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Journal articles on the topic 'Prp45'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Dellaire, Graham, Evgeny M. Makarov, JeffJ M. Cowger, et al. "Mammalian PRP4 Kinase Copurifies and Interacts with Components of Both the U5 snRNP and the N-CoR Deacetylase Complexes." Molecular and Cellular Biology 22, no. 14 (2002): 5141–56. http://dx.doi.org/10.1128/mcb.22.14.5141-5156.2002.

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ABSTRACT A growing body of evidence supports the coordination of pre-mRNA processing and transcriptional regulation. We demonstrate here that mammalian PRP4 kinase (PRP4K) is associated with complexes involved in both of these processes. PRP4K is implicated in pre-mRNA splicing as the homologue of the Schizosaccharomyces pombe pre-mRNA splicing kinase Prp4p, and it is enriched in SC35-containing nuclear splicing speckles. RNA interference of Caenorhabditis elegans PRP4K indicates that it is essential in metazoans. In support of a role for PRP4K in pre-mRNA splicing, we identified PRP6, SWAP, and pinin as interacting proteins and demonstrated that PRP4K is a U5 snRNP-associated kinase. In addition, BRG1 and N-CoR, components of nuclear hormone coactivator and corepressor complexes, also interact with PRP4K. PRP4K coimmunoprecipitates with N-CoR, BRG1, pinin, and PRP6, and we present data suggesting that PRP6 and BRG1 are substrates of this kinase. Lastly, PRP4K, BRG1, and PRP6 can be purified as components of the N-CoR-2 complex, and affinity-purified PRP4K/N-CoR complexes exhibit deacetylase activity. We suggest that PRP4K is an essential kinase that, in association with the both U5 snRNP and N-CoR deacetylase complexes, demonstrates a possible coordination of pre-mRNA splicing with chromatin remodeling events involved in transcriptional regulation.

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2

Figueroa, Jonine D., and Michael J. Hayman. "The human Ski-interacting protein functionally substitutes for the yeast PRP45 gene." Biochemical and Biophysical Research Communications 319, no. 4 (2004): 1105–9. http://dx.doi.org/10.1016/j.bbrc.2004.05.096.

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3

Gahura, Ondřej, Kateřina Abrhámová, Michal Skružný, et al. "Prp45 affects Prp22 partition in spliceosomal complexes and splicing efficiency of non-consensus substrates." Journal of Cellular Biochemistry 106, no. 1 (2009): 139–51. http://dx.doi.org/10.1002/jcb.21989.

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4

Martinkova, K., P. Lebduska, M. Skruzny, P. Folk, and F. Puta. "Functional Mapping of Saccharomyces cerevisiae Prp45 Identifies the SNW Domain as Essential for Viability." Journal of Biochemistry 132, no. 4 (2002): 557–63. http://dx.doi.org/10.1093/oxfordjournals.jbchem.a003257.

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5

Hálová, Martina, Ondřej Gahura, Martin Převorovský, et al. "Nineteen complex–related factor Prp45 is required for the early stages of cotranscriptional spliceosome assembly." RNA 23, no. 10 (2017): 1512–24. http://dx.doi.org/10.1261/rna.061986.117.

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6

Maddock, J. R., E. M. Weidenhammer, C. C. Adams, R. L. Lunz, and J. L. Woolford. "Extragenic suppressors of Saccharomyces cerevisiae prp4 mutations identify a negative regulator of PRP genes." Genetics 136, no. 3 (1994): 833–47. http://dx.doi.org/10.1093/genetics/136.3.833.

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Abstract The PRP4 gene encodes a protein that is a component of the U4/U6 small nuclear ribonucleoprotein particle and is necessary for both spliceosome assembly and pre-mRNA splicing. To identify genes whose products interact with the PRP4 gene or gene product, we isolated second-site suppressors of temperature-sensitive prp4 mutations. We limited ourselves to suppressors with a distinct phenotype, cold sensitivity, to facilitate analysis of mutants. Ten independent recessive suppressors were obtained that identified four complementation groups, spp41, spp42, spp43 and spp44 (suppressor of prp4, numbers 1-4). spp41-spp44 suppress the pre-mRNA splicing defect as well as the temperature-sensitive phenotype of prp4 strains. Each of these spp mutations also suppresses prp3; spp41 and spp42 suppress prp11 as well. Neither spp41 nor spp42 suppressors null alleles of prp3 or prp4, indicating that the suppression does not occur via a bypass mechanism. The spp41 and spp42 mutations are neither allele- nor gene-specific in their pattern of suppression and do not result in a defect in pre-mRNA splicing. Thus the SPP41 and SPP42 gene products are unlikely to participate directly in mRNA splicing or interact directly with Prp3p or Prp4p. Expression of PRP3-lacZ and PRP4-lacZ gene fusions is increased in spp41 strains, suggesting that wild-type Spp41p represses expression of PRP3 and PRP4. SPP41 was cloned and sequenced and found to be essential. spp43 is allelic to the previously identified suppressor srn1, which encodes a negative regulator of gene expression.

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7

Gahura, Ondrej, Anna Valentova, Katerina Abrhamova, Petr Folk, and Frantisek Puta. "Prp45, the homolog of SNW1/SKIP, functionally interacts with the DEAH‐box helicase Prp22 to affect splicing fidelity in S. cerevisiae." FASEB Journal 22, S2 (2008): 210. http://dx.doi.org/10.1096/fasebj.22.2_supplement.210.

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8

Schneider, Cornelius, Dmitry E. Agafonov, Jana Schmitzová, Klaus Hartmuth, Patrizia Fabrizio, and Reinhard Lührmann. "Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes." PLOS Genetics 11, no. 9 (2015): e1005539. http://dx.doi.org/10.1371/journal.pgen.1005539.

