1
|
Tseng CK, Cheng SC. Arresting Spliceosome Intermediates at Various Stages of the Splicing Pathway. Methods Mol Biol 2023; 2666:193-211. [PMID: 37166667 DOI: 10.1007/978-1-0716-3191-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The spliceosome is a dynamic ribonucleoprotein particle and is assembled via sequential binding of five snRNAs and numerous protein factors. To understand the molecular mechanism of the splicing reaction, it is necessary to dissect the spliceosome pathway and isolate spliceosome intermediates in various stages of the pathway for biochemical and structural analysis. Here, we describe protocols for preparing intron-containing transcripts, cell-free splicing extracts, and in vitro splicing reactions, as well as procedures to arrest the spliceosome at different stages of the pathway for characterization of specific splicing complexes from the budding yeast Saccharomyces cerevisiae. Methods for arresting spliceosomes at specific stages include depletion with antibodies against factors required for specific steps of the pathway, use of extracts prepared from temperature-sensitive mutants, use of dominant negative mutants of DExD/H-box proteins, and use of mutant substrates.
Collapse
Affiliation(s)
- Chi-Kang Tseng
- Graduate Institute of Microbiology, National Taiwan University, College of Medicine, Taipei, Taiwan, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China.
| |
Collapse
|
2
|
Transcriptomic analysis reveals process of autolysis of Kluyveromyces marxianus in vacuum negative pressure and the higher temperature. Int Microbiol 2022; 25:515-529. [DOI: 10.1007/s10123-022-00240-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/23/2022] [Accepted: 02/07/2022] [Indexed: 10/19/2022]
|
3
|
Liu X, Pan X, Chen D, Yin C, Peng J, Shi W, Qi L, Wang R, Zhao W, Zhang Z, Yang J, Peng YL. Prp19-associated splicing factor Cwf15 regulates fungal virulence and development in the rice blast fungus. Environ Microbiol 2021; 23:5901-5916. [PMID: 34056823 DOI: 10.1111/1462-2920.15616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
The splicing factor Cwf15 is an essential component of the Prp19-associated component of the spliceosome and regulates intron splicing in several model species, including yeasts and human cells. However, the roles of Cwf15 remain unexplored in plant pathogenic fungi. Here, we report that MoCWF15 in the rice blast fungus Magnaporthe oryzae is non-essential to viability and important to fungal virulence, growth and conidiation. MoCwf15 contains a putative nuclear localization signal (NLS) and is localized into the nucleus. The NLS sequence but not the predicted phosphorylation site or two sumoylation sites was essential for the biological functions of MoCwf15. Importantly, MoCwf15 physically interacted with the Prp19-associated splicing factors MoCwf4, MoSsa1 and MoCyp1, and negatively regulated protein accumulations of MoCyp1 and MoCwf4. Furthermore, with the deletion of MoCWF15, aberrant intron splicing occurred in near 400 genes, 20 of which were important to the fungal development and virulence. Taken together, MoCWF15 regulates fungal growth and infection-related development by modulating the intron splicing efficiency of a subset of genes in the rice blast fungus.
Collapse
Affiliation(s)
- Xinsen Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xiao Pan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Deng Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Changfa Yin
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Junbo Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Shi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Linlu Qi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ruijin Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Yang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - You-Liang Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
4
|
Petasny M, Bentata M, Pawellek A, Baker M, Kay G, Salton M. Splicing to Keep Cycling: The Importance of Pre-mRNA Splicing during the Cell Cycle. Trends Genet 2020; 37:266-278. [PMID: 32950269 DOI: 10.1016/j.tig.2020.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022]
Abstract
Pre-mRNA splicing is a fundamental process in mammalian gene expression, and alternative splicing plays an extensive role in generating protein diversity. Because the majority of genes undergo pre-mRNA splicing, most cellular processes depend on proper spliceosome function. We focus on the cell cycle and describe its dependence on pre-mRNA splicing and accurate alternative splicing. We outline the key cell-cycle factors and their known alternative splicing isoforms. We discuss different levels of pre-mRNA splicing regulation such as post-translational modifications and changes in the expression of splicing factors. We describe the effect of chromatin dynamics on pre-mRNA splicing during the cell cycle. In addition, we focus on spliceosome component SF3B1, which is mutated in many types of cancer, and describe the link between SF3B1 and its inhibitors and the cell cycle.
Collapse
Affiliation(s)
- Mayra Petasny
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mercedes Bentata
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Andrea Pawellek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mai Baker
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| |
Collapse
|
5
|
Tseng CK, Chung CS, Chen HC, Cheng SC. A central role of Cwc25 in spliceosome dynamics during the catalytic phase of pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2017; 23:546-556. [PMID: 28057857 PMCID: PMC5340917 DOI: 10.1261/rna.059204.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/03/2017] [Indexed: 05/22/2023]
Abstract
Splicing of precursor mRNA occurs via two consecutive steps of transesterification reaction; both require ATP and several proteins. Despite the energy requirement in the catalytic phase, incubation of the purified spliceosome under proper ionic conditions can elicit competitive reversible transesterification, debranching, and spliced-exon-reopening reactions without the necessity for ATP or other factors, suggesting that small changes in the conformational state of the spliceosome can lead to disparate chemical consequences for the substrate. We show here that Cwc25 plays a central role in modulating the conformational state of the catalytic spliceosome during normal splicing reactions. Cwc25 binds tightly to the spliceosome after the reaction and is then removed from the spliceosome, which normally requires DExD/H-box protein Prp16 and ATP hydrolysis, to allow the occurrence of the second reaction. When deprived of Cwc25, the purified first-step spliceosome catalyzes both forward and reverse splicing reactions under normal splicing conditions without requiring energy. Both reactions are inhibited when Cwc25 is added back, presumably due to the stabilization of first-step conformation. Prp16 is dispensable for the second reaction when splicing is carried out under conditions that destabilize Cwc25. We also show that the purified precatalytic spliceosome can catalyze two steps of the reaction at a low efficiency without requiring Cwc25, Slu7, or Prp18 when incubated under proper conditions. Our study reveals conformational modulation of the spliceosome by Cwc25 and Prp16 in stabilization and destabilization of first-step conformation, respectively, to facilitate the splicing process.
Collapse
Affiliation(s)
- Chi-Kang Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Che-Sheng Chung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Hsin-Chou Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| |
Collapse
|
6
|
Role of Cwc24 in the First Catalytic Step of Splicing and Fidelity of 5' Splice Site Selection. Mol Cell Biol 2017; 37:MCB.00580-16. [PMID: 27994011 DOI: 10.1128/mcb.00580-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/11/2016] [Indexed: 12/17/2022] Open
Abstract
Cwc24 is an essential splicing factor but only transiently associates with the spliceosome, with an unknown function. The protein contains a RING finger and a zinc finger domain in the carboxyl terminus. The human ortholog of Cwc24, RNF113A, has been associated with the disorder trichothiodystrophy. Here, we show that the zinc finger domain is essential for Cwc24 function, while the RING finger domain is dispensable. Cwc24 binds to the spliceosome after the Prp19-associated complex and is released upon Prp2 action. Cwc24 is not required for Prp2-mediated remodeling of the spliceosome, but the spliceosome becomes inactive if remodeling occurs before the addition of Cwc24. Cwc24 binds directly to pre-mRNA at the 5' splice site, spanning the splice junction. In the absence of Cwc24, U5 and U6 modes of interaction with the 5' splice site are altered, and splicing is very inefficient, with aberrant cleavage at the 5' splice site. Our data suggest roles for Cwc24 in orchestrating organization of the spliceosome into an active configuration prior to Prp2-mediated spliceosome remodeling and in promoting specific interaction of U5 and U6 with the 5' splice site for fidelity of 5' splice site selection.
Collapse
|
7
|
Collier SE, Voehler M, Peng D, Ohi R, Gould KL, Reiter NJ, Ohi MD. Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5. Biochemistry 2014; 53:6439-51. [PMID: 25263959 PMCID: PMC4204884 DOI: 10.1021/bi5008639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The
spliceosome is a dynamic macromolecular machine composed of
five small nuclear ribonucleoparticles (snRNPs), the NineTeen Complex
(NTC), and other proteins that catalyze the removal of introns mature
to form the mature message. The NTC, named after its founding member Saccharomyces cerevisiae Prp19, is a conserved spliceosome
subcomplex composed of at least nine proteins. During spliceosome
assembly, the transition to an active spliceosome correlates with
stable binding of the NTC, although the mechanism of NTC function
is not understood. Schizosaccharomyces pombe Cdc5, a core subunit of the NTC, is an essential protein required
for pre-mRNA splicing. The highly conserved Cdc5 N-terminus contains
two canonical Myb (myeloblastosis) repeats (R1 and R2) and a third
domain (D3) that was previously classified as a Myb-like repeat. Although
the N-terminus of Cdc5 is required for its function, how R1, R2, and
D3 each contribute to functionality is unclear. Using a combination
of yeast genetics, structural approaches, and RNA binding assays,
we show that R1, R2, and D3 are all required for the function of Cdc5
in cells. We also show that the N-terminus of Cdc5 binds RNA in vitro. Structural and functional analyses of Cdc5-D3
show that, while this domain does not adopt a Myb fold, Cdc5-D3 preferentially
binds double-stranded RNA. Our data suggest that the Cdc5 N-terminus
interacts with RNA structures proposed to be near the catalytic core
of the spliceosome.
