Prp24: Difference between revisions
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< | <StructureSection load='2ghp' size='450' side='right' scene='Sandbox_Reserved_340/2ghp/1' caption='Yeast N-terminal 3 RNA binding domains of splicing factor Prp24 (PDB code [[2ghp]]).'> | ||
'''Prp24''' ('''Pr'''e-mRNA splicing '''P'''rotein '''24''') is a [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae ''Saccharomyces cerevisiae''] yeast protein that functions in the formation of base pair interactions between the [http://en.wikipedia.org/wiki/U6_spliceosomal_RNA U6] and [http://en.wikipedia.org/wiki/U4_spliceosomal_RNA U4] [http://en.wikipedia.org/wiki/SnRNP snRNPs (small nuclear ribonucleoproteins)] to form the U4/U6 di-snRNP during the assembly of the [http://en.wikipedia.org/wiki/Spliceosome spliceosome] <ref name="Bae">PMID:17320109</ref>. This protein contains four RNA recognition motifs (RRMs) that function in the binding of Prp24 to U6 snRNA <ref name="Bae"/>. These RRM domains are conserved in structure and sequence in proteins orthologous to Prp24 in ''Homo sapiens'' and ''Schizosaccharomyces pombe'', as well as in other proteins containing RRMs <ref name="Rader">PMID:12458792</ref>. | '''Prp24''' ('''Pr'''e-mRNA splicing '''P'''rotein '''24''') is a [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae ''Saccharomyces cerevisiae''] yeast protein that functions in the formation of base pair interactions between the [http://en.wikipedia.org/wiki/U6_spliceosomal_RNA U6] and [http://en.wikipedia.org/wiki/U4_spliceosomal_RNA U4] [http://en.wikipedia.org/wiki/SnRNP snRNPs (small nuclear ribonucleoproteins)] to form the U4/U6 di-snRNP during the assembly of the [http://en.wikipedia.org/wiki/Spliceosome spliceosome] <ref name="Bae">PMID:17320109</ref>. This protein contains four RNA recognition motifs (RRMs) that function in the binding of Prp24 to U6 snRNA <ref name="Bae"/>. These RRM domains are conserved in structure and sequence in proteins orthologous to Prp24 in ''Homo sapiens'' and ''Schizosaccharomyces pombe'', as well as in other proteins containing RRMs <ref name="Rader">PMID:12458792</ref>. | ||
== Introduction == | == Introduction == | ||
[[Image:Spliceosome.jpg |frame|left| Figure 1. Assembly and disassembly of the spliceosome in ''Saccharomyces cerevisiae'' (after Staley and Guthrie 1998 <ref name="Staley"/>)]] | |||
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[[Image:Transester.jpg |frame|left| Figure 2. The transesterificiation reactions of pre-mRNA splicing (after Brow 2002<ref name="Brow review"/>) ]] | |||
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=== Pre-mRNA Splicing === | |||
Pre-mRNA splicing is an essential process in eukaryotes that removes non-coding introns from a pre-mRNA transcript and splices coding exons together before the mRNA is exported from the nucleus for translation into a protein<ref name="Staley">PMID:9476892</ref>. Splicing requires five snRNPs (U1, U2, U4, U5, U6), several other proteins, and the input of energy from ATP. The U1 and U2 snRNPs assemble individually on the pre-mRNA transcript, while U4 and U6 form a U4/U6 di-snRNP before interacting with U5 to form a U4/U6.U5 tri-snRNP that combines with U1 and U2 at the pre-mRNA transcript (Fig 1)<ref name="Staley"/>. U4 and U1 then depart, and after conformational changes and base pair formation with the pre-mRNA the remaining snRNPs form the catalytically active spliceosome<ref name="Staley"/>. Two transesterification reactions then occur; the first reaction is the nucleophillic attack of the phosphate group at the end of the 5' exon by the 2' hydroxyl of a specific adenosine at the branch point sequence of the intron (Fig 2)<ref name="Brow review">PMID:12429696</ref>. This is then followed by the nucleophillic attack of the phosphate group linking the 3' exon to the intron by the 3' hydroxyl of the 5' exon<ref name="Brow review"/>. These splicing reactions, as well as the addition of 7-methylguanosine 5' cap and a 3' polyadenosine tail, results in a mature mRNA transcript that can be exported from the nucleus and translated into a protein. | |||