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9

Kao, H. Y., and P. G. Siliciano. "Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle." Molecular and Cellular Biology 16, no. 3 (1996): 960–67. http://dx.doi.org/10.1128/mcb.16.3.960.

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We have used suppressor genetics to identify factors that interact with Saccharomyces cerevisiae U1 small nuclear RNA (snRNA). In this way, we isolated PRP40-1, a suppressor that restores growth at 18 degrees C to a strain bearing a cold-sensitive mutation in U1 RNA. A gene disruption experiment shows that PRP40 is an essential gene. To study the role of PRP40 in splicing, we created a pool of temperature-sensitive prp40 strains. Primer extension analysis of intron-containing transcripts in prp40 temperature-sensitive strains reveals a splicing defect, indicating that Prp40 plays a direct role in pre-mRNA splicing. In addition, U1 RNA coimmunoprecipitates with Pro40, indicating that Prp40 is bound to the U1 small nuclear ribonucleoprotein particle in vivo. Therefore, we conclude that PRP40 encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle.

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10

Pichugin, V., S. Domnin, I. Kurapeev, and V. Bober. "Abstract PR045." Anesthesia & Analgesia 123 (September 2016): 70. http://dx.doi.org/10.1213/01.ane.0000492455.68115.b5.

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11

Dsouza, S. L., A. Kulkarni, and A. Shetty. "Abstract PR145." Anesthesia & Analgesia 123 (September 2016): 188–89. http://dx.doi.org/10.1213/01.ane.0000492548.65230.a9.

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12

Yoon, M. H., K. S. Park, J. I. Choi, and Y. O. Kim. "Abstract PR345." Anesthesia & Analgesia 123 (September 2016): 443. http://dx.doi.org/10.1213/01.ane.0000492740.56818.0a.

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13

Wang, B., K. lv, and Q. Q. Lian. "Abstract PR445." Anesthesia & Analgesia 123 (September 2016): 563. http://dx.doi.org/10.1213/01.ane.0000492832.73370.45.

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14

Mathew, J. J., and S. Gvalani. "Abstract PR545." Anesthesia & Analgesia 123 (September 2016): 691–92. http://dx.doi.org/10.1213/01.ane.0000492927.18431.10.

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15

Tsai, Rong-Tzong, Chi-Kang Tseng, Pei-Jung Lee, et al. "Dynamic Interactions of Ntr1-Ntr2 with Prp43 and with U5 Govern the Recruitment of Prp43 To Mediate Spliceosome Disassembly." Molecular and Cellular Biology 27, no. 23 (2007): 8027–37. http://dx.doi.org/10.1128/mcb.01213-07.

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ABSTRACT The Saccharomyces cerevisiae splicing factors Ntr1 (also known as Spp382) and Ntr2 form a stable complex and can further associate with DExD/H-box RNA helicase Prp43 to form a functional complex, termed the NTR complex, which catalyzes spliceosome disassembly. We show that Prp43 interacts with Ntr1-Ntr2 in a dynamic manner. The Ntr1-Ntr2 complex can also bind to the spliceosome first, before recruiting Prp43 to catalyze disassembly. Binding of Ntr1-Ntr2 or Prp43 does not require ATP, but disassembly of the spliceosome requires hydrolysis of ATP. The NTR complex also dynamically interacts with U5 snRNP. Ntr2 interacts with U5 component Brr2 and is essential for both interactions of NTR with U5 and with the spliceosome. Ntr2 alone can also bind to U5 and to the spliceosome, suggesting a role of Ntr2 in mediating the binding of NTR to the spliceosome through its interaction with U5. Our results demonstrate that dynamic interactions of NTR with U5, through the interaction of Ntr2 with Brr2, and interactions of Ntr1 and Prp43 govern the recruitment of Prp43 to the spliceosome to mediate spliceosome disassembly.

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16

Banroques, J., and J. N. Abelson. "PRP4: a protein of the yeast U4/U6 small nuclear ribonucleoprotein particle." Molecular and Cellular Biology 9, no. 9 (1989): 3710–19. http://dx.doi.org/10.1128/mcb.9.9.3710.

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The Saccharomyces cerevisiae prp mutants (prp2 through prp11) are known to be defective in pre-mRNA splicing at nonpermissive temperatures. We have sequenced the PRP4 gene and shown that it encodes a 52-kilodalton protein. We obtained PRP4 protein-specific antibodies and found that they inhibited in vitro pre-mRNA splicing, which confirms the essential role of PRP4 in splicing. Moreover, we found that PRP4 is required early in the spliceosome assembly pathway. Immunoprecipitation experiments with anti-PRP4 antibodies were used to demonstrate that PRP4 is a protein of the U4/U6 small nuclear ribonucleoprotein particle (snRNP). Furthermore, the U5 snRNP could be immunoprecipitated through snRNP-snRNP interactions in the large U4/U5/U6 complex.

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17

Banroques, J., and J. N. Abelson. "PRP4: a protein of the yeast U4/U6 small nuclear ribonucleoprotein particle." Molecular and Cellular Biology 9, no. 9 (1989): 3710–19. http://dx.doi.org/10.1128/mcb.9.9.3710-3719.1989.

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The Saccharomyces cerevisiae prp mutants (prp2 through prp11) are known to be defective in pre-mRNA splicing at nonpermissive temperatures. We have sequenced the PRP4 gene and shown that it encodes a 52-kilodalton protein. We obtained PRP4 protein-specific antibodies and found that they inhibited in vitro pre-mRNA splicing, which confirms the essential role of PRP4 in splicing. Moreover, we found that PRP4 is required early in the spliceosome assembly pathway. Immunoprecipitation experiments with anti-PRP4 antibodies were used to demonstrate that PRP4 is a protein of the U4/U6 small nuclear ribonucleoprotein particle (snRNP). Furthermore, the U5 snRNP could be immunoprecipitated through snRNP-snRNP interactions in the large U4/U5/U6 complex.