Collapse
Affiliation(s)
- Scott E Collier
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center , Nashville, Tennessee 37232, United States
| | | | | | | | | | | | | |
Collapse
|
8
|
Chen HC, Chang KJ, Su YL, Huang YH, Cheng SC. Structural requirement of Ntc77 for spliceosome activation and first catalytic step. Nucleic Acids Res 2014; 42:12261-71. [PMID: 25294830 PMCID: PMC4231770 DOI: 10.1093/nar/gku914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Prp19-associated complex is required for spliceosome activation by stabilizing the binding of U5 and U6 on the spliceosome after the release of U4. The complex comprises at least eight proteins, among which Ntc90 and Ntc77 contain multiple tetratricopeptide repeat (TPR) elements. We have previously shown that Ntc90 is not involved in spliceosome activation, but is required for the recruitment of essential first-step factor Yju2 to the spliceosome. We demonstrate here that Ntc77 has dual functions in both spliceosome activation and the first catalytic step in recruiting Yju2. We have identified an amino-terminal region of Ntc77, which encompasses the N-terminal domain and the first three TPR motifs, dispensable for spliceosome activation but required for stable interaction of Yju2 with the spliceosome. Deletion of this region had no severe effect on the integrity of the NTC, binding of NTC to the spliceosome or spliceosome activation, but impaired splicing and exhibited a dominant-negative growth phenotype. Our data reveal functional roles of Ntc77 in both spliceosome activation and the first catalytic step, and distinct structural domains of Ntc77 required for these two steps.
Collapse
Affiliation(s)
- Hsin-Chou Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan 112, Republic of China
| | - Kae-Jiun Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Yu-Lun Su
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Yu-Hsin Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| |
Collapse
|
9
|
Benjamin AB, Zhou X, Isaac O, Zhao H, Song Y, Chi X, Sun B, Hao L, Zhang L, Liu L, Guan H, Shao S. PRP19 upregulation inhibits cell proliferation in lung adenocarcinomas by p21-mediated induction of cell cycle arrest. Biomed Pharmacother 2014; 68:463-70. [DOI: 10.1016/j.biopha.2014.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/04/2014] [Indexed: 11/25/2022] Open
|
10
|
The SPF27 homologue Num1 connects splicing and kinesin 1-dependent cytoplasmic trafficking in Ustilago maydis. PLoS Genet 2014; 10:e1004046. [PMID: 24391515 PMCID: PMC3879195 DOI: 10.1371/journal.pgen.1004046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 10/30/2013] [Indexed: 12/23/2022] Open
Abstract
The conserved NineTeen protein complex (NTC) is an integral subunit of the spliceosome and required for intron removal during pre-mRNA splicing. The complex associates with the spliceosome and participates in the regulation of conformational changes of core spliceosomal components, stabilizing RNA-RNA- as well as RNA-protein interactions. In addition, the NTC is involved in cell cycle checkpoint control, response to DNA damage, as well as formation and export of mRNP-particles. We have identified the Num1 protein as the homologue of SPF27, one of NTC core components, in the basidiomycetous fungus Ustilago maydis. Num1 is required for polarized growth of the fungal hyphae, and, in line with the described NTC functions, the num1 mutation affects the cell cycle and cell division. The num1 deletion influences splicing in U. maydis on a global scale, as RNA-Seq analysis revealed increased intron retention rates. Surprisingly, we identified in a screen for Num1 interacting proteins not only NTC core components as Prp19 and Cef1, but several proteins with putative functions during vesicle-mediated transport processes. Among others, Num1 interacts with the motor protein Kin1 in the cytoplasm. Similar phenotypes with respect to filamentous and polar growth, vacuolar morphology, as well as the motility of early endosomes corroborate the genetic interaction between Num1 and Kin1. Our data implicate a previously unidentified connection between a component of the splicing machinery and cytoplasmic transport processes. As the num1 deletion also affects cytoplasmic mRNA transport, the protein may constitute a novel functional interconnection between the two disparate processes of splicing and trafficking. In eukaryotic cells, nascent mRNA is processed by splicing to remove introns and to join the exon sequences. The processed mRNA is then transported out of the nucleus and employed by ribosomes to synthesize proteins. Splicing is achieved by the spliceosome and associated protein complexes, among them the so-called NineTeen complex (NTC). We have identified the Num1 protein as one of the core components of the NTC in the fungus Ustilago maydis, and could show that it is required for polarized growth of the filamentous fungal cells. Consistent with the NTC function, cells with a num1-deletion show reduced splicing of mRNA. Moreover, we uncover a novel cytoplasmic function of the Num1 protein: It physically interacts with the microtubule-associated Kinesin 1 motor protein, and phenotypic analyses corroborate that both proteins are functionally connected. Our findings reveal a yet unidentified role of a global splicing factor during intracellular trafficking processes. A possible connection between these disparate mechanisms presumably resides in mRNA-export out of the nucleus and/or the transport of mRNA within the cytoplasm.
Collapse
|
11
|
Structural and functional characterization of the N terminus of Schizosaccharomyces pombe Cwf10. EUKARYOTIC CELL 2013; 12:1472-89. [PMID: 24014766 DOI: 10.1128/ec.00140-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members are highly homologous to eukaryotic translation elongation factor EF2, and they contain a conserved N-terminal extension (NTE) to the EF2-like portion, predicted to be an intrinsically unfolded domain. Using S. pombe as a model system, we show that the NTE is not essential, but cells lacking this domain are defective in pre-mRNA splicing. Genetic interactions between cwf10-ΔNTE and other pre-mRNA splicing mutants are consistent with a role for the NTE in spliceosome activation and second-step catalysis. Characterization of Cwf10-NTE by various biophysical techniques shows that in solution the NTE contains regions of both structure and disorder. The first 23 highly conserved amino acids of the NTE are essential for its role in splicing but when overexpressed are not sufficient to restore pre-mRNA splicing to wild-type levels in cwf10-ΔNTE cells. When the entire NTE is overexpressed in the cwf10-ΔNTE background, it can complement the truncated Cwf10 protein in trans, and it immunoprecipitates a complex similar in composition to the late-stage U5.U2/U6 spliceosome. These data show that the structurally flexible NTE is capable of independently incorporating into the spliceosome and improving splicing function, possibly indicating a role for the NTE in stabilizing conformational rearrangements during a splice cycle.
Collapse
|
12
|
Abstract
RNA splicing is one of the fundamental processes in gene expression in eukaryotes. Splicing of pre-mRNA is catalysed by a large ribonucleoprotein complex called the spliceosome, which consists of five small nuclear RNAs and numerous protein factors. The spliceosome is a highly dynamic structure, assembled by sequential binding and release of the small nuclear RNAs and protein factors. DExD/H-box RNA helicases are required to mediate structural changes in the spliceosome at various steps in the assembly pathway and have also been implicated in the fidelity control of the splicing reaction. Other proteins also play key roles in mediating the progression of the spliceosome pathway. In this review, we discuss the functional roles of the protein factors involved in the spliceosome pathway primarily from studies in the yeast system.
Collapse
|
13
|
Ohrt T, Prior M, Dannenberg J, Odenwälder P, Dybkov O, Rasche N, Schmitzová J, Gregor I, Fabrizio P, Enderlein J, Lührmann R. Prp2-mediated protein rearrangements at the catalytic core of the spliceosome as revealed by dcFCCS. RNA (NEW YORK, N.Y.) 2012; 18:1244-56. [PMID: 22535589 PMCID: PMC3358646 DOI: 10.1261/rna.033316.112] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 05/18/2023]
Abstract
The compositional and conformational changes during catalytic activation of the spliceosome promoted by the DEAH box ATPase Prp2 are only poorly understood. Here, we show by dual-color fluorescence cross-correlation spectroscopy (dcFCCS) that the binding affinity of several proteins is significantly changed during the Prp2-mediated transition of precatalytic B(act) spliceosomes to catalytically activated B* spliceosomes from Saccharomyces cerevisiae. During this step, several proteins, including the zinc-finger protein Cwc24, are quantitatively displaced from the B* complex. Consistent with this, we show that Cwc24 is required for step 1 but not for catalysis per se. The U2-associated SF3a and SF3b proteins Prp11 and Cus1 remain bound to the B* spliceosome under near-physiological conditions, but their binding is reduced at high salt. Conversely, high-affinity binding sites are created for Yju2 and Cwc25 during catalytic activation, consistent with their requirement for step 1 catalysis. Our results suggest high cooperativity of multiple Prp2-mediated structural rearrangements at the spliceosome's catalytic core. Moreover, dcFCCS represents a powerful tool ideally suited to study quantitatively spliceosomal protein dynamics in equilibrium.
