Spliceosomal immunophilins

Mesa, Annia; Somarelli, Jason A.; Herrera, René J.

doi:10.1016/j.febslet.2008.06.006

Cited by 22 publications

(23 citation statements)

References 52 publications

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“…While there are several reports of cyclophilin and parvulin isomerases being linked to mRNA splicing (62), FKBP25 is so far the only FKBP family member that has demonstrated direct binding to RNA, and is the only prolyl isomerase shown to bind dsRNA. Interestingly, two cyclophilin prolyl isomerases are able to bind ssRNA due to an auxiliary RNA recognition motif (RRM) domain.…”

Section: Discussionmentioning

confidence: 99%

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

Dilworth¹,

Upadhyay²,

Bonnafous³

et al. 2017

Nucleic Acids Research

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Prolyl isomerases are defined by a catalytic domain that facilitates the cis–trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets.

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Section: Discussionmentioning

confidence: 99%

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

Dilworth¹,

Upadhyay²,

Bonnafous³

et al. 2017

Nucleic Acids Research

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“…Cyclophilins in Pre-mRNA Splicing-Human spliceosomes contain at least eight cyclophilin family proteins (3,45), and they are recruited at different stages during splicing. Cyclophilins are PPIases.…”

Section: Mansoni and Skip In Aedes Aegypti Bos Taurus Caenorhabditmentioning

confidence: 99%

A Large Intrinsically Disordered Region in SKIP and Its Disorder-Order Transition Induced by PPIL1 Binding Revealed by NMR

Wang

Zhang

et al. 2010

Journal of Biological Chemistry

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Pre-mRNA splicing, the removal of introns from mRNA precursors, is a dynamic process and requires many conformational rearrangements (1). It is catalyzed by the spliceosome, which is a large machine formed by ordered interactions of several small nuclear ribonucleoproteins (snRNPs), 3 U1, U2, U5, and U4/U6, and numerous other less stably associated nonsnRNP splicing factors (2). The assembly of the spliceosome goes through many intermediate stages. The stable intermediate complexes are the A, B, and C complexes. After the complex A is formed by pre-mRNA binding to the U1 and U2, it recruits U4/U6⅐U5 tri-snRNP, forming the B complex. The B complex is still inactive and requires conformational and compositional rearrangements to form active spliceosome, complex B* (3). Complex B* undergoes the first catalytic step of splicing to generate complex C. After additional rearrangements occur in the spliceosomal RNP network (4), complex C undergoes a second catalytic step and releases the mRNA.Mass spectrometric analyses of the human A (5), B (6, 7), B* (8), and C (7) complexes indicate that there are dramatic changes in protein content during splicing. For example, in the A complex to B complex transition, ϳ25 proteins are recruited and more than 35 non-snRNP proteins associated. These include the Prp19⅐CDC5 complex and Prp19-related factors. Subunits of these become more stably integrated in the B* complex (8, 9). Recently, Bessonov et al. (7) purified the catalytically active C complex and identified its stable RNP core, which constituted with Prp19⅐CDC5 and Prp19-related factors. Ski interaction protein (SKIP) and peptidylprolyl isomerase-like protein 1 (PPIL1) belong to Prp19-related factors and are included in this stable RNP core. Both of them are believed to be involved in the activation of the spliceosome (2,8,9).Human SKIP (536 residues) is colocalized with SC35, a splicing factor at nuclear speckles (11). Expression of a dominant negative SKIP (residues 87-342 of SKIP) results in a 1,25-(OH) 2 D 3 -dependent transient accumulation of the unspliced transcripts (12), indicting that SKIP influences pre-mRNA splicing. Nagai et al. (13) reported that SKIP affected the splicing of a natural gene product, the downstream intron, and aber-* This work was supported by the Chinese National Fundamental Research Project (Grants 2006CB806507, 2006CB910201, 2002CB713806, and 2006AA02A315) and the Chinese National Natural Science Foundation (Grants 30121001, 30570361, and 30830031

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“…In fact, a recent mass spectroscopy analysis of B and C spliceosomal complexes purified from Drosophila melanogaster indicates that many of the proteins identified in the Bombyx mori genome are, in fact, part of the Drosophila melanogaster spliceosome (Herold et al, 2009). The spliceosomal B1 complex is made up of the U1 snRNP, U2 snRNP, and U4/U6.U5 tri-snRNP (Moore and Sharp, 1993;Mesa et al, 2008). Seven Sm core proteins each bind as heptameric rings to U1, U2, U4, and U5 (Jurica and Moore, 2003).…”

Section: Discussionmentioning

confidence: 99%

“…Seven Sm core proteins each bind as heptameric rings to U1, U2, U4, and U5 (Jurica and Moore, 2003). In the B2 and C assemblies, U1 and U4 detach from the spliceosome with U2, U5, and U6 remaining to carry out the final transesterification reaction (Mesa et al, 2008). In addition to the core RNPs, a series of additional splicing factors make up the B and C complexes, including SR proteins, hnRNPs, and a variety of tissueand/or developmental stage-specific proteins (Stickeler et al, 1999;Matsui et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

Genome‐based identification of spliceosomal proteins in the silk moth Bombyx mori

Somarelli

Mesa

Fuller

et al. 2010

Arch Insect Biochem Physiol

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Pre-messenger RNA splicing is a highly conserved eukaryotic cellular function that takes place by way of a large, RNA-protein assembly known as the spliceosome. In the mammalian system, nearly 300 proteins associate with uridine-rich small nuclear (sn)RNAs to form this complex. Some of these splicing factors are ubiquitously present in the spliceosome, whereas others are involved only in the processing of specific transcripts. Several proteomics analyses have delineated the proteins of the spliceosome in several species. In this study, we mine multiple sequence data sets of the silk moth Bombyx mori in an attempt to identify the entire set of known spliceosomal proteins. Five data sets were utilized, including the 3X, 6X, and Build 2.0 genomic contigs as well as the expressed sequence tag and protein libraries. While homologs for 88% of vertebrate splicing factors were delineated in the Bombyx mori genome, there appear to be several spliceosomal polypeptides absent in Bombyx mori and seven additional insect species. This apparent increase in spliceosomal complexity in vertebrates may reflect the tissue-specific and developmental stage-specific alternative pre-mRNA splicing requirements in vertebrates. Phylogenetic analyses of 15 eukaryotic taxa using the core splicing factors suggest that the essential functional units of the pre-mRNA processing machinery have remained highly conserved from yeast to humans. The Sm and LSm proteins are the most conserved, whereas proteins of the U1 small nuclear ribonucleoprotein particle are the most divergent. These data highlight both the differential conservation and relative phylogenetic signals of the essential spliceosomal components throughout evolution.

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Spliceosomal immunophilins

Cited by 22 publications

References 52 publications

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

A Large Intrinsically Disordered Region in SKIP and Its Disorder-Order Transition Induced by PPIL1 Binding Revealed by NMR

Genome‐based identification of spliceosomal proteins in the silk moth Bombyx mori

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