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18

Beier, David H., Tucker J. Carrocci, Clarisse van der Feltz, et al. "Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly." Nucleic Acids Research 47, no. 20 (2019): 10842–51. http://dx.doi.org/10.1093/nar/gkz765.

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Abstract The DEAD-box family of proteins are ATP-dependent, RNA-binding proteins implicated in many aspects of RNA metabolism. Pre-mRNA splicing in eukaryotes requires three DEAD-box ATPases (Prp5, Prp28 and Sub2), the molecular mechanisms of which are poorly understood. Here, we use single molecule FRET (smFRET) to study the conformational dynamics of yeast Prp5. Prp5 is essential for stable association of the U2 snRNP with the intron branch site (BS) sequence during spliceosome assembly. Our data show that the Prp5 RecA-like domains undergo a large conformational rearrangement only in response to binding of both ATP and RNA. Mutations in Prp5 impact the fidelity of BS recognition and change the conformational dynamics of the RecA-like domains. We propose that BS recognition during spliceosome assembly involves a set of coordinated conformational switches among U2 snRNP components. Spontaneous toggling of Prp5 into a stable, open conformation may be important for its release from U2 and to prevent competition between Prp5 re-binding and subsequent steps in spliceosome assembly.

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19

Montembault, Emilie, Stéphanie Dutertre, Claude Prigent, and Régis Giet. "PRP4 is a spindle assembly checkpoint protein required for MPS1, MAD1, and MAD2 localization to the kinetochores." Journal of Cell Biology 179, no. 4 (2007): 601–9. http://dx.doi.org/10.1083/jcb.200703133.

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The spindle checkpoint delays anaphase onset until every chromosome kinetochore has been efficiently captured by the mitotic spindle microtubules. In this study, we report that the human pre–messenger RNA processing 4 (PRP4) protein kinase associates with kinetochores during mitosis. PRP4 depletion by RNA interference induces mitotic acceleration. Moreover, we frequently observe lagging chromatids during anaphase leading to aneuploidy. PRP4-depleted cells do not arrest in mitosis after nocodazole treatment, indicating a spindle assembly checkpoint (SAC) failure. Thus, we find that PRP4 is necessary for recruitment or maintenance of the checkpoint proteins MPS1, MAD1, and MAD2 at the kinetochores. Our data clearly identify PRP4 as a previously unrecognized kinetochore component that is necessary to establish a functional SAC.

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20

Bjørn, S. P., A. Soltyk, J. D. Beggs, and J. D. Friesen. "PRP4 (RNA4) from Saccharomyces cerevisiae: its gene product is associated with the U4/U6 small nuclear ribonucleoprotein particle." Molecular and Cellular Biology 9, no. 9 (1989): 3698–709. http://dx.doi.org/10.1128/mcb.9.9.3698.

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The PRP4 (RNA4) gene product is involved in nuclear mRNA processing in yeast cells; we have previously cloned the gene by complementation of a temperature-sensitive mutation. Sequence and transcript analyses of the cloned gene predicted the gene product to be a 52-kilodalton protein, which was confirmed with antibodies raised against the PRP4 gene product. These antibodies inhibited precursor mRNA splicing in vitro, demonstrating a direct role of PRP4 in splicing. Immunoprecipitations with the antibodies indicated that the PRP4 protein is associated with the U4/U6 small nuclear ribonucleoprotein particle.

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21

Bjørn, S. P., A. Soltyk, J. D. Beggs, and J. D. Friesen. "PRP4 (RNA4) from Saccharomyces cerevisiae: its gene product is associated with the U4/U6 small nuclear ribonucleoprotein particle." Molecular and Cellular Biology 9, no. 9 (1989): 3698–709. http://dx.doi.org/10.1128/mcb.9.9.3698-3709.1989.

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The PRP4 (RNA4) gene product is involved in nuclear mRNA processing in yeast cells; we have previously cloned the gene by complementation of a temperature-sensitive mutation. Sequence and transcript analyses of the cloned gene predicted the gene product to be a 52-kilodalton protein, which was confirmed with antibodies raised against the PRP4 gene product. These antibodies inhibited precursor mRNA splicing in vitro, demonstrating a direct role of PRP4 in splicing. Immunoprecipitations with the antibodies indicated that the PRP4 protein is associated with the U4/U6 small nuclear ribonucleoprotein particle.

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22

Schmidt, Henning, Kathrin Richert, Robert A. Drakas, and Norbert F. Käufer. "spp42, Identified as a Classical Suppressor of prp4-73, Which Encodes a Kinase Involved in Pre-mRNA Splicing in Fission Yeast, Is a Homologue of the Splicing Factor Prp8p." Genetics 153, no. 3 (1999): 1183–91. http://dx.doi.org/10.1093/genetics/153.3.1183.

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Abstract We have identified two classical extragenic suppressors, spp41 and spp42, of the temperature sensitive (ts) allele prp4-73. The prp4+ gene of Schizosaccharomyces pombe encodes a protein kinase. Mutations in both suppressor genes suppress the growth and the pre-mRNA splicing defect of prp4-73ts at the restrictive temperature (36°). spp41 and spp42 are synthetically lethal with each other in the presence of prp4-73ts, indicating a functional relationship between spp41 and spp42. The suppressor genes were mapped on the left arm of chromosome I proximal to the his6 gene. Based on our mapping data we isolated spp42 by screening PCR fragments for functional complementation of the prp4-73ts mutant at the restrictive temperature. spp42 encodes a large protein (p275), which is the homologue of Prp8p. This protein has been shown in budding yeast and mammalian cells to be a bona fide pre-mRNA splicing factor. Taken together with other recent genetic and biochemical data, our results suggest that Prp4 kinase plays an important role in the formation of catalytic spliceosomes.

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23

Nordzieke, Steffen, Thomas Zobel, Benjamin Fränzel, Dirk A. Wolters, Ulrich Kück, and Ines Teichert. "A Fungal Sarcolemmal Membrane-Associated Protein (SLMAP) Homolog Plays a Fundamental Role in Development and Localizes to the Nuclear Envelope, Endoplasmic Reticulum, and Mitochondria." Eukaryotic Cell 14, no. 4 (2014): 345–58. http://dx.doi.org/10.1128/ec.00241-14.

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ABSTRACT S arco l emmal m embrane- a ssociated p rotein (SLMAP) is a tail-anchored protein involved in fundamental cellular processes, such as myoblast fusion, cell cycle progression, and chromosomal inheritance. Further, SLMAP misexpression is associated with endothelial dysfunctions in diabetes and cancer. SLMAP is part of the conserved str iatin- i nteracting p hosphatase a nd k inase (STRIPAK) complex required for specific signaling pathways in yeasts, filamentous fungi, insects, and mammals. In filamentous fungi, STRIPAK was initially discovered in Sordaria macrospora , a model system for fungal differentiation. Here, we functionally characterize the STRIPAK subunit PRO45, a homolog of human SLMAP. We show that PRO45 is required for sexual propagation and cell-to-cell fusion and that its f ork h ead- a ssociated (FHA) domain is essential for these processes. Protein-protein interaction studies revealed that PRO45 binds to STRIPAK subunits PRO11 and SmMOB3, which are also required for sexual propagation. Superresolution s tructured- i llumination m icroscopy (SIM) further established that PRO45 localizes to the nuclear envelope, endoplasmic reticulum, and mitochondria. SIM also showed that localization to the nuclear envelope requires STRIPAK subunits PRO11 and PRO22, whereas for mitochondria it does not. Taken together, our study provides important insights into fundamental roles of the fungal SLMAP homolog PRO45 and suggests STRIPAK-related and STRIPAK-unrelated functions.

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24

Shao, Wei, Zhan Ding, Zeng-Zhang Zheng, et al. "Prp5−Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription." Nucleic Acids Research 48, no. 11 (2020): 5799–813. http://dx.doi.org/10.1093/nar/gkaa311.

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Abstract Transcription and pre-mRNA splicing are coupled to promote gene expression and regulation. However, mechanisms by which transcription and splicing influence each other are still under investigation. The ATPase Prp5p is required for pre-spliceosome assembly and splicing proofreading at the branch-point region. From an open UV mutagenesis screen for genetic suppressors of prp5 defects and subsequent targeted testing, we identify components of the TBP-binding module of the Spt–Ada–Gcn5 Acetyltransferase (SAGA) complex, Spt8p and Spt3p. Spt8Δ and spt3Δ rescue the cold-sensitivity of prp5-GAR allele, and prp5 mutants restore growth of spt8Δ and spt3Δ strains on 6-azauracil. By chromatin immunoprecipitation (ChIP), we find that prp5 alleles decrease recruitment of RNA polymerase II (Pol II) to an intron-containing gene, which is rescued by spt8Δ. Further ChIP-seq reveals that global effects on Pol II-binding are mutually rescued by prp5-GAR and spt8Δ. Inhibited splicing caused by prp5-GAR is also restored by spt8Δ. In vitro assays indicate that Prp5p directly interacts with Spt8p, but not Spt3p. We demonstrate that Prp5p's splicing proofreading is modulated by Spt8p and Spt3p. Therefore, this study reveals that interactions between the TBP-binding module of SAGA and the spliceosomal ATPase Prp5p mediate a balance between transcription initiation/elongation and pre-spliceosome assembly.

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25

Tauchert, Marcel J., Jean-Baptiste Fourmann, Henning Christian, Reinhard Lührmann, and Ralf Ficner. "Structural and functional analysis of the RNA helicase Prp43 from the thermophilic eukaryoteChaetomium thermophilum." Acta Crystallographica Section F Structural Biology Communications 72, no. 2 (2016): 112–20. http://dx.doi.org/10.1107/s2053230x15024498.

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RNA helicases are indispensable for all organisms in each domain of life and have implications in numerous cellular processes. The DEAH-box RNA helicase Prp43 is involved in pre-mRNA splicing as well as rRNA maturation. Here, the crystal structure ofChaetomium thermophilumPrp43 at 2.9 Å resolution is revealed. Furthermore, it is demonstrated that Prp43 fromC. thermophilumis capable of functionally replacing its orthologue fromSaccharomyces cerevisiaein spliceosomal disassembly assays.

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26

Ahmed, Muhammad Bilal, Salman Ul Islam, and Young Sup Lee. "PRP4 Promotes Skin Cancer by Inhibiting Production of Melanin, Blocking Influx of Extracellular Calcium, and Remodeling Cell Actin Cytoskeleton." International Journal of Molecular Sciences 22, no. 13 (2021): 6992. http://dx.doi.org/10.3390/ijms22136992.

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Pre-mRNA processing factor 4B (PRP4) has previously been shown to induce epithelial-mesenchymal transition (EMT) and drug resistance in cancer cell lines. As melanin plays an important photoprotective role in the risk of sun-induced skin cancers, we have investigated whether PRP4 can induce drug resistance and regulate melanin biosynthesis in a murine melanoma (B16F10) cell line. Cells were incubated with a crucial melanogenesis stimulator, alpha-melanocyte-stimulating hormone, followed by transfection with PRP4. This resulted in the inhibition of the production of melanin via the downregulation of adenylyl cyclase-cyclic adenosine 3′,5′-monophosphate (AC)–(cAMP)–tyrosinase synthesis signaling pathway. Inhibition of melanin production by PRP4 leads to the promotion of carcinogenesis and induced drug resistance in B16F10 cells. Additionally, PRP4 overexpression upregulated the expression of β-arrestin 1 and desensitized the extracellular calcium-sensing receptor (CaSR), which in turn, inhibited the influx of extracellular Ca2+ ions. The decreased influx of Ca2+ was confirmed by a decreased expression level of calmodulin. We have demonstrated that transient receptor potential cation channel subfamily C member 1 was involved in the influx of CaSR-induced Ca2+ via a decreasing level of its expression. Furthermore, PRP4 overexpression downregulated the expression of AC, decreased the synthesis of cAMP, and modulated the actin cytoskeleton by inhibiting the expression of Ras homolog family member A (RhoA). Our investigation suggests that PRP4 inhibits the production of melanin in B16F10 cells, blocks the influx of Ca2+ through desensitization of CaSR, and modulates the actin cytoskeleton through downregulating the AC–cAMP pathway; taken together, these observations collectively lead to the promotion of skin carcinogenesis.

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27

Hamann, Florian, Lars C. Zimmerningkat, Robert A. Becker, et al. "The structure of Prp2 bound to RNA and ADP-BeF3−reveals structural features important for RNA unwinding by DEAH-box ATPases." Acta Crystallographica Section D Structural Biology 77, no. 4 (2021): 496–509. http://dx.doi.org/10.1107/s2059798321001194.

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Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excisedviathe spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct ofChaetomium thermophilumPrp2 was crystallized in the presence of ADP-BeF3−and a poly-U12RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3−- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.

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Robert-Paganin, Julien, Stéphane Réty, and Nicolas Leulliot. "Regulation of DEAH/RHA Helicases by G-Patch Proteins." BioMed Research International 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/931857.

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RNA helicases from the DEAH/RHA family are present in all the processes of RNA metabolism. The function of two helicases from this family, Prp2 and Prp43, is regulated by protein partners containing a G-patch domain. The G-patch is a glycine-rich domain discovered by sequence alignment, involved in protein-protein and protein-nucleic acid interaction. Although it has been shown to stimulate the helicase’s enzymatic activities, the precise role of the G-patch domain remains unclear. The role of G-patch proteins in the regulation of Prp43 activity has been studied in the two biological processes in which it is involved: splicing and ribosome biogenesis. Depending on the pathway, the activity of Prp43 is modulated by different G-patch proteins. A particular feature of the structure of DEAH/RHA helicases revealed by the Prp43 structure is the OB-fold domain in C-terminal part. The OB-fold has been shown to be a platform responsible for the interaction with G-patch proteins and RNA. Though there is still no structural data on the G-patch domain, in the current model, the interaction between the helicase, the G-patch protein, and RNA leads to a cooperative binding of RNA and conformational changes of the helicase.

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29

Xu, Y., S. Petersen-Bjørn, and J. D. Friesen. "The PRP4 (RNA4) protein of Saccharomyces cerevisiae is associated with the 5' portion of the U4 small nuclear RNA." Molecular and Cellular Biology 10, no. 3 (1990): 1217–25. http://dx.doi.org/10.1128/mcb.10.3.1217.

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We have combined oligonucleotide-directed RNase H degradation and immunoprecipitation in a study of the association of the Saccharomyces cerevisiae PRP4 protein with the U4-U6 complex. We have found that three oligonucleotides were able to direct nearly to completion the RNase H-specific cleavage of the target RNA molecules as they exist in splicing extracts. Immunoprecipitation of the degradation products with PRP4 antibody showed that the 5' portion of U4 small nuclear RNA (snRNA) and the 3' portion of U6 snRNA coimmunoprecipitated with the PRP4 protein. Micrococcal nuclease protection experiments confirmed further that the 5' portion and 3' end of U4 snRNA were very resistant to nuclease digestion, whereas the 3' portion of U6 snRNA was protected to only a very small extent. We conclude that the PRP4 protein of S. cerevisiae is associated primarily with the 5' portion of U4 snRNA in the U4-U6 small nuclear ribonucleoprotein (snRNP).

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30

Xu, Y., S. Petersen-Bjørn, and J. D. Friesen. "The PRP4 (RNA4) protein of Saccharomyces cerevisiae is associated with the 5' portion of the U4 small nuclear RNA." Molecular and Cellular Biology 10, no. 3 (1990): 1217–25. http://dx.doi.org/10.1128/mcb.10.3.1217-1225.1990.

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We have combined oligonucleotide-directed RNase H degradation and immunoprecipitation in a study of the association of the Saccharomyces cerevisiae PRP4 protein with the U4-U6 complex. We have found that three oligonucleotides were able to direct nearly to completion the RNase H-specific cleavage of the target RNA molecules as they exist in splicing extracts. Immunoprecipitation of the degradation products with PRP4 antibody showed that the 5' portion of U4 small nuclear RNA (snRNA) and the 3' portion of U6 snRNA coimmunoprecipitated with the PRP4 protein. Micrococcal nuclease protection experiments confirmed further that the 5' portion and 3' end of U4 snRNA were very resistant to nuclease digestion, whereas the 3' portion of U6 snRNA was protected to only a very small extent. We conclude that the PRP4 protein of S. cerevisiae is associated primarily with the 5' portion of U4 snRNA in the U4-U6 small nuclear ribonucleoprotein (snRNP).

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Bennett, Erin M., Andrew M. L. Lever, and Jane F. Allen. "Human Immunodeficiency Virus Type 2 Gag Interacts Specifically with PRP4, a Serine-Threonine Kinase, and Inhibits Phosphorylation of Splicing Factor SF2." Journal of Virology 78, no. 20 (2004): 11303–12. http://dx.doi.org/10.1128/jvi.78.20.11303-11312.2004.