Collapse
Affiliation(s)
- Thomas Ohrt
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Mira Prior
- III. Physikalisches Institut (Biophysik), University of Göttingen, D-37077 Göttingen, Germany
| | - Julia Dannenberg
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Peter Odenwälder
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Olexandr Dybkov
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Nicolas Rasche
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Jana Schmitzová
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Ingo Gregor
- III. Physikalisches Institut (Biophysik), University of Göttingen, D-37077 Göttingen, Germany
| | - Patrizia Fabrizio
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Physikalisches Institut (Biophysik), University of Göttingen, D-37077 Göttingen, Germany
- Corresponding authors.E-mail .E-mail .
| | - Reinhard Lührmann
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
- Corresponding authors.E-mail .E-mail .
| |
Collapse
|
14
|
Query CC, Konarska MM. CEF1/CDC5 alleles modulate transitions between catalytic conformations of the spliceosome. RNA (NEW YORK, N.Y.) 2012; 18:1001-13. [PMID: 22408182 PMCID: PMC3334688 DOI: 10.1261/rna.029421.111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Conformational change within the spliceosome is required between the first and second catalytic steps of pre-mRNA splicing. A prior genetic screen for suppressors of an intron mutant that stalls between the two steps yielded both prp8 and non-prp8 alleles that suppressed second-step splicing defects. We have now identified the strongest non-prp8 suppressors as alleles of the NTC (Prp19 complex) component, CEF1. These cef1 alleles generally suppress second-step defects caused by a variety of intron mutations, mutations in U6 snRNA, or deletion of the second-step protein factor Prp17, and they can activate alternative 3' splice sites. Genetic and functional interactions between cef1 and prp8 alleles suggest that they modulate the same event(s) in the first-to-second-step transition, most likely by stabilization of the second-step spliceosome; in contrast, alleles of U6 snRNA that also alter this transition modulate a distinct event, most likely by stabilization of the first-step spliceosome. These results implicate a myb-like domain of Cef1/CDC5 in interactions that modulate conformational states of the spliceosome and suggest that alteration of these events affects splice site use, resulting in alternative splicing-like patterns in yeast.
Collapse
Affiliation(s)
- Charles C. Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Corresponding authors.E-mail .E-mail .
| | - Maria M. Konarska
- The Rockefeller University, New York, New York 10065, USA
- Corresponding authors.E-mail .E-mail .
| |
Collapse
|
15
|
Saha D, Khandelia P, O'Keefe RT, Vijayraghavan U. Saccharomyces cerevisiae NineTeen complex (NTC)-associated factor Bud31/Ycr063w assembles on precatalytic spliceosomes and improves first and second step pre-mRNA splicing efficiency. J Biol Chem 2012; 287:5390-9. [PMID: 22215661 DOI: 10.1074/jbc.m111.298547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pre-mRNA splicing occurs in spliceosomes whose assembly and activation are critical for splice site selection and catalysis. The highly conserved NineTeen complex protein complex stabilizes various snRNA and protein interactions early in the spliceosome assembly pathway. Among several NineTeen complex-associated proteins is the nonessential protein Bud31/Ycr063w, which is also a component of the Cef1p subcomplex. A role for Bud31 in pre-mRNA splicing is implicated by virtue of its association with splicing factors, but its specific functions and spliceosome interactions are uncharacterized. Here, using in vitro splicing assays with extracts from a strain lacking Bud31, we illustrate its role in efficient progression to the first catalytic step and its requirement for the second catalytic step in reactions at higher temperatures. Immunoprecipitation of functional epitope-tagged Bud31 from in vitro reactions showed that its earliest association is with precatalytic B complex and that the interaction continues in catalytically active complexes with stably bound U2, U5, and U6 small nuclear ribonucleoproteins. In complementary experiments, wherein precatalytic spliceosomes are selected from splicing reactions, we detect the occurrence of Bud31. Cross-linking of proteins to pre-mRNAs with a site-specific 4-thio uridine residue at the -3 position of exon 1 was tested in reactions with WT and bud31 null extracts. The data suggest an altered interaction between a ∼25-kDa protein and this exonic residue of pre-mRNAs in the arrested bud31 null spliceosomes. These results demonstrate the early spliceosomal association of Bud31 and provide plausible functions for this factor in stabilizing protein interactions with the pre-mRNA.
Collapse
Affiliation(s)
- Debjani Saha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | | | | |
Collapse
|
16
|
Abstract
AbstractRecent work in plant immunity has shown that MOS4, a known intermediate in R protein mediated resistance, is a core member of the nuclear MOS4-associated complex (MAC). This complex is highly conserved in eukaryotes, as orthologous complexes known as the CDC5L-SNEVPrp19-Pso4 complex and the Nineteen complex (NTC) were previously identified in human and yeast, respectively. The involvement of these complexes in pre-mRNA splicing and spliceosome assembly suggests that the MAC probably has a similar function in plants. Double mutants of any two MAC components are lethal, whereas single mutants of the MAC core components mos4, Atcdc5, mac3, and prl1 are all viable and display pleiotropic defects. This suggests that while the MAC is required for some essential biological function such as splicing, individual MAC components are not crucial for complex functionality and likely have regulatory roles in other biological processes such as plant immunity and flowering time control. Future studies on MAC components in Arabidopsis will provide further insight into the regulatory mechanisms of the MAC on specific biological processes.
Collapse
|
17
|
Brown HF, Wang L, Khadka S, Fields S, LaCount DJ. A densely overlapping gene fragmentation approach improves yeast two-hybrid screens for Plasmodium falciparum proteins. Mol Biochem Parasitol 2011; 178:56-9. [PMID: 21530591 DOI: 10.1016/j.molbiopara.2011.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 04/08/2011] [Accepted: 04/14/2011] [Indexed: 01/18/2023]
Abstract
Use of the yeast two-hybrid assay to study Plasmodium falciparum protein-protein interactions is limited by poor expression of P. falciparum genes in yeast and lack of easily implemented assays to confirm the results. We report here two methods to create gene fragments - random fragmentation by partial DNAse I digestion and generation of densely overlapping fragments by PCR - that enable most portions of P. falciparum genes to be expressed and screened in the yeast two-hybrid assay. The PCR-based method is less technically challenging and facilitates fine-scale mapping of protein interaction domains. Both approaches revealed a putative interaction between PfMyb2 (PF10_0327) and PFC0365w. We developed new plasmids to express the proteins in wheat germ extracts and confirmed the interaction in both the split-luciferase assay and in co-purification experiments with glutathione-S-transferase and HA-tagged proteins. The combination of improved yeast two-hybrid screening approaches and convenient systems to validate interactions enhances the utility of yeast two-hybrid assays for P. falciparum.
Collapse
Affiliation(s)
- Hakeenah F Brown
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | | | | | | | | |
Collapse
|
18
|
Ganesh K, Adam S, Taylor B, Simpson P, Rada C, Neuberger M. CTNNBL1 is a novel nuclear localization sequence-binding protein that recognizes RNA-splicing factors CDC5L and Prp31. J Biol Chem 2011; 286:17091-102. [PMID: 21385873 PMCID: PMC3089553 DOI: 10.1074/jbc.m110.208769] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear proteins typically contain short stretches of basic amino acids (nuclear localization sequences; NLSs) that bind karyopherin α family members, directing nuclear import. Here, we identify CTNNBL1 (catenin-β-like 1), an armadillo motif-containing nuclear protein that exhibits no detectable primary sequence homology to karyopherin α, as a novel, selective NLS-binding protein. CTNNBL1 (a single-copy gene conserved from fission yeast to man) was previously found associated with Prp19-containing RNA-splicing complexes as well as with the antibody-diversifying enzyme AID. We find that CTNNBL1 association with the Prp19 complex is mediated by recognition of the NLS of the CDC5L component of the complex and show that CTNNBL1 also interacts with Prp31 (another U4/U6.U5 tri-snRNP-associated splicing factor) through its NLS. As with karyopherin αs, CTNNBL1 binds NLSs via its armadillo (ARM) domain, but displays a separate, more selective NLS binding specificity. Furthermore, the CTNNBL1/AID interaction depends on amino acids forming the AID conformational NLS with CTNNBL1-deficient cells showing a partial defect in AID nuclear accumulation. However, in further contrast to karyopherin αs, the CTNNBL1 N-terminal region itself binds karyopherin αs (rather than karyopherin β), suggesting a function divergent from canonical nuclear transport. Thus, CTNNBL1 is a novel NLS-binding protein, distinct from karyopherin αs, with the results suggesting a possible role in the selective intranuclear targeting or interactions of some splicing-associated complexes.
Collapse
Affiliation(s)
- Karuna Ganesh
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | | | | | | | | | | |
Collapse
|
19
|
Splicing factor Cwc22 is required for the function of Prp2 and for the spliceosome to escape from a futile pathway. Mol Cell Biol 2010; 31:43-53. [PMID: 20956557 DOI: 10.1128/mcb.00801-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cwc22 was previously identified to associate with the pre-mRNA splicing factor Cef1/Ntc85, a component of the Prp19-associated complex (nineteen complex [NTC]) involved in spliceosome activation. We show here that Cwc22 is required for pre-mRNA splicing both in vivo and in vitro but is neither tightly associated with the NTC nor required for spliceosome activation. Cwc22 is associated with the spliceosome prior to catalytic steps and remains associated throughout the reaction. The stable association of Cwc22 with the spliceosome requires the presence of the NTC but is independent of Prp2. Although Cwc22 is not required for the recruitment of Prp2 to the spliceosome, it is essential for the function of Prp2 in promoting the release of the U2 components SF3a and SF3b. In the absence of Cwc22, Prp2 can bind to the spliceosome but is dissociated upon ATP hydrolysis without promoting the release of SF3a/b. Thus, Cwc22 represents a novel ATP-dependent step one factor besides Prp2 and Spp2 and has a distinct role from that of Spp2 in mediating the function of Prp2.
Collapse
|
20
|
Grainger RJ, Barrass JD, Jacquier A, Rain JC, Beggs JD. Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome. RNA (NEW YORK, N.Y.) 2009; 15:2161-73. [PMID: 19854871 PMCID: PMC2779682 DOI: 10.1261/rna.1908309] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 09/15/2009] [Indexed: 05/20/2023]
Abstract
In Saccharomyces cerevisiae, Cwc21p is a protein of unknown function that is associated with the NineTeen Complex (NTC), a group of proteins involved in activating the spliceosome to promote the pre-mRNA splicing reaction. Here, we show that Cwc21p binds directly to two key splicing factors-namely, Prp8p and Snu114p-and becomes the first NTC-related protein known to dock directly to U5 snRNP proteins. Using a combination of proteomic techniques we show that the N-terminus of Prp8p contains an intramolecular fold that is a Snu114p and Cwc21p interacting domain (SCwid). Cwc21p also binds directly to the C-terminus of Snu114p. Complementary chemical cross-linking experiments reveal reciprocal protein footprints between the interacting Prp8 and Cwc21 proteins, identifying the conserved cwf21 domain in Cwc21p as a Prp8p binding site. Genetic and functional interactions between Cwc21p and Isy1p indicate that they have related functions at or prior to the first catalytic step of splicing, and suggest that Cwc21p functions at the catalytic center of the spliceosome, possibly in response to environmental or metabolic changes. We demonstrate that SRm300, the only SR-related protein known to be at the core of human catalytic spliceosomes, is a functional ortholog of Cwc21p, also interacting directly with Prp8p and Snu114p. Thus, the function of Cwc21p is likely conserved from yeast to humans.
Collapse
Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
| | | | | | | | | |
Collapse
|
21
|
Chiu YF, Liu YC, Chiang TW, Yeh TC, Tseng CK, Wu NY, Cheng SC. Cwc25 is a novel splicing factor required after Prp2 and Yju2 to facilitate the first catalytic reaction. Mol Cell Biol 2009; 29:5671-8. [PMID: 19704000 PMCID: PMC2772750 DOI: 10.1128/mcb.00773-09] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/10/2009] [Accepted: 08/17/2009] [Indexed: 11/20/2022] Open
Abstract
Cwc25 has previously been identified to associate with pre-mRNA splicing factor Cef1/Ntc85, a component of the Prp19-associated complex (nineteen complex, or NTC) involved in spliceosome activation. We show here that Cwc25 is neither tightly associated with NTC nor required for spliceosome activation but is required for the first catalytic reaction. The affinity-purified spliceosome formed in Cwc25-depleted extracts contained only pre-mRNA and could be chased into splicing intermediates upon the addition of recombinant Cwc25 in an ATP-independent manner, suggesting that Cwc25 functions in the final step of the first catalytic reaction after the action of Prp2. Yju2 and a heat-resistant factor of unknown identity, HP, have previously been shown to be required for the same step of the splicing pathway. Cwc25, although resistant to heat treatment, is not sufficient to replace the function of HP, indicating that another heat-resistant factor, which we named HP-X, is involved. The requirement of Cwc25 and HP-X for the first catalytic reaction could be partially compensated for when the affinity-purified spliceosome was incubated in the presence of low concentrations of Mn(2+). These results have implications for the possible roles of Cwc25 and HP-X in facilitating juxtaposition of the 5' splice site and the branch point during the first catalytic reaction.
Collapse
Affiliation(s)
- Ying-Fang Chiu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Yen-Chi Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Ting-Wei Chiang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Tzu-Chi Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Chi-Kang Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Nan-Ying Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, Faculty of Life Science and Institute of Genomic Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| |
Collapse
|
22
|
The homologue of Lentinula edodes ctg1, a target for CDC5 and its interacting partner CIPB, from Coprinopsis cinerea is involved in fruitingbody morphogenesis of C. cinerea. MYCOSCIENCE 2009. [DOI: 10.1007/s10267-009-0489-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
23
|
Chang KJ, Chen HC, Cheng SC. Ntc90 is required for recruiting first step factor Yju2 but not for spliceosome activation. RNA (NEW YORK, N.Y.) 2009; 15:1729-39. [PMID: 19617314 PMCID: PMC2743064 DOI: 10.1261/rna.1625309] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The Prp19-associated complex (NineTeen Complex [NTC]) is required for spliceosome activation by specifying interactions of U5 and U6 with pre-mRNA on the spliceosome after the release of U4. The NTC consists of at least eight protein components, including two tetratricopeptide repeat (TPR)-containing proteins, Ntc90 and Ntc77. Ntc90 has nine copies of the TPR with seven clustered in the carboxy-terminal half of the protein, and interacts with all identified NTC components except for Prp19 and Ntc25. It forms a stable complex with Ntc31, Ntc30, and Ntc20 in the absence of Ntc25, when other interactions between NTC components are disrupted. In this study, we used both biochemical and genetic methods to analyze the structure of Ntc90, and its function in maintaining the integrity of the NTC and in NTC-mediated spliceosome activation. Our results show that Ntc90 interacts with Ntc31, Ntc30, and other NTC components through different regions of the protein, and that its function may be regulated by Ntc31 and Ntc30. Ntc90 is not required for the association of Prp19, Ntc85, Ntc77, Ntc25, and Ntc20, or for their binding to the spliceosome. It is also not required for NTC-mediated spliceosome activation, but is required for the recruitment of Yju2, which is involved in the first catalytic reaction after the function of Prp2. Our results demonstrate a novel role of the NTC in recruiting splicing factors to the spliceosome after its activation.
Collapse
Affiliation(s)
- Kae-Jiun Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | | | | |
Collapse
|
24
|
Monaghan J, Xu F, Gao M, Zhao Q, Palma K, Long C, Chen S, Zhang Y, Li X. Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity. PLoS Pathog 2009; 5:e1000526. [PMID: 19629177 PMCID: PMC2709443 DOI: 10.1371/journal.ppat.1000526] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 06/30/2009] [Indexed: 01/01/2023] Open
Abstract
Plant Resistance (R) proteins play an integral role in defense against pathogen infection. A unique gain-of-function mutation in the R gene SNC1, snc1, results in constitutive activation of plant immune pathways and enhanced resistance against pathogen infection. We previously found that mutations in MOS4 suppress the autoimmune phenotypes of snc1, and that MOS4 is part of a nuclear complex called the MOS4-Associated Complex (MAC) along with the transcription factor AtCDC5 and the WD-40 protein PRL1. Here we report the immuno-affinity purification of the MAC using HA-tagged MOS4 followed by protein sequence analysis by mass spectrometry. A total of 24 MAC proteins were identified, 19 of which have predicted roles in RNA processing based on their homology to proteins in the Prp19-Complex, an evolutionarily conserved spliceosome-associated complex containing homologs of MOS4, AtCDC5, and PRL1. Among these were two highly similar U-box proteins with homology to the yeast and human E3 ubiquitin ligase Prp19, which we named MAC3A and MAC3B. MAC3B was recently shown to exhibit E3 ligase activity in vitro. Through reverse genetics analysis we show that MAC3A and MAC3B are functionally redundant and are required for basal and R protein-mediated resistance in Arabidopsis. Like mos4-1 and Atcdc5-1, mac3a mac3b suppresses snc1-mediated autoimmunity. MAC3 localizes to the nucleus and interacts with AtCDC5 in planta. Our results suggest that MAC3A and MAC3B are members of the MAC that function redundantly in the regulation of plant innate immunity.
Collapse
Affiliation(s)
- Jacqueline Monaghan
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fang Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Minghui Gao
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Qingguo Zhao
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Kristoffer Palma
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chengzu Long
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - She Chen
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Yuelin Zhang
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
25
|
Gahura O, Abrhámová K, Skruzný M, Valentová A, Munzarová V, Folk P, Půta F. Prp45 affects Prp22 partition in spliceosomal complexes and splicing efficiency of non-consensus substrates. J Cell Biochem 2009; 106:139-51. [PMID: 19016306 DOI: 10.1002/jcb.21989] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human transcription co-regulator SNW1/SKIP is implicated in the regulation of both transcription elongation and alternative splicing. Prp45, the SNW/SKIP ortholog in yeast, is assumed to be essential for pre-mRNA processing. Here, we characterize prp45(1-169), a temperature sensitive allele of PRP45, which at permissive temperature elicits cell division defects and hypersensitivity to microtubule inhibitors. Using a synthetic lethality screen, we found that prp45(1-169) genetically interacts with alleles of NTC members SYF1, CLF1/SYF3, NTC20, and CEF1, and 2nd step splicing factors SLU7, PRP17, PRP18, and PRP22. Cwc2-associated spliceosomal complexes purified from prp45(1-169) cells showed decreased stoichiometry of Prp22, suggesting its deranged interaction with the spliceosome. In vivo splicing assays in prp45(1-169) cells revealed that branch point mutants accumulated more pre-mRNA whereas 5' and 3' splice site mutants showed elevated levels of lariat-exon intermediate as compared to wild-type cells. Splicing of canonical intron was unimpeded. Notably, the expression of Prp45(119-379) in prp45(1-169) cells restored Prp22 partition in the Cwc2-pulldowns and rescued temperature sensitivity and splicing phenotype of prp45(1-169) strain. Our data suggest that Prp45 contributes, in part through its interaction with the 2nd step-proofreading helicase Prp22, to splicing efficiency of substrates non-conforming to the consensus.