Pre-mRNA splicing is an essential process in eukaryotes that removes non-coding introns from a pre-mRNA transcript and splices coding exons together before the mRNA is exported from the nucleus for translation into a protein<ref name="Staley">PMID:9476892</ref>. Splicing requires five snRNPs (U1, U2, U4, U5, U6), several other proteins, and the input of energy from ATP. The U1 and U2 snRNPs assemble individually on the pre-mRNA transcript, while U4 and U6 form a U4/U6 di-snRNP before interacting with U5 to form a U4/U6.U5 tri-snRNP that combines with U1 and U2 at the pre-mRNA transcript (Fig 1)<ref name="Staley"/>. U4 and U1 then depart, and after conformational changes and base pair formation with the pre-mRNA the remaining snRNPs form the catalytically active spliceosome<ref name="Staley"/>. Two transesterification reactions then occur; the first reaction is the nucleophillic attack of the phosphate group at the end of the 5' exon by the 2' hydroxyl of a specific adenosine at the branch point sequence of the intron (Fig 2)<ref name="Brow review">PMID:12429696</ref>. | |||
===U6 and U4 snRNPs=== | ===U6 and U4 snRNPs=== | ||
U6 is considered to be one of the most catalytically important snRNAs in the spliceosome, as it interacts directly with the 5' splice site through base pairing <ref name="Fortner">PMID:8299941</ref>. It is thought to undergo three conformational changes throughout the entire process of splicing and splicesome assembly; it exists as one conformation as free U6 snRNP, another as part of the U4/U6 di-snRNP and as a third when associated with U2 and the pre-mRNA <ref name="Jandrositz">PMID:7882985</ref>. In addition to Prp24, U6 is associated with seven other proteins, Lsm 2-8, which form a ring around the 3' portion of the U6 snRNA <ref name="Karaduman2008">PMID:18971323</ref>. | U6 is considered to be one of the most catalytically important snRNAs in the spliceosome, as it interacts directly with the 5' splice site through base pairing <ref name="Fortner">PMID:8299941</ref>. It is thought to undergo three conformational changes throughout the entire process of splicing and splicesome assembly; it exists as one conformation as free U6 snRNP, another as part of the U4/U6 di-snRNP and as a third when associated with U2 and the pre-mRNA <ref name="Jandrositz">PMID:7882985</ref> <ref name="Dunn">PMID:20659011</ref>. In addition to Prp24, U6 is associated with seven other proteins, Lsm 2-8, which form a ring around the 3' portion of the U6 snRNA <ref name="Karaduman2008">PMID:18971323</ref>. | ||
The U4 snRNA is thought to be non-catalytic because it leaves the spliceosome before the transesterification reactions occur <ref name="Staley"/>. Its function is instead thought to be aiding U6 in maintaining a conformation that will enable it to interact with U2 and the 5' splice site <ref name="Madhani">PMID:2149118</ref>. The U4 snRNP contains the U4 snRNA, a ring complex of the Sm proteins B-G, and the proteins Prp3, Prp4, and Snu13 <ref name="Brow review"/>. | The U4 snRNA is thought to be non-catalytic because it leaves the spliceosome before the transesterification reactions occur <ref name="Staley"/>. Its function is instead thought to be aiding U6 in maintaining a conformation that will enable it to interact with U2 and the 5' splice site <ref name="Madhani">PMID:2149118</ref>. The U4 snRNP contains the U4 snRNA, a ring complex of the Sm proteins B-G, and the proteins Prp3, Prp4, and Snu13 <ref name="Brow review"/>. | ||
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===Role of Prp24 in Splicing=== | ===Role of Prp24 in Splicing=== | ||
Prp24 is a U6 snNRP protein that functions in the annealing of the U4 and U6 snRNPs during the assembly of the spliceosome. This protein was first identified in a genetic screen as mutated gene that caused an accumulation of pre-mRNA <ref name="Vij">PMID:2676722</ref>. Its first functional role was suggested after several mutant forms of the protein were found to suppress a cold sensitive growth defect caused by mutations in the U4 snRNA <ref name="Shannon">PMID:1827420</ref>. It is thought that Prp24 helps to stabilize the U6 snRNA and hold it in a conformation that promotes base pairing interactions with the U4 snRNA to form the stem I and stem II structures of the U4/U6 di-snRNP <ref name="Vidaver">PMID:10545453</ref>. Although Prp24 departs from the U4/U6 complex before the formation of the U4/U6.U5 tri-snRNP, it has been suggested that Prp24 may also play a role in the dissociation of U4 from U6 during the base pairing of U6 with U2 and the 5' splice site <ref name="Vaidya">Vaidya V, Vijayraghavan U. Prp21, a U2-snRNP-associated protein, and Prp24, a U6-snRNP-associated protein, functionally interact during spliceosome assembly. J Genet. 