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ABSTRACT Using a yeast two-hybrid screen of a T-cell cDNA library to identify cellular proteins that bind to the human immunodeficiency virus type 2 (HIV-2) Gag polyprotein, we identified PRP4, a serine-threonine protein kinase. Specific interaction of PRP4 and HIV-2 Gag was confirmed in in vitro and in vivo assays. The interacting region of HIV-2 Gag is located in the conserved matrix and capsid domains, while both the RS (arginine-serine-rich) domain and the KS (kinase) domain of PRP4 are able to bind to HIV-2 Gag. PRP4 is not incorporated into virus particles. HIV-2 Gag is able to inhibit PRP4-mediated phosphorylation of the splicing factor SF2. This is also observed with Gag from simian immunodeficiency virus, a closely related virus, but not with Gag from human T-cell lymphotropic virus type 1. Our results provide evidence for a novel interaction between Gag and a cellular protein kinase involved in the control of constitutive splicing in two closely related retroviruses. We hypothesize that as Gag accumulates in the cell, down regulation of splicing occurs through reduced phosphorylation of SF2. At late stages of infection, this interaction may replace the function of the early viral regulatory protein Rev.

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Leeds, Nina B., Eliza C. Small, Shawna L. Hiley, Timothy R. Hughes, and Jonathan P. Staley. "The Splicing Factor Prp43p, a DEAH Box ATPase, Functions in Ribosome Biogenesis." Molecular and Cellular Biology 26, no. 2 (2006): 513–22. http://dx.doi.org/10.1128/mcb.26.2.513-522.2006.

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ABSTRACT Biogenesis of the small and large ribosomal subunits requires modification, processing, and folding of pre-rRNA to yield mature rRNA. Here, we report that efficient biogenesis of both small- and large-subunit rRNAs requires the DEAH box ATPase Prp43p, a pre-mRNA splicing factor. By steady-state analysis, a cold-sensitive prp43 mutant accumulates 35S pre-rRNA and depletes 20S, 27S, and 7S pre-rRNAs, precursors to the small- and large-subunit rRNAs. By pulse-chase analysis, the prp43 mutant is defective in the formation of 20S and 27S pre-rRNAs and in the accumulation of 18S and 25S mature rRNAs. Wild-type Prp43p immunoprecipitates pre-rRNAs and mature rRNAs, indicating a direct role in ribosome biogenesis. The Prp43p-Q423N mutant immunoprecipitates 27SA2 pre-rRNA threefold more efficiently than the wild type, suggesting a critical role for Prp43p at the earliest stages of large-subunit biogenesis. Consistent with an early role for Prp43p in ribosome biogenesis, Prp43p immunoprecipitates the majority of snoRNAs; further, compared to the wild type, the prp43 mutant generally immunoprecipitates the snoRNAs more efficiently. In the prp43 mutant, the snoRNA snR64 fails to methylate residue C2337 in 27S pre-rRNA, suggesting a role in snoRNA function. We propose that Prp43p promotes recycling of snoRNAs and biogenesis factors during pre-rRNA processing, similar to its recycling role in pre-mRNA splicing. The dual function for Prp43p in the cell raises the possibility that ribosome biogenesis and pre-mRNA splicing may be coordinately regulated.

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Combs, D. Joshua, Roland J. Nagel, Manuel Ares, and Scott W. Stevens. "Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis." Molecular and Cellular Biology 26, no. 2 (2006): 523–34. http://dx.doi.org/10.1128/mcb.26.2.523-534.2006.

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ABSTRACT The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis.

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U. Ito, Takashi, Nobuhiko Nishida, Kazuki Ohishi, Wataru Higemoto, Yoshitomo Karaki, and Hidehiko Ishimoto. "Investigation of Bulk Superconductivity in PrPt5." Journal of the Physical Society of Japan 75, Suppl (2006): 189–91. http://dx.doi.org/10.1143/jpsjs.75s.189.

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Zhang, Zhenwei, Norbert Rigo, Olexandr Dybkov, et al. "Structural insights into how Prp5 proofreads the pre-mRNA branch site." Nature 596, no. 7871 (2021): 296–300. http://dx.doi.org/10.1038/s41586-021-03789-5.

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AbstractDuring the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex—a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. 1–4). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2–BS helix), which is proofread by Prp5 at this stage through an unclear mechanism5. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2–BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155HEAT), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155HEAT to the bulged BS-A of the U2–BS helix triggers closure of Hsh155HEAT, which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155HEAT. Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing.

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Wiseman, Colette, Luanne Freer, and Erick Hung. "Physical and Medical Characteristics of Successful and Unsuccessful Summiteers of Mount Everest in 2003." Wilderness & Environmental Medicine 17, no. 2 (2006): 103–8. http://dx.doi.org/10.1580/pr45-04.1.

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Panjwani, Usha, Lalan Thakur, Jag Parvesh Anand, et al. "Effect of l-Carnitine Supplementation on Endurance Exercise in Normobaric/Normoxic and Hypobaric/Hypoxic Conditions." Wilderness & Environmental Medicine 18, no. 3 (2007): 169–76. http://dx.doi.org/10.1580/pr45-05.1.

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38

Hoffmann, Andrea, Torsten Thimm, Marcus Dröge, Edward R. B. Moore, Jean Charles Munch, and Christoph C. Tebbe. "Intergeneric Transfer of Conjugative and Mobilizable Plasmids Harbored by Escherichia coli in the Gut of the Soil Microarthropod Folsomia candida(Collembola)." Applied and Environmental Microbiology 64, no. 7 (1998): 2652–59. http://dx.doi.org/10.1128/aem.64.7.2652-2659.1998.