Collapse
Affiliation(s)
- Ondrej Gahura
- Faculty of Science, Department of Cell Biology, Charles University in Prague, Prague 128 00, Czech Republic
| | | | | | | | | | | | | |
Collapse
|
26
|
The splicing factor Prp17 interacts with the U2, U5 and U6 snRNPs and associates with the spliceosome pre- and post-catalysis. Biochem J 2008; 416:365-74. [DOI: 10.1042/bj20081195] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Saccharomyces cerevisiae PRP17-null mutants are temperature-sensitive for growth. In vitro splicing with extracts lacking Prp17 are kinetically slow for the first step of splicing and are arrested for the second step at temperatures greater than 34 °C. In the present study we show that these stalled spliceosomes are compromised for an essential conformational switch that is triggered by Prp16 helicase. These results suggest a plausible mechanistic basis for the second-step arrest in prp17Δ extracts and support a role for Prp17 in conjunction with Prp16. To understand the association of Prp17 with spliceosomes we used a functional epitope-tagged protein in co-immunoprecipitation experiments. Examination of co-precipitated snRNAs (small nuclear RNAs) show that Prp17 interacts with U2, U5 and U6 snRNPs (small nuclear ribonucleoproteins) but it is not a core component of any one snRNP. Prp17 association with in-vitro-assembled spliceosome complexes on actin pre-mRNAs was also investigated. Although the U5 snRNP proteins Prp8 and Snu114 are found in early pre-spliceosomes that contain all five snRNPs, Prp17 is not detectable at this step; however, Prp17 is present in the subsequent pre-catalytic A1 complex, containing unspliced pre-mRNA, formed after the dissociation of U4 snRNP. Thus Prp17 joins the spliceosome prior to both catalytic reactions. Our results indicate continued interactions in catalytic spliceosomes that contain reaction intermediates and in post-splicing complexes containing the lariat intron. These Prp17–spliceosome association analyses provide a biochemical basis for the delayed first step in prp17Δ and explain the previously known multiple genetic interactions between Prp17, factors of the Prp19-complex [NTC (nineteen complex)], functional elements in U2 and U5 snRNAs and other second-step splicing factors.
Collapse
|
27
|
Andersen DS, Tapon N. Drosophila MFAP1 is required for pre-mRNA processing and G2/M progression. J Biol Chem 2008; 283:31256-67. [PMID: 18765666 DOI: 10.1074/jbc.m803512200] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The mammalian spliceosome has mainly been studied using proteomics. The isolation and comparison of different splicing intermediates has revealed the dynamic association of more than 200 splicing factors with the spliceosome, relatively few of which have been studied in detail. Here, we report the characterization of the Drosophila homologue of microfibril-associated protein 1 (dMFAP1), a previously uncharacterized protein found in some human spliceosomal fractions ( Jurica, M. S., and Moore, M. J. (2003) Mol. Cell 12, 5-14 ). We show that dMFAP1 binds directly to the Drosophila homologue of Prp38p (dPrp38), a tri-small nuclear ribonucleoprotein component ( Xie, J., Beickman, K., Otte, E., and Rymond, B. C. (1998) EMBO J. 17, 2938-2946 ), and is required for pre-mRNA processing. dMFAP1, like dPrp38, is essential for viability, and our in vivo data show that cells with reduced levels of dMFAP1 or dPrp38 proliferate more slowly than normal cells and undergo apoptosis. Consistent with this, double-stranded RNA-mediated depletion of dPrp38 or dMFAP1 causes cells to arrest in G(2)/M, and this is paralleled by a reduction in mRNA levels of the mitotic phosphatase string/cdc25. Interestingly double-stranded RNA-mediated depletion of a wide range of core splicing factors elicits a similar phenotype, suggesting that the observed G(2)/M arrest might be a general consequence of interfering with spliceosome function.
Collapse
Affiliation(s)
- Ditte S Andersen
- Cancer Research UK, London Research Institute, London WC2A 3PX, UK
| | | |
Collapse
|
28
|
Tian W, Zhang LV, Taşan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 2008; 9 Suppl 1:S7. [PMID: 18613951 PMCID: PMC2447541 DOI: 10.1186/gb-2008-9-s1-s7] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Learning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling', which exploits correlation between function and other gene characteristics; and 'guilt-by-association', which transfers function from one gene to another via biological relationships. Results: We have developed a strategy ('Funckenstein') that performs guilt-by-profiling and guilt-by-association and combines the results. Using a benchmark set of functional categories and input data for protein-coding genes in Saccharomyces cerevisiae, Funckenstein was compared with a previous combined strategy. Subsequently, we applied Funckenstein to 2,455 Gene Ontology terms. In the process, we developed 2,455 guilt-by-profiling classifiers based on 8,848 gene characteristics and 12 functional linkage graphs based on 23 biological relationships. Conclusion: Funckenstein outperforms a previous combined strategy using a common benchmark dataset. The combination of 'guilt-by-profiling' and 'guilt-by-association' gave significant improvement over the component classifiers, showing the greatest synergy for the most specific functions. Performance was evaluated by cross-validation and by literature examination of the top-scoring novel predictions. These quantitative predictions should help prioritize experimental study of yeast gene functions.
Collapse
Affiliation(s)
- Weidong Tian
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Gräub R, Lancero H, Pedersen A, Chu M, Padmanabhan K, Xu XQ, Spitz P, Chalkley R, Burlingame AL, Stokoe D, Bernstein HS. Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing. Cell Cycle 2008; 7:1795-803. [PMID: 18583928 DOI: 10.4161/cc.7.12.6017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CDC5 proteins are components of the pre-mRNA splicing complex and essential for cell cycle progression in yeast, plants and mammals. Human CDC5 is phosphorylated in a mitogen-dependent manner, and its association with the spliceosome is ATP-dependent. Examination of the amino acid sequence suggests that CDC5L may be phosphorylated at up to 28 potential consensus recognition sequences for known kinases, however, the identity of actual phosphorylation sites, their role in regulating CDC5L activity, and the kinases responsible for their phosphorylation have not previously been determined. Using two-dimensional phosphopeptide mapping and nanoelectrospray mass spectrometry, we now show that CDC5L is phosphorylated on at least nine sites in vivo. We demonstrate that while CDC5L is capable of forming homodimers in vitro and in vivo, neither homodimerization nor nuclear localization is dependent on phosphorylation at these sites. Using an in vitro splicing assay, we show that phosphorylation of CDC5L at threonines 411 and 438 within recognition sequences for CDKs are required for CDC5L-mediated pre-mRNA splicing. We also demonstrate that a specific inhibitor of CDK2, CVT-313, inhibits CDC5L phosphorylation in both in vitro kinase assays and in vivo radiolabeling experiments in cycling cells. These studies represent the first demonstration of a regulatory role for phosphorylation of CDC5L, and suggest that targeting these sites or the implicated kinases may provide novel strategies for treating disorders of unguarded cellular proliferation, such as cancer.
Collapse
Affiliation(s)
- Remo Gräub
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143-0130, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Nakazawa T, Kaneko S, Miyazaki Y, Jojima T, Yamazaki T, Katsukawa S, Shishido K. Basidiomycete Lentinula edodes CDC5 and a novel interacting protein CIPB bind to a newly isolated target gene in an unusual manner. Fungal Genet Biol 2008; 45:818-28. [DOI: 10.1016/j.fgb.2008.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 02/25/2008] [Accepted: 02/25/2008] [Indexed: 11/27/2022]
|
31
|
Lin Z, Yin K, Zhu D, Chen Z, Gu H, Qu LJ. AtCDC5 regulates the G2 to M transition of the cell cycle and is critical for the function of Arabidopsis shoot apical meristem. Cell Res 2008; 17:815-28. [PMID: 17768399 DOI: 10.1038/cr.2007.71] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
As a cell cycle regulator, the Myb-related CDC5 protein was reported to be essential for the G2 phase of the cell cycle in yeast and animals, but little is known about its function in plants. Here we report the functional characterization of the CDC5 gene in Arabidopsis thaliana. Arabidopsis CDC5 (AtCDC5) is mainly expressed in tissues with high cell division activity, and is expressed throughout the entire process of embryo formation. The AtCDC5 loss-of-function mutant is embryonic lethal. In order to investigate the function of AtCDC5 in vivo, we generated AtCDC5-RNAi plants in which the expression of AtCDC5 was reduced by RNA interference. We found that the G2 to M (G2/M) phase transition was affected in the AtCDC5-RNAi plants, and that endoreduplication was increased. Additionally, the maintenance of shoot apical meristem (SAM) function was disturbed in the AtCDC5-RNAi plants, in which both the WUSCHEL (WUS)-CLAVATA (CLV) and the SHOOT MERISTEMLESS (STM) pathways were impaired. In situ hybridization analysis showed that the expression of STM was greatly reduced in the shoot apical cells of the AtCDC5-RNAi plants. Moreover, cyclinB1 or Histone4 was found to be expressed in some of these cells when the transcript of STM was undetectable. These results suggest that AtCDC5 is essential for the G2/M phase transition and may regulate the function of SAM by controlling the expression of STM and WUS.
Collapse
Affiliation(s)
- Zhiqiang Lin
- National Laboratory for Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing, China
| | | | | | | | | | | |
Collapse
|
32
|
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.
