ABSTRACT
The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with â¼1.5-2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.
Subject(s)
Adenine/chemistry , Multiprotein Complexes/chemistry , Nerve Tissue Proteins/chemistry , Protein Conformation , RNA Splicing Factors/chemistry , DNA/chemistry , DNA/genetics , DNA/ultrastructure , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/genetics , Histone Demethylases/genetics , Humans , Methylation , Methyltransferases/genetics , Multiprotein Complexes/genetics , Multiprotein Complexes/ultrastructure , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/ultrastructure , Protein Domains/genetics , RNA Splicing Factors/genetics , RNA Splicing Factors/ultrastructure , RNA-Binding Proteins/geneticsABSTRACT
Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the Saccharomyces cerevisiae C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in S. cerevisiae, respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition.
Subject(s)
DEAD-box RNA Helicases/chemistry , RNA Splicing Factors/chemistry , RNA Splicing , Spliceosomes/chemistry , Amino Acid Sequence , Biocatalysis , Catalytic Domain , Cryoelectron Microscopy , DEAD-box RNA Helicases/ultrastructure , Humans , Models, Molecular , RNA Splicing Factors/ultrastructure , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/ultrastructure , Spliceosomes/ultrastructureABSTRACT
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, Bact, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release. Here we report a cryo-electron microscopy structure of the postcatalytic P complex at 3.3-angstrom resolution, revealing that the 3' ss is mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point. Furthermore, one or more unidentified proteins become stably associated with the P complex, securing the 3' exon and potentially regulating activity of the helicase Prp22. Prp22 binds nucleotides 15 to 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively.
Subject(s)
DEAD-box RNA Helicases/chemistry , Multienzyme Complexes/chemistry , RNA Splicing Factors/chemistry , RNA Splicing , Ribonucleoprotein, U4-U6 Small Nuclear/chemistry , Ribonucleoprotein, U5 Small Nuclear/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/metabolism , Spliceosomes/chemistry , Base Pairing , Biocatalysis , Catalytic Domain , Cryoelectron Microscopy , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/ultrastructure , Exons , Introns , Multienzyme Complexes/genetics , Multienzyme Complexes/ultrastructure , Mutation , Protein Conformation , RNA Splice Sites , RNA Splicing Factors/genetics , RNA Splicing Factors/ultrastructure , Ribonucleoprotein, U4-U6 Small Nuclear/genetics , Ribonucleoprotein, U4-U6 Small Nuclear/ultrastructure , Ribonucleoprotein, U5 Small Nuclear/genetics , Ribonucleoprotein, U5 Small Nuclear/ultrastructure , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/ultrastructure , Spliceosomes/ultrastructureABSTRACT
The spliceosome excises introns from pre-mRNAs in two sequential transesterifications-branching and exon ligation-catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5' exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5' splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3' exon docking, and restructures the pairