes in chromatin modification and ribosome biogenesis.
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Affiliation(s)
- Insuk Lee
- Center for Systems and Synthetic Biology, Institute for Molecular Biology, University of Texas at Austin, Austin, TX 78712-1064, USA
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134
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Abdelhaleem M. Do human RNA helicases have a role in cancer? Biochim Biophys Acta Rev Cancer 2004; 1704:37-46. [PMID: 15238243 DOI: 10.1016/j.bbcan.2004.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Accepted: 05/06/2004] [Indexed: 11/24/2022]
Abstract
Human RNA helicases (HRH) represent a large family of enzymes that play important roles in RNA processing. The biochemical characteristics and biological functions of the majority of HRH are still to be determined. However, there are examples of dysregulation of HRH expression in various types of cancer. In addition, some HRH have been shown to be involved in the regulation of, or the molecular interaction with, molecules implicated in cancer. Other helicases take part in fusion transcripts resulting from cancer-associated chromosomal translocation. These findings raise the question of whether HRH can contribute to cancer development/progression. In this review, I summarize the cancer-related features of HRH.
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Affiliation(s)
- Mohamed Abdelhaleem
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Room 3691 Atrium, 555 University Avenue, Toronto, ON M5G 1X8, Canada.
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135
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Dez C, Froment C, Noaillac-Depeyre J, Monsarrat B, Caizergues-Ferrer M, Henry Y. Npa1p, a component of very early pre-60S ribosomal particles, associates with a subset of small nucleolar RNPs required for peptidyl transferase center modification. Mol Cell Biol 2004; 24:6324-37. [PMID: 15226434 PMCID: PMC434229 DOI: 10.1128/mcb.24.14.6324-6337.2004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Revised: 02/08/2004] [Accepted: 04/09/2004] [Indexed: 11/20/2022] Open
Abstract
We have identified a novel essential nucleolar factor required for the synthesis of 5.8S and 25S rRNAs termed Npa1p. In the absence of Npa1p, the pre-rRNA processing pathway leading to 5.8S and 25S rRNA production is perturbed such that the C2 cleavage within internal transcribed spacer 2 occurs prematurely. Npa1p accumulates in the immediate vicinity of the dense fibrillar component of the nucleolus and is predominantly associated with the 27SA2 pre-rRNA, the RNA component of the earliest pre-60S ribosomal particles. By mass spectrometry, we have identified the protein partners of Npa1p, which include eight putative helicases as well as the novel Npa2p factor. Strikingly, we also show that Npa1p can associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase center. Our results suggest that 27SA2-containing pre-60S ribosomal particles are located at the interface between the dense fibrillar and the granular components of the nucleolus and that these particles can contain a subset of snoRNPs.
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Affiliation(s)
- Christophe Dez
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099 CNRS-Université Paul Sabatier, IFR 109, Toulouse, France
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136
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Schneider S, Campodonico E, Schwer B. Motifs IV and V in the DEAH Box Splicing Factor Prp22 Are Important for RNA Unwinding, and Helicase-defective Prp22 Mutants Are Suppressed by Prp8. J Biol Chem 2004; 279:8617-26. [PMID: 14688266 DOI: 10.1074/jbc.m312715200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast pre-mRNA splicing factor Prp22 is a member of the DEAH box family of nucleic acid-stimulated ATPases and RNA helicases. Here we report a mutational analysis of 16 conserved residues in motifs Ia ((534)TQPRRVAA(541)), IV ((695)LVFLTG(700)), and V ((757)TNIAETSIT(765)). Mutants T757A, I764A, and T765A were lethal, and F697A cells did not grow at < or =30 degrees C. The mutant proteins failed to catalyze mRNA release from the spliceosome in vitro, and they were deficient for RNA unwinding. The F697A, I764A, and T765A proteins were active for ATP hydrolysis in the presence of RNA cofactor. The T757A mutant retained basal ATPase activity but was not stimulated by RNA, whereas ATP hydrolysis by T765A was strictly dependent on the RNA cofactor. Thus Thr-757 and Thr-765 in motif V link ATP hydrolysis to the RNA cofactor. To illuminate the mechanism of Prp22-catalyzed mRNA release, we performed a genetic screen to identify extragenic suppressors of the cold-sensitive growth defect of a helicase/release-defective Prp22 mutant. We identified one of the suppressors as a missense mutation of PRP8 (R1753K), a protein component of the U5 small nuclear ribonucleoprotein. We show that PRP8-R1753K suppressed multiple helicase-deficient prp22 mutations, including the lethal I764A mutation. Replacing Arg-1753 of Prp8 by either Lys, Ala, Gln, or Glu resulted in suppression of helicase-defective Prp22 mutants. Prp8-Arg1753 mutations by themselves caused temperature-sensitive growth defects in a PRP22 strain. These findings suggest a model whereby Prp22 disrupts an RNA/protein or RNA/RNA interaction in the spliceosome that is normally stabilized by Prp8.