Collapse
Affiliation(s)
- Mauricio B Goldfeder
- Department of Biochemistry, Chemistry Institute, University of São Paulo, 748 Av. Prof. Lineu Prestes, São Paulo, SP, Brazil
| | | |
Collapse
|
33
|
Palma K, Zhao Q, Cheng YT, Bi D, Monaghan J, Cheng W, Zhang Y, Li X. Regulation of plant innate immunity by three proteins in a complex conserved across the plant and animal kingdoms. Genes Dev 2007; 21:1484-93. [PMID: 17575050 PMCID: PMC1891426 DOI: 10.1101/gad.1559607] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Innate immunity against pathogen infection is an evolutionarily conserved process among multicellular organisms. Arabidopsis SNC1 encodes a Resistance protein that combines attributes of multiple mammalian pattern recognition receptors. Utilizing snc1 as an autoimmune model, we identified a discrete protein complex containing at least three members--MOS4 (Modifier Of snc1, 4), AtCDC5, and PRL1 (Pleiotropic Regulatory Locus 1)--that are all essential for plant innate immunity. AtCDC5 has DNA-binding activity, suggesting that this complex probably regulates defense responses through transcriptional control. Since the complex components along with their interactions are highly conserved from fission yeast to Arabidopsis and human, they may also have a yet-to-be-identified function in mammalian innate immunity.
Collapse
Affiliation(s)
- Kristoffer Palma
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Qingguo Zhao
- National Institute of Biological Sciences (NIBS), Zhongguancun Life Science Park, Beijing 102206, People’s Republic of China
| | - Yu Ti Cheng
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Dongling Bi
- National Institute of Biological Sciences (NIBS), Zhongguancun Life Science Park, Beijing 102206, People’s Republic of China
| | - Jacqueline Monaghan
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Wei Cheng
- National Institute of Biological Sciences (NIBS), Zhongguancun Life Science Park, Beijing 102206, People’s Republic of China
| | - Yuelin Zhang
- National Institute of Biological Sciences (NIBS), Zhongguancun Life Science Park, Beijing 102206, People’s Republic of China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Corresponding author.E-MAIL ; FAX (604) 822-2114
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Liu YC, Chen HC, Wu NY, Cheng SC. A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing. Mol Cell Biol 2007; 27:5403-13. [PMID: 17515604 PMCID: PMC1952081 DOI: 10.1128/mcb.00346-07] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Prp19-associated complex (NTC) is essential for pre-mRNA splicing and is associated with the spliceosome during spliceosome activation. NTC is required for specifying interactions of U5 and U6 with pre-mRNA to stabilize their association with the spliceosome after dissociation of U4. Here, we show that a novel splicing factor, Yju2, is associated with components of NTC, and that it is required for pre-mRNA splicing both in vivo and in vitro. During spliceosome assembly, Yju2 is associated with the spliceosome at nearly the same time as NTC but is destabilized after the first catalytic reaction, whereas other NTC components remain associated until the reaction is complete. Extracts depleted of Yju2 could be complemented by recombinant Yju2, suggesting that Yju2 and NTC are not entirely in association with each other. Yju2 is not required for the binding of NTC to the spliceosome or for NTC-mediated spliceosome activation. Complementation analysis of the affinity-isolated spliceosome formed in Yju2-depleted extracts demonstrated that Yju2 acts in concert with an unidentified heat-resistant factor(s) in an ATP-independent manner to promote the first catalytic reaction of pre-mRNA splicing after Prp2-mediated structural rearrangement of the spliceosome.
Collapse
Affiliation(s)
- Yen-Chi Liu
- Institute of Microbiology Biology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | | | | | | |
Collapse
|
36
|
Behzadnia N, Golas MM, Hartmuth K, Sander B, Kastner B, Deckert J, Dube P, Will CL, Urlaub H, Stark H, Lührmann R. Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes. EMBO J 2007; 26:1737-48. [PMID: 17332742 PMCID: PMC1829389 DOI: 10.1038/sj.emboj.7601631] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Accepted: 02/02/2007] [Indexed: 11/09/2022] Open
Abstract
Little is known about the higher-order structure of prespliceosomal A complexes, in which pairing of the pre-mRNA's splice sites occurs. Here, human A complexes were isolated under physiological conditions by double-affinity selection. Purified complexes contained stoichiometric amounts of U1, U2 and pre-mRNA, and crosslinking studies indicated that these form concomitant base pairing interactions with one another. A complexes contained nearly all U1 and U2 proteins plus approximately 50 non-snRNP proteins. Unexpectedly, proteins of the hPrp19/CDC5 complex were also detected, even when A complexes were formed in the absence of U4/U6 snRNPs, demonstrating that they associate independent of the tri-snRNP. Double-affinity purification yielded structurally homogeneous A complexes as evidenced by electron microscopy, and allowed for the first time the generation of a three-dimensional structure. A complexes possess an asymmetric shape (approximately 260 x 200 x 195 angstroms) and contain a main body with various protruding elements, including a head-like domain and foot-like protrusions. Complexes isolated here are well suited for in vitro assembly studies to determine factor requirements for the A to B complex transition.
Collapse
Affiliation(s)
- Nastaran Behzadnia
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Monika M Golas
- 3D Electron Cryomicroscopy Group, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Bjoern Sander
- 3D Electron Cryomicroscopy Group, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Jochen Deckert
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Prakash Dube
- 3D Electron Cryomicroscopy Group, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, MPI of Biophysical Chemistry, Göttingen, Germany
| | - Holger Stark
- 3D Electron Cryomicroscopy Group, MPI of Biophysical Chemistry, Göttingen, Germany
- 3D Electron Cryomicroscopy Group, MPI for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany. Tel.: +49 551 2011305; Fax: +49 551 2011197; E-mail:
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany. Tel.: +49 551 2011407; Fax: +49 551 2011197; E-mail:
| |
Collapse
|
37
|
Lin Z, Yin K, Wang X, Liu M, Chen Z, Gu H, Qu LJ. Virus induced gene silencing of AtCDC5 results in accelerated cell death in Arabidopsis leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2007; 45:87-94. [PMID: 17298883 DOI: 10.1016/j.plaphy.2006.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 12/19/2006] [Indexed: 05/14/2023]
Abstract
CDC5, a Myb-related protein, is reported to be essential for the G(2) phase of cell cycle in yeast and animals, but little is known about its function in plants. In this study, Arabidopsis thaliana CDC5 (AtCDC5) is found to be nuclear localized, and the C-terminus of this protein is of transcriptional activation activity in yeast. By taking advantage of the virus induced gene silencing (VIGS) technique, we analyzed the phenotypes of the plants in which AtCDC5 is specifically silenced. The AtCDC5 VIGS plants died before bolting, in which accelerated cell death was detected. Further analysis showed that the transcripts of AtSPT and SAG13, but not SAG12, accumulated in these AtCDC5 VIGS plants, suggesting that the accelerated cell death is different from that occurred during leaf senescence. Furthermore, silencing of AtCDC5 by VIGS in either wild-type, npr1 or nahG plants all induces cell death, suggesting that SA is not crucial for the AtCDC5-associated cell death.
Collapse
Affiliation(s)
- Zhiqiang Lin
- National Laboratory for Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
38
|
Chen CH, Kao DI, Chan SP, Kao TC, Lin JY, Cheng SC. Functional links between the Prp19-associated complex, U4/U6 biogenesis, and spliceosome recycling. RNA (NEW YORK, N.Y.) 2006; 12:765-74. [PMID: 16540691 PMCID: PMC1440898 DOI: 10.1261/rna.2292106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The Prp19-associated complex, consisting of at least eight protein components, is involved in spliceosome activation by specifying the interaction of U5 and U6 with pre-mRNA for their stable association with the spliceosome after U4 dissociation. We show here that yeast cells depleted of one or two of the Prp19-associated components, accumulate the free form of U4. In NTC25-deleted cells, the level of U6 was also reduced. Extracts prepared from NTC25-deleted cells contained neither free U4 nor U6 and were ineffective in spliceosome recycling in the in vitro splicing reaction. Overexpression of U6 partially rescued the temperature-sensitive growth defect and decreased the relative amount of free U4 in NTC25-deleted cells, indicating that the accumulation of free U4 was a consequence of insufficient amounts of U6 snRNA. Extracts prepared from U6-overproducing NTC25-deleted cells containing free-form U6 were capable of spliceosome recycling, suggesting a role of free U6 RNP in spliceosome recycling. Our results demonstrate that in addition to direct participation in spliceosome activation, the Prp19-associated complex has an indirect role in spliceosome recycling through affecting the biogenesis of U4/U6 snRNP in the in vivo splicing reaction.
Collapse
Affiliation(s)
- Chun-Hong Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taiwan, Republic of China
| | | | | | | | | | | |
Collapse
|
39
|
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.