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ABSTRACT The gut of the soil microarthropod Folsomia candidaprovides a habitat for a high density of bacterial cells (T. Thimm, A. Hoffmann, H. Borkott, J. C. Munch, and C. C. Tebbe, Appl. Environ. Microbiol. 64:2660–2669, 1998). We investigated whether these gut bacteria act as recipients for plasmids from Escherichia coli. Filter mating with E. coli donor cells and collected feces of F. candida revealed that the broad-host-range conjugative plasmid pRP4-luc (pRP4 with a luciferase marker gene) transferred to fecal bacteria at estimated frequencies of 5.4 × 10−1 transconjugants per donor. The mobilizable plasmid pSUP104-luc was transferred from the IncQ mobilizing strain E. coli S17-1 and less efficiently from the IncF1 mobilizing strain NM522 but not from the nonmobilizing strain HB101. When S17-1 donor strains were fed to F. candida, transconjugants of pRP4-luc and pSUP104-luc were isolated from feces. Additionally, the narrow-host-range plasmid pSUP202-luc was transferred to indigenous bacteria, which, however, could not maintain this plasmid. Inhibition experiments with nalidixic acid indicated that pRP4-luc plasmid transfer took place in the gut rather than in the feces. A remarkable diversity of transconjugants was isolated in this study: from a total of 264 transconjugants, 15 strains belonging to the alpha, beta, or gamma subclass of the class Proteobacteriawere identified by DNA sequencing of the PCR-amplified 16S rRNA genes and substrate utilization assays (Biolog). Except forAlcaligenes faecalis, which was identified by the Biolog assay, none of the isolates was identical to reference strains from data banks. This study indicates the importance of the microarthropod gut for enhanced conjugative gene transfer in soil microbial communities.

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Malhan, S., E. Oksuz, B. Antmen, C. Ar, C. Balkan, and K. Kavakli. "PRO45 NATIONAL BURDEN OF HEMOPHILIA A IN TURKEY." Value in Health 22 (November 2019): S849. http://dx.doi.org/10.1016/j.jval.2019.09.2375.

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40

Becerra, Soraya, Eduardo Andrés-León, Silvia Prieto-Sánchez, Cristina Hernández-Munain, and Carlos Suñé. "Prp40 and early events in splice site definition." Wiley Interdisciplinary Reviews: RNA 7, no. 1 (2015): 17–32. http://dx.doi.org/10.1002/wrna.1312.

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Boon, Kum-Loong, Tatsiana Auchynnikava, Gretchen Edwalds-Gilbert, et al. "Yeast Ntr1/Spp382 Mediates Prp43 Function in Postspliceosomes." Molecular and Cellular Biology 26, no. 16 (2006): 6016–23. http://dx.doi.org/10.1128/mcb.02347-05.

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ABSTRACT The Ntr1 and Ntr2 proteins of Saccharomyces cerevisiae have been reported to interact with proteins involved in pre-mRNA splicing, but their roles in the splicing process are unknown. We show here that they associate with a postsplicing complex containing the excised intron and the spliceosomal U2, U5, and U6 snRNAs, supporting a link with a late stage in the pre-mRNA splicing process. Extract from cells that had been metabolically depleted of Ntr1 has low splicing activity and accumulates the excised intron. Also, the level of U4/U6 di-snRNP is increased but those of the free U5 and U6 snRNPs are decreased in Ntr1-depleted extract, and increased levels of U2 and decreased levels of U4 are found associated with the U5 snRNP protein Prp8. These results suggest a requirement for Ntr1 for turnover of the excised intron complex and recycling of snRNPs. Ntr1 interacts directly or indirectly with the intron release factor Prp43 and is required for its association with the excised intron. We propose that Ntr1 promotes release of excised introns from splicing complexes by acting as a spliceosome receptor or RNA-targeting factor for Prp43, possibly assisted by the Ntr2 protein.

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Díaz Casas, Adalberto, Walter J. Chazin, and Belinda Pastrana-Ríos. "Prp40 Homolog A Is a Novel Centrin Target." Biophysical Journal 112, no. 12 (2017): 2529–39. http://dx.doi.org/10.1016/j.bpj.2017.03.042.

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Qiu, Rongde, Jun Zhang, and Xin Xiang. "The splicing-factor Prp40 affects dynein–dynactin function in Aspergillus nidulans." Molecular Biology of the Cell 31, no. 12 (2020): 1289–301. http://dx.doi.org/10.1091/mbc.e20-03-0166.

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We performed a genomewide mutant screen for genes affecting dynein-mediated early-endosome distribution in Aspergillus nidulans, and we unexpectedly identified Prp40A, a homologue of the yeast splicing factor Prp40. Prp40A and its higher eukaryotic homologues may represent new factors affecting the assembly and function of dynein-dynactin.

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Corkery, Dale P., Cécile Le Page, Liliane Meunier, Diane Provencher, Anne-Marie Mes-Masson, and Graham Dellaire. "PRP4K is a HER2-regulated modifier of taxane sensitivity." Cell Cycle 14, no. 7 (2015): 1059–69. http://dx.doi.org/10.1080/15384101.2015.1007775.

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Sami, Manabu, Koji Suzuki, Kanta Sakamoto, Hiroshi Kadokura, Katsuhiko Kitamoto, and Koji Yoda. "A plasmid pRH45 of Lactobacillus brevis confers hop resistance." Journal of General and Applied Microbiology 44, no. 5 (1998): 361–63. http://dx.doi.org/10.2323/jgam.44.361.

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Kulaeva, Olga A., Emma S. Gribchenko, Evgeny A. Zorin, Marina S. Kliukova, and Vladimir A. Zhukov. "Comparative analysis of the expression of stress-related genes in two pea genotypes contrasting in tolerance to cadmium." Ecological genetics 16, no. 4 (2018): 75–84. http://dx.doi.org/10.17816/ecogen16475-84.