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Affiliation(s)
- Susanne Schneider
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10021, USA
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137
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Abstract
Specific systems of nuclear RNA degradation appear to target and degrade aberrant pre-mRNA molecules. In this work we report on a Dbr1p-dependent RNA decay pathway that limits the accumulation of splice-defective lariat intermediates stalled at the second step of splicing. In this pathway, splice-defective lariat intermediates are debranched by Dbr1p and subsequently degraded 5' to 3' primarily by the cytoplasmic exonuclease, Xrn1p. When debranching is blocked, these splicing intermediates can be degraded in a 3' to 5' direction in a manner dependent on Ski2p, a cofactor for the cytoplasmic exosome. In that Xrn1p and Ski2p are cytoplasmic and Dbr1p localizes to both the nucleus and the cytoplasm, these data suggest that this decay pathway occurs within the cytoplasm. Furthermore, the finding that lariat intermediates accumulate in the dbr1Delta strain suggests that this pathway also functions as an inherent quality control mechanism for the process of pre-mRNA splicing.
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Affiliation(s)
- Patricia J Hilleren
- Department of Biology, 815 North Broadway, Skidmore College, Saratoga Springs, NY 12866, USA.
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138
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Edwalds-Gilbert G, Kim DH, Silverman E, Lin RJ. Definition of a spliceosome interaction domain in yeast Prp2 ATPase. RNA (NEW YORK, N.Y.) 2004; 10:210-20. [PMID: 14730020 PMCID: PMC1370533 DOI: 10.1261/rna.5151404] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The Saccharomyces cerevisiae splicing factor Prp2 is an RNA-dependent ATPase required before the first transesterification reaction in pre-mRNA splicing. Prp2 binds to the spliceosome in the absence of ATP and is released following ATP hydrolysis. It contains three domains: a unique N-terminal domain, a helicase domain that is highly conserved in the DExD/H protein family, and a C-terminal domain that is conserved in spliceosomal DEAH proteins Prp2, Prp16, Prp22, and Prp43. We examined the role of each domain of Prp2 by deletion mutagenesis. Whereas deletions of either the helicase or C-terminal domain are lethal, deletions in the N-terminal domain have no detectable effect on Prp2 activity. Overexpression of the C-terminal domain of Prp2 exacerbates the temperature-sensitive phenotype of a prp2(Ts) strain, suggesting that the C-domain interferes with the activity of the Prp2(Ts) protein. A genetic approach was then taken to study interactions between Prp2 and the spliceosome. Previously, we isolated dominant negative mutants in the helicase domain of Prp2 that inhibit the activity of wild-type Prp2 when the mutant protein is overexpressed. We mutagenized one prp2 release mutant gene and screened for loss of dominant negative function. Several weak binding mutants were isolated and mapped to the C terminus of Prp2, further indicating the importance of the C terminus in spliceosome binding. This study is the first to indicate that amino acid substitutions outside the helicase domain can abolish spliceosome contact and splicing activity of a spliceosomal DEAH protein.
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Affiliation(s)
- Gretchen Edwalds-Gilbert
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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139
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Xu YZ, Newnham CM, Kameoka S, Huang T, Konarska MM, Query CC. Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA. EMBO J 2004; 23:376-85. [PMID: 14713954 PMCID: PMC1271757 DOI: 10.1038/sj.emboj.7600050] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Accepted: 11/28/2003] [Indexed: 11/08/2022] Open
Abstract
Communication between U1 and U2 snRNPs is critical during pre-spliceosome assembly; yet, direct connections have not been observed. To investigate this assembly step, we focused on Prp5, an RNA-dependent ATPase of the DExD/H family. We identified homologs of Saccharomyces cerevisiae Prp5 in humans (hPrp5) and Schizosaccharomyces pombe (SpPrp5), and investigated their interactions and function. Depletion and reconstitution of SpPrp5 from extracts demonstrate that ATP binding and hydrolysis by Prp5 are required for pre-spliceosome complex A formation. hPrp5 and SpPrp5 are each physically associated with both U1 and U2 snRNPs; Prp5 contains distinct U1- and U2-interacting domains that are required for pre-spliceosome assembly; and, we observe a Prp5-associated U1/U2 complex in S. pombe. Together, these data are consistent with Prp5 being a bridge between U1 and U2 snRNPs at the time of pre-spliceosome formation.