Collapse
Affiliation(s)
- Rong-Tzong Tsai
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan, Republic of China
| | | | | | | | | | | | | |
Collapse
|
40
|
Grillari J, Ajuh P, Stadler G, Löscher M, Voglauer R, Ernst W, Chusainow J, Eisenhaber F, Pokar M, Fortschegger K, Grey M, Lamond AI, Katinger H. SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly. Nucleic Acids Res 2005; 33:6868-83. [PMID: 16332694 PMCID: PMC1310963 DOI: 10.1093/nar/gki986] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 11/11/2005] [Accepted: 11/11/2005] [Indexed: 11/25/2022] Open
Abstract
We have isolated the human protein SNEV as downregulated in replicatively senescent cells. Sequence homology to the yeast splicing factor Prp19 suggested that SNEV might be the orthologue of Prp19 and therefore might also be involved in pre-mRNA splicing. We have used various approaches including gene complementation studies in yeast using a temperature sensitive mutant with a pleiotropic phenotype and SNEV immunodepletion from human HeLa nuclear extracts to determine its function. A human-yeast chimera was indeed capable of restoring the wild-type phenotype of the yeast mutant strain. In addition, immunodepletion of SNEV from human nuclear extracts resulted in a decrease of in vitro pre-mRNA splicing efficiency. Furthermore, as part of our analysis of protein-protein interactions within the CDC5L complex, we found that SNEV interacts with itself. The self-interaction domain was mapped to amino acids 56-74 in the protein's sequence and synthetic peptides derived from this region inhibit in vitro splicing by surprisingly interfering with spliceosome formation and stability. These results indicate that SNEV is the human orthologue of yeast PRP19, functions in splicing and that homo-oligomerization of SNEV in HeLa nuclear extract is essential for spliceosome assembly and that it might also be important for spliceosome stability.
Collapse
Affiliation(s)
- Johannes Grillari
- Institute of Applied Microbiology, University of Natural Resources and Applied Life Sciences Vienna, Austria Muthgasse 18, A-1190 Vienna.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Zhang N, Kaur R, Lu X, Shen X, Li L, Legerski RJ. The Pso4 mRNA splicing and DNA repair complex interacts with WRN for processing of DNA interstrand cross-links. J Biol Chem 2005; 280:40559-67. [PMID: 16223718 DOI: 10.1074/jbc.m508453200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA interstrand cross-links (ICLs) are perhaps the most formidable lesion encountered by the cellular DNA repair machinery, and the elucidation of the process by which they are removed in eukaryotic cells has proved a daunting task. In particular, the early stages of adduct recognition and uncoupling of the cross-link have remained elusive principally because genetic studies have not been highly revealing. We have developed a biochemical assay in which processing of a DNA substrate containing a site-specific psoralen ICL can be monitored in vitro. Using this assay we have shown previously that the mismatch repair factor MutSbeta, the nucleotide excision repair heterodimer Ercc1-Xpf, and the replication proteins RPA and PCNA are involved in an early stage of psoralen ICL processing. Here, we report the identification of two additional factors required in the ICL repair process, a previously characterized pre-mRNA splicing complex composed of Pso4/Prp19, Cdc5L, Plrg1, and Spf27 (Pso4 complex), and WRN the protein deficient in Werner syndrome. Analysis of the WRN protein indicates that its DNA helicase function, but not its exonuclease activity, is required for ICL processing in vitro. In addition, we show that WRN and the Pso4 complex interact through a direct physical association between WRN and Cdc5L. A putative model for uncoupling of ICLs in mammalian cells is presented.
Collapse
Affiliation(s)
- Nianxiang Zhang
- Department of Molecular Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | | | | | | | |
Collapse
|
42
|
Chan SP, Cheng SC. The Prp19-associated complex is required for specifying interactions of U5 and U6 with pre-mRNA during spliceosome activation. J Biol Chem 2005; 280:31190-9. [PMID: 15994330 DOI: 10.1074/jbc.m505060200] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activation of the spliceosome involves a major structural change in the spliceosome, including release of U1 and U4 small nuclear ribonucleoprotein particles and the addition of a large protein complex, the Prp19-associated complex. We previously showed that the Prp19-associated complex is required for stable association of U5 and U6 with the spliceosome after U4 is released. Changes within the spliceosome upon binding of the Prp19-associated complex include remodeling of the U6/5' splice site interaction and destabilization of Lsm proteins to allow further interaction of U6 with the intron sequence. Here, we further analyzed interactions of U5 and U6 with pre-mRNA at various stages of spliceosome assembly from initial binding of tri-small nuclear ribonucleoprotein complex to the activated spliceosome to reveal stepwise changes of interactions. We demonstrate that both U5 and U6 interacted with pre-mRNA in dynamic manners spanning over a large region of U6 and the 5' exon sequences prior to the activation of the spliceosome. During spliceosome activation, interactions were locked down to small regions, and the Prp19-associated complex was required for defining the specificity of interaction of U5 and U6 with the 5' splice site to stabilize their association with the spliceosome after U4 is dissociated.
Collapse
Affiliation(s)
- Shih-Peng Chan
- Institute of Molecular Biology, Academia Sinica, Nankang 115, Taiwan, Republic of China
| | | |
Collapse
|
43
|
Ohi MD, Vander Kooi CW, Rosenberg JA, Ren L, Hirsch JP, Chazin WJ, Walz T, Gould KL. Structural and functional analysis of essential pre-mRNA splicing factor Prp19p. Mol Cell Biol 2005; 25:451-60. [PMID: 15601865 PMCID: PMC538785 DOI: 10.1128/mcb.25.1.451-460.2005] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
U-box-containing Prp19p is an integral component of the Prp19p-associated complex (the nineteen complex, or NTC) that is essential for activation of the spliceosome. Prp19p makes numerous protein-protein contacts with other NTC components and is required for NTC stability. Here we show that Prp19p forms a tetramer in vitro and in vivo and we map the domain required for its oligomerization to a central tetrameric coiled-coil. Biochemical and in vivo analyses are consistent with Prp19p tetramerization providing an interaction surface for a single copy of its binding partner, Cef1p. Electron microscopy showed that the isolated Prp19p tetramer is an elongated particle consisting of four globular WD40 domains held together by a central stalk consisting of four N-terminal U-boxes and four coiled-coils. These structural and functional data provide a basis for understanding the role of Prp19p as a key architectural component of the NTC.
Collapse
Affiliation(s)
- Melanie D Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Miyazaki Y, Jojima T, Ono T, Yamazaki T, Shishido K. A cDNA homologue of Schizosaccharomyces pombe cdc5(+) from the mushroom Lentinula edodes: characterization of the cDNA and its expressed product. ACTA ACUST UNITED AC 2004; 1680:93-102. [PMID: 15488989 DOI: 10.1016/j.bbaexp.2004.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2001] [Revised: 06/02/2004] [Accepted: 08/27/2004] [Indexed: 10/26/2022]
Abstract
A cDNA homologue of Schizosaccharomyces pombe cdc5(+) was isolated from the basidiomycete mushroom Lentinula edodes and it was named Le.cdc5 cDNA. The deduced Le.CDC5 (842 amino acid residues) possessed N-terminal amino acid sequence highly homologous to those of S. pombe cdc5(+) gene product (Sp.cdc5p) and Sp.cdc5p-related proteins (SPCDC5RPs). The N-terminal 185 amino acid peptide of Le.CDC5 (Le.CDC5(1-185) peptide) produced in Escherichia coli was subjected to random binding-site selection analysis, revealing that Le.CDC5(1-185) peptide binds to a 7-bp sequence with the consensus sequence of 5'GCAATGT3' (complementary; 5'ACATTGC3'). Genomic binding-site (GBS) cloning by using Le.CDC5(1-185) peptide resulted in an isolation of the DNA fragment that contained three sets of 7-bp consensus-like sequence and TATA box. The Le.CDC5 protein contained two putative phosphorylation sites of cAMP-dependent protein kinase (A kinase) in its C-terminus. There exists a possible leucine zipper between the two phosphorylation sites. The Le.CDC5 fragment containing the two phosphorylation sites was actually phosphorylated by commercially available A kinase. Yeast two-hybrid analysis suggested the homodimerization of Le.CDC5 protein probably through the leucine zipper. Northern blot analysis showed that Le.cdc5 gene is most actively transcribed in primordia and small immature fruiting bodies of L. edodes, implying that Le.cdc5 may play a role in the beginning and early stage of fruiting-body formation.
Collapse
Affiliation(s)
- Yasumasa Miyazaki
- Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | | | | | | | | |
Collapse
|
45
|
Makarova OV, Makarov EM, Urlaub H, Will CL, Gentzel M, Wilm M, Lührmann R. A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing. EMBO J 2004; 23:2381-91. [PMID: 15175653 PMCID: PMC423283 DOI: 10.1038/sj.emboj.7600241] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 04/27/2004] [Indexed: 11/09/2022] Open
Abstract
During catalytic activation of the spliceosome, snRNP remodeling events occur, leading to the formation of a 35S U5 snRNP that contains a large group of proteins, including Prp19 and CDC5, not found in 20S U5 snRNPs. To investigate the function of 35S U5 proteins, we immunoaffinity purified human spliceosomes that had not yet undergone catalytic activation (designated BDeltaU1), which contained U2, U4, U5, and U6, but lacked U1 snRNA. Comparison of the protein compositions of BDeltaU1 and activated B* spliceosomes revealed that, whereas U4/U6 snRNP proteins are stably associated with BDeltaU1 spliceosomes, 35S U5-associated proteins (which are present in B*) are largely absent, suggesting that they are dispensable for complex B formation. Indeed, immunodepletion/complementation experiments demonstrated that a subset of 35S U5 proteins including Prp19, which form a stable heteromeric complex, are required prior to catalytic step 1 of splicing, but not for stable integration of U4/U6.U5 tri-snRNPs. Thus, comparison of the proteomes of spliceosomal complexes at defined stages can provide information as to which proteins function as a group at a particular step of splicing.