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Background. A major problem of the environmental pollution with heavy metals, including cadmium, requires an intensive study of the molecular and genetic mechanisms underlying the tolerance of plants to these toxic substances. In this study we present a comparative analysis of the expression of stress-related genes in two pea genotypes contrasting in tolerance to cadmium. Materials and methods. A unique mutant of pea SGECdt, characterized by the increased tolerance to cadmium, and initial line SGE were used. Gene expression was analyzed by Real Time PCR. Results. In the line SGE cadmium increase the expression of genes, encoding catalase, chitinase, chitinase-like protein PRP4A and dirigent protein PI206. In the mutant SGECdt cadmium increase the expression of genes, encoding chitinase, glutathione reductase and defensin DRR230. In control samples expression of genes encoding PRP4A and DRRR230 was enhanced in mutant SGECdt versus line SGE. Conclusion. It was shown that, the reaction of the mutant SGECdt at the molecular level differs from that of the line SGE. In the mutant SGECdt, a change in the expression of a number of genes is observed, which may indicate that cadmium entering the cell causes activation of defense reactions.

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Kudlinzki, Denis, Andreas Schmitt, Henning Christian, and Ralf Ficner. "Structural analysis of the C-terminal domain of the spliceosomal helicase Prp22." Biological Chemistry 393, no. 10 (2012): 1131–40. http://dx.doi.org/10.1515/hsz-2012-0158.

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Abstract Splicing of pre-mRNA requires the activity of at least eight different DEAD/H-box proteins that are involved in distinct steps of the splicing process. These proteins are driving the spliceosomal machinery by ATP-dependent unwinding of dsRNA and/or disrupting protein-RNA complexes. The spliceosomal DEAH-box proteins Prp2, Prp16, Prp22 and Prp43 share homologous C-terminal domains (CTD). We have determined the crystal structure of the CTD of human Prp22 by means of MAD. The fold of the human Prp22-CTD closely resembles that of the yeast Prp43-CTD. The similarity of these helicase-associated CTDs to the winged-helix and ratchet domains of the DNA helicase Hel308 suggests an analogous function in dsRNA binding and unwinding. Here, we also demonstrate that the CTD has a significant impact on the ATPase activity of yPrp22 in vitro. Homology modeling of the CTDs of hPrp2, hPrp16 and hPrp43 suggests that the CTDs of spliceosomal helicases contain conserved positively charged patches on their surfaces representing a common RNA-binding surface as well as divergent regions most likely mediating specific interactions with different proteins of the spliceosome.

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Murakami, Karin, Kenji Nakano, Toshiyuki Shimizu, and Umeharu Ohto. "The crystal structure of human DEAH-box RNA helicase 15 reveals a domain organization of the mammalian DEAH/RHA family." Acta Crystallographica Section F Structural Biology Communications 73, no. 6 (2017): 347–55. http://dx.doi.org/10.1107/s2053230x17007336.

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DEAH-box RNA helicase 15 (DHX15) plays important roles in RNA metabolism, including in splicing and in ribosome biogenesis. In addition, mammalian DHX15 also mediates the innate immune sensing of viral RNA. However, structural information on this protein is not available, although the structure of the fungal orthologue of this protein, Prp43, has been elucidated. Here, the crystal structure of the ADP-bound form of human DHX15 is reported at a resolution of 2.0 Å. This is the first structure to be revealed of a member of the mammalian DEAH-box RNA helicase (DEAH/RHA) family in a nearly complete form, including the catalytic core consisting of the two N-terminal RecA domains and the C-terminal regulatory domains (CTD). The ADP-bound form of DHX15 displayed a compact structure, in which the RecA domains made extensive contacts with the CTD. Notably, a potential RNA-binding site was found on the surface of a RecA domain with positive electrostatic potential. Almost all structural features were conserved between the fungal Prp43 and the human DHX15, suggesting that they share a fundamentally common mechanism of action and providing a better understanding of the specific mammalian functions of DHX15.

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Kojima, Tatsuya, Takeru Zama, Kazuhiro Wada, Hiroshi Onogi, and Masatoshi Hagiwara. "Cloning of Human PRP4 Reveals Interaction with Clk1." Journal of Biological Chemistry 276, no. 34 (2001): 32247–56. http://dx.doi.org/10.1074/jbc.m103790200.

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Chen, Hsin-Chou, Chi-Kang Tseng, Rong-Tzong Tsai, Che-Sheng Chung, and Soo-Chen Cheng. "Link of NTR-Mediated Spliceosome Disassembly with DEAH-Box ATPases Prp2, Prp16, and Prp22." Molecular and Cellular Biology 33, no. 3 (2012): 514–25. http://dx.doi.org/10.1128/mcb.01093-12.

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ABSTRACTThe DEAH-box ATPase Prp43 is required for disassembly of the spliceosome after the completion of splicing or after the discard of the spliceosome due to a splicing defect. Prp43 associates with Ntr1 and Ntr2 to form the NTR complex and is recruited to the spliceosome via the interaction of Ntr2 and U5 component Brr2. Ntr2 alone can bind to U5 and to the spliceosome. To understand how NTR might mediate the disassembly of spliceosome intermediates, we arrested the spliceosome at various stages of the assembly pathway and assessed its susceptibility to disassembly. We found that NTR could catalyze the disassembly of affinity-purified spliceosomes arrested specifically after the ATP-dependent action of DEAH-box ATPase Prp2, Prp16, or Prp22 but not at steps before the action of these ATPases or upon their binding to the spliceosome. These results link spliceosome disassembly to the functioning of splicing ATPases. Analysis of the binding of Ntr2 to each splicing complex has revealed that the presence of Prp16 and Slu7, which also interact with Brr2, has a negative impact on Ntr2 binding. Our study provides insights into the mechanism by which NTR can be recruited to the spliceosome to mediate the disassembly of spliceosome intermediates when the spliceosome pathway is retarded, while disassembly is prevented in normal reactions.

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