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Affiliation(s)
- Yong-Zhen Xu
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Catherine M Newnham
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sei Kameoka
- The Rockefeller University, New York, NY, USA
| | - Tao Huang
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461-1975, USA. Tel.: +1 718 430 4174; Fax: +1 718 430 8574; E-mail:
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140
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Perriman R, Barta I, Voeltz GK, Abelson J, Ares M. ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA. Proc Natl Acad Sci U S A 2003; 100:13857-62. [PMID: 14610285 PMCID: PMC283511 DOI: 10.1073/pnas.2036312100] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stable addition of U2 small nuclear ribonucleoprotein (snRNP) to form the prespliceosome is the first ATP-dependent step in splicing, and it requires the DEXD/H box ATPase Prp5p. However, prespliceosome formation occurs without ATP in extracts lacking the U2 snRNP protein Cus2p. Here we show that Prp5p is required for the ATP-independent prespliceosome assembly that occurs in the absence of Cus2p. Addition of recombinant Cus2p can restore the ATP dependence of prespliceosome assembly, but only if it is added before Prp5p. Prp5p with an altered ATP-binding domain (Prp5-GNTp) can support growth in vivo, but only in a cus2 deletion strain, mirroring the in vitro results. Other Prp5 ATP-binding domain substitutions are lethal, even in the cus2 deletion strain, but can be suppressed by U2 small nuclear RNA mutations that hyperstabilize U2 stem IIa. We infer that the presence of Cus2p and stem IIa-destabilized forms of U2 small nuclear RNA places high demands on the ATP-driven function of Prp5p. Because Prp5p is not dispensable in vitro even in the absence of ATP, we propose that the core Prp5p function in bringing U2 to the branchpoint is not directly ATP-dependent. The positive role of Cus2p in rescuing mutant U2 can be reconciled with its antagonistic effect on Prp5 function in a model whereby Cus2p first helps Prp5p to activate the U2 snRNP for prespliceosome formation but then is displaced by Prp5p before or during the stabilization of U2 at the branchpoint.
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MESH Headings
- Adenosine Triphosphate/metabolism
- Base Sequence
- Binding Sites
- DEAD-box RNA Helicases
- Genes, Fungal
- Models, Biological
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Protein Structure, Tertiary
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Splicing
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/metabolism
- Trans-Activators/chemistry
- Trans-Activators/genetics
- Trans-Activators/metabolism
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Affiliation(s)
- Rhonda Perriman
- Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
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141
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Abstract
Introns are removed from precursor messenger RNAs in the cell nucleus by a large ribonucleoprotein complex called the spliceosome. The spliceosome contains five subcomplexes called snRNPs, each with one RNA and several protein components. Interactions of the snRNPs with each other and the intron are highly dynamic, changing in an ordered progression throughout the splicing process. This allosteric cascade of interactions is programmed into the RNA and protein components of the spliceosome, and is driven by a family of DExD/H-box RNA-dependent ATPases. The dependence of cascade progression on multiple intron-recognition events likely serves to enforce the accuracy of splicing. Here, the progression of the allosteric cascade from the first recognition event to the first catalytic step of splicing is reviewed.
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Affiliation(s)
- David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1532, USA.
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142
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Abstract
In this report, I describe the co-purification of a novel 70-kDa RNA helicase (RH70) and U1snRNP through six column steps. Peptide sequence analysis by mass spectrometry and Edman degradation revealed that RH70 is the previously reported DDX17. Biochemical characterization of RH70, obtained by partial separation from U1snRNP, yielded the following results. (a) RH70 mediates the unwinding of duplex RNA but not DNA in an ATP-dependent manner. (b) Both the RNA-dependent ATPase and RNA helicase activities of RH70 are highly specific for ATP, exhibiting an apparent K(m) of 0.5 mm. (c) RH70 catalyzes the unwinding of duplex RNA containing single-stranded regions at either the 5'- or 3'-end. Its association with U1snRNP and ATP specificity suggest a role for RH70 in pre-mRNA splicing, in particular, at the early stages of the splicing reaction involving U1snRNP.
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Affiliation(s)
- Chee-Gun Lee
- Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA.
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143
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Huang T, Vilardell J, Query CC. Pre-spliceosome formation in S.pombe requires a stable complex of SF1-U2AF(59)-U2AF(23). EMBO J 2002; 21:5516-26. [PMID: 12374752 PMCID: PMC129087 DOI: 10.1093/emboj/cdf555] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have initiated a biochemical analysis of splicing complexes in extracts from the fission yeast Schizosaccharomyces pombe. Extracts of S.pombe contain high levels of the spliceosome-like U2/5/6 tri-snRNP, which dissociates into mono-snRNPs in the presence of ATP, and supports binding of U2 snRNP to the 3' end of introns, yielding a weak ATP-independent E complex and the stable ATP-dependent complex A. The requirements for S.pombe complex A formation (pre-mRNA sequence elements, protein splicing factors, SF1/BBP and both subunits of U2AF) are analogous to those of mammalian complex A. The S.pombe SF1/BBP, U2AF(59) and U2AF(23) are tightly associated in a novel complex that is required for complex A formation. This pre-formed SF1- U2AF(59)-U2AF(23) complex may represent a streamlined mechanism for recognition of the branch site, pyrimidine tract and 3' splice site at the 3' end of introns.
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Affiliation(s)
| | - Josep Vilardell
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461-1975, USA
Present address: Centre de Regulació Genòmica, Passeig Marítim, 37–49, 08003 Barcelona, Spain Corresponding author e-mail:
| | - Charles C. Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461-1975, USA
Present address: Centre de Regulació Genòmica, Passeig Marítim, 37–49, 08003 Barcelona, Spain Corresponding author e-mail:
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144
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Luz JS, Georg RC, Gomes CH, Machado-Santelli GM, Oliveira CC. Sdo1p, the yeast orthologue of Shwachman-Bodian-Diamond syndrome protein, binds RNA and interacts with nuclear rRNA-processing factors. Yeast 1990; 26:287-98. [DOI: 10.1002/yea.1668] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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