Collapse
Affiliation(s)
- Olga V Makarova
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Evgeny M Makarov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marc Gentzel
- EMBL, Bioanalytical Research Group, Heidelberg, Germany
| | - Matthias Wilm
- EMBL, Bioanalytical Research Group, Heidelberg, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Tel.: +49 551 201 1407; Fax: +49 551 201 1197; E-mail:
| |
Collapse
|
46
|
Sun X, Zhang H, Wang D, Ma D, Shen Y, Shang Y. DLP, a novel Dim1 family protein implicated in pre-mRNA splicing and cell cycle progression. J Biol Chem 2004; 279:32839-47. [PMID: 15161931 DOI: 10.1074/jbc.m402522200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, primary transcripts undergo a splicing process that removes intronic sequences by a macromolecular enzyme known as the spliceosome. Both genetic and biochemical studies have revealed that essential components of the spliceosome include five small RNAs, U1, U2, U4, U5, and U6, and as many as 300 distinct proteins. Here we report the molecular cloning and functional analysis of a novel cDNA encoding for a protein of 149 amino acids. This protein has 38% amino acid sequence identity with and is evolutionally related to yeast Dim1 protein. Hence we named this protein DLP for Dim1-like protein. We showed that DLP is required for S/G(2) transition. We also demonstrated that DLP functions in cell nucleus and interacts with the U5-102-kDa protein subunit of the spliceosome, and blocking DLP protein activity led to an insufficient pre-mRNA splicing, suggesting that DLP is yet another protein component involved in pre-mRNA splicing. Collectively, our experiments indicated that DLP is implicated in not only cell cycle progression but also in a more specific molecular process such as pre-mRNA splicing.
Collapse
MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Blotting, Western
- Cell Cycle
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/metabolism
- Cell Division
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cloning, Molecular
- Computational Biology
- DNA, Complementary/metabolism
- Genome
- Glutathione Transferase/metabolism
- HeLa Cells
- Humans
- Microscopy, Confocal
- Microscopy, Fluorescence
- Models, Genetic
- Molecular Sequence Data
- Nuclear Proteins
- Phylogeny
- Plasmids/metabolism
- Precipitin Tests
- Protein Binding
- RNA/metabolism
- RNA Splicing
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Spliceosomes/metabolism
- Transfection
- Two-Hybrid System Techniques
Collapse
Affiliation(s)
- Xiaojing Sun
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xue Yuan Road, Beijing 100083, China
| | | | | | | | | | | |
Collapse
|
47
|
Ajuh P, Lamond AI. Identification of peptide inhibitors of pre-mRNA splicing derived from the essential interaction domains of CDC5L and PLRG1. Nucleic Acids Res 2003; 31:6104-16. [PMID: 14576297 PMCID: PMC275459 DOI: 10.1093/nar/gkg817] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
CDC5L and PLRG1 are both spliceosomal proteins that are highly conserved across species. They have both been shown to be part of sub- spliceosomal protein complexes that are essential for pre-mRNA splicing in yeast and humans. CDC5L and PLRG1 interact directly in vitro. This interaction is mediated by WD40 regions in PLRG1 and the C-terminal domain of CDC5L. In order to determine whether this interaction is important for the splicing mechanism, we have designed peptides corresponding to highly conserved sequences in the interaction domains of both proteins. These peptides were used in in vitro splicing experiments as competitors to the cognate sequences in the endogenous proteins. Certain peptides derived from the binding domains of both proteins were found to inhibit in vitro splicing. This splicing inhibition could be prevented by preincubating the peptides with the corresponding partner protein that had been expressed in Escherichia coli. The results from this study indicate that the interaction between CDC5L and PLRG1 is essential for pre-mRNA splicing and further demonstrate that small peptides can be used as effective splicing inhibitors.
Collapse
Affiliation(s)
- Paul Ajuh
- The University of Dundee, School of Life Sciences, Wellcome Trust Biocentre, Dow Street, Dundee DD1 5EH, UK
| | | |
Collapse
|
48
|
Abstract
During spliceosome activation, a large structural rearrangement occurs that involves the release of two small nuclear RNAs, U1 and U4, and the addition of a protein complex associated with Prp19p. We show here that the Prp19p-associated complex is required for stable association of U5 and U6 with the spliceosome after U4 is dissociated. Ultraviolet crosslinking analysis revealed the existence of two modes of base pairing between U6 and the 5' splice site, as well as a switch of such base pairing from one to the other that required the Prp19p-associated complex during spliceosome activation. Moreover, a Prp19p-dependent structural change in U6 small nuclear ribonucleoprotein particles was detected that involves destabilization of Sm-like (Lsm) proteins to bring about interactions between the Lsm binding site of U6 and the intron sequence near the 5' splice site, indicating dynamic association of Lsm with U6 and a direct role of Lsm proteins in activation of the spliceosome.
Collapse
Affiliation(s)
- Shih-Peng Chan
- Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taiwan, Republic of China
| | | | | | | |
Collapse
|
49
|
Leonard D, Ajuh P, Lamond AI, Legerski RJ. hLodestar/HuF2 interacts with CDC5L and is involved in pre-mRNA splicing. Biochem Biophys Res Commun 2003; 308:793-801. [PMID: 12927788 DOI: 10.1016/s0006-291x(03)01486-4] [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: 11/29/2022]
Abstract
hLodestar/HuF2 belongs to the SNF2 family of proteins. This family of proteins has been shown to play a critical role in altering protein-DNA interactions in a variety of cellular contexts. We have identified an unexpected interaction between hLodestar/HuF2 and CDC5L in both the yeast two-hybrid system and HeLa nuclear extract. CDC5L is a well-characterized pre-mRNA splicing factor in yeast and humans. Our findings demonstrate that hLodestar/HuF2 associates with human splicing complexes. We also found that a truncated hLodestar/HuF2 polypeptide that overlaps with the CDC5L-binding region can inhibit pre-mRNA splicing by disrupting spliceosome assembly. These findings indicate that hLodestar/HuF2 may have a role in pre-mRNA splicing. These data are consistent with a close co-ordination of the transcription and splicing pathways in eukaryotes. Although many members of the DExH/D helicase superfamily have been linked to pre-mRNA splicing, this is the first SNF2 family member to be implicated in this pathway.
Collapse
Affiliation(s)
- Deana Leonard
- Department of Molecular Genetics, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
| | | | | | | |
Collapse
|
50
|
Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 2003; 100:8348-53. [PMID: 12826619 PMCID: PMC166232 DOI: 10.1073/pnas.0832373100] [Citation(s) in RCA: 410] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic sequencing is no longer a novelty, but gene function annotation remains a key challenge in modern biology. A variety of functional genomics experimental techniques are available, from classic methods such as affinity precipitation to advanced high-throughput techniques such as gene expression microarrays. In the future, more disparate methods will be developed, further increasing the need for integrated computational analysis of data generated by these studies. We address this problem with MAGIC (Multisource Association of Genes by Integration of Clusters), a general framework that uses formal Bayesian reasoning to integrate heterogeneous types of high-throughput biological data (such as large-scale two-hybrid screens and multiple microarray analyses) for accurate gene function prediction. The system formally incorporates expert knowledge about relative accuracies of data sources to combine them within a normative framework. MAGIC provides a belief level with its output that allows the user to vary the stringency of predictions. We applied MAGIC to Saccharomyces cerevisiae genetic and physical interactions, microarray, and transcription factor binding sites data and assessed the biological relevance of gene groupings using Gene Ontology annotations produced by the Saccharomyces Genome Database. We found that by creating functional groupings based on heterogeneous data types, MAGIC improved accuracy of the groupings compared with microarray analysis alone. We describe several of the biological gene groupings identified.
Collapse
Affiliation(s)
- Olga G. Troyanskaya
- Department of Genetics and
Saccharomyces Genome Database,
Stanford University School of Medicine, and
Department of Statistics, Stanford University,
Stanford, CA 94305
| | - Kara Dolinski
- Department of Genetics and
Saccharomyces Genome Database,
Stanford University School of Medicine, and
Department of Statistics, Stanford University,
Stanford, CA 94305
| | - Art B. Owen
- Department of Genetics and
Saccharomyces Genome Database,
Stanford University School of Medicine, and
Department of Statistics, Stanford University,
Stanford, CA 94305
| | - Russ B. Altman
- Department of Genetics and
Saccharomyces Genome Database,
Stanford University School of Medicine, and
Department of Statistics, Stanford University,
Stanford, CA 94305
- To whom correspondence may be addressed at the present
address: Lewis-Sigler Institute, Carl Icahn Laboratory, Princeton University,
Princeton, NJ 08544. E-mail:
. To
whom correspondence may be addressed at: 251 Campus Drive, MSOB X-215,
Stanford, CA 94305-5479. E-mail:
| | - David Botstein
- Department of Genetics and
Saccharomyces Genome Database,
Stanford University School of Medicine, and
Department of Statistics, Stanford University,
Stanford, CA 94305
- To whom correspondence may be addressed at the present
address: Lewis-Sigler Institute, Carl Icahn Laboratory, Princeton University,
Princeton, NJ 08544. E-mail:
. To
whom correspondence may be addressed at: 251 Campus Drive, MSOB X-215,
Stanford, CA 94305-5479. E-mail:
| |
Collapse
|