1998 Dec; 77(3):85-94</ref>. This additional role for Prp24, however, has not been sufficiently supported experimentally. | Prp24 is a U6 snNRP protein that functions in the annealing of the U4 and U6 snRNPs during the assembly of the spliceosome. This protein was first identified in a genetic screen as a mutated gene that caused an accumulation of pre-mRNA <ref name="Vij">PMID:2676722</ref>. Its first functional role was suggested after several mutant forms of the protein were found to suppress a cold sensitive growth defect caused by mutations in the U4 snRNA <ref name="Shannon">PMID:1827420</ref>. It is thought that Prp24 helps to stabilize the U6 snRNA and hold it in a conformation that promotes base pairing interactions with the U4 snRNA to form the stem I and stem II structures of the U4/U6 di-snRNP <ref name="Vidaver">PMID:10545453</ref>. Although Prp24 departs from the U4/U6 complex before the formation of the U4/U6.U5 tri-snRNP, it has been suggested that Prp24 may also play a role in the dissociation of U4 from U6 during the base pairing of U6 with U2 and the 5' splice site <ref name="Vaidya">Vaidya V, Vijayraghavan U. Prp21, a U2-snRNP-associated protein, and Prp24, a U6-snRNP-associated protein, functionally interact during spliceosome assembly. J Genet. 1998 Dec; 77(3):85-94</ref>. This additional role for Prp24, however, has not been sufficiently supported experimentally. | ||
== Structure == | == Structure == | ||
The key structural elements of Prp24 are the conserved RNA recognition motifs (RRMs). These motifs are found in many proteins with RNA binding properties and contain conserved RNP elements that are recognizable by their primary sequence <ref name="Shannon"/>. For several years, Prp24 was thought to contain three RRMs, termed RRM 1, RRM 2, and RRM 3 <ref name="Shannon"/>. However, analysis of homologs of Prp24 from several different species allowed the identification of a fourth RRM in Prp24 of ''S. cerevisiae'', albeit one that was much less highly conserved and not easily recognizable by its RNP-consensus domain <ref name="Rader"/>. | The key structural elements of Prp24 are the conserved RNA recognition motifs (RRMs). These motifs are found in many proteins with RNA binding properties and contain conserved RNP elements that are recognizable by their primary sequence <ref name="Shannon"/>. For several years, Prp24 was thought to contain three RRMs, termed RRM 1, RRM 2, and RRM 3 <ref name="Shannon"/>. However, analysis of homologs of Prp24 from several different species allowed the identification of a fourth RRM in Prp24 of ''S. cerevisiae'', albeit one that was much less highly conserved and not easily recognizable by its RNP-consensus domain <ref name="Rader"/>. | ||
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U6 is arguably the most structurally dynamic snRNA involved in the splicing process, seemingly undergoing at least three different structures: it exists in one conformation as free U6 snRNP, another when base paired in the U4/U6 di-snRNP, and a third in base pairing interactions with U2 and the 5' splice site <ref name="Jandrositz"/>. One large role suggested for Prp24 has been in assisting in the conformational changes between the free U6 structure and the U4/U6 conformation. | U6 is arguably the most structurally dynamic snRNA involved in the splicing process, seemingly undergoing at least three different structures: it exists in one conformation as free U6 snRNP, another when base paired in the U4/U6 di-snRNP, and a third in base pairing interactions with U2 and the 5' splice site <ref name="Jandrositz"/>. One large role suggested for Prp24 has been in assisting in the conformational changes between the free U6 structure and the U4/U6 conformation. | ||
Prp24 co-immunoprecipitates with free U6 and U4/U6 di-snRNP, indicating that it is closely associated with these | Prp24 co-immunoprecipitates with free U6 and U4/U6 di-snRNP, indicating that it is closely associated with these particles <ref name="Shannon"/><ref name="Ghetti">PMID:7585243</ref>. Initial investigation of the structure showed that Prp24 very likely binds directly to the 40-43 nucleotides of U6 based on chemical modification of naked U6 snRNA compared to free U6 snRNP<ref name="Jandrositz"/>. Further investigation suggested that Prp24 binds within the 30-56 nucleotide region of free U6, as well as to stem II of U4/U6 in the 39-56 and 67-70 nucleotide regions of U6 <ref name="Ghetti"/>. | ||
The main function of Prp24 seems to be directly related to formation of the U4/U6 complex, particularly based on the evidence that Prp24 is present in U6 and U4/U6, but not U4/U6.U5 <ref name="Shannon"/><ref name="Ghetti"/><ref name="Jandrositz"/>. Prp24 greatly increases the rate and efficiency of U4/U6 annealing <ref name="Raghunathan">PMID:9452384</ref> and mutations in Prp24 have been shown to prevent the formation of the U4/U6 di-snRNP <ref name="Lygerou">PMID:10022888</ref>. Although the exact mechanism by which Prp24 promotes annealing of U4 and U6 is not known, it has been suggested that Prp24 may stabilize the secondary structure of U6 to allow it to interact with U4 in order to allow formation of U4/U6 <ref name="Vidaver"/>. | The main function of Prp24 seems to be directly related to formation of the U4/U6 complex, particularly based on the evidence that Prp24 is present in U6 and U4/U6, but not U4/U6.U5 <ref name="Shannon"/><ref name="Ghetti"/><ref name="Jandrositz"/>. Prp24 greatly increases the rate and efficiency of U4/U6 annealing <ref name="Raghunathan">PMID:9452384</ref> and mutations in Prp24 have been shown to prevent the formation of the U4/U6 di-snRNP <ref name="Lygerou">PMID:10022888</ref>. Although the exact mechanism by which Prp24 promotes annealing of U4 and U6 is not known, it has been suggested that Prp24 may stabilize the secondary structure of U6 to allow it to interact with U4 in order to allow formation of U4/U6 <ref name="Vidaver"/>. | ||
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Several additional roles for Prp24 have been suggested in spliceosome assembly/disassembly, although nothing has been sufficiently supported. A genetic interaction in which Prp24 mutation suppressed a Prp21 (a component of the U2 snRNP) mutation suggested that the two proteins may interact during the base pairing of U2 and U6 at the 5' splice site; however, further investigation failed to produce evidence of a definite interaction between the two proteins, although the authors maintained that a transient interaction between Prp24 and Prp21 may exist in an intermediate form of the assembling spliceosome <ref name="Vaidya"/>. It has also been suggested that Prp24 may also assist in the formation of U4/U5.U6 <ref name="Ryan">PMID:12212846</ref> or in the destabilization of U6 from U2 upon completion of splicing to release free U6 snRNP,<ref name="Vidaver"/>, but there is insufficient evidence to conclusively support these functions of Prp24. | Several additional roles for Prp24 have been suggested in spliceosome assembly/disassembly, although nothing has been sufficiently supported. A genetic interaction in which Prp24 mutation suppressed a Prp21 (a component of the U2 snRNP) mutation suggested that the two proteins may interact during the base pairing of U2 and U6 at the 5' splice site; however, further investigation failed to produce evidence of a definite interaction between the two proteins, although the authors maintained that a transient interaction between Prp24 and Prp21 may exist in an intermediate form of the assembling spliceosome <ref name="Vaidya"/>. It has also been suggested that Prp24 may also assist in the formation of U4/U5.U6 <ref name="Ryan">PMID:12212846</ref> or in the destabilization of U6 from U2 upon completion of splicing to release free U6 snRNP,<ref name="Vidaver"/>, but there is insufficient evidence to conclusively support these functions of Prp24. | ||
</StructureSection> | |||
__NOTOC__ | |||
==3D structures of pre-mRNA-splicing factors== | |||
[[pre-mRNA-splicing factor]] | |||
== References == | == References == | ||
<references/> | <references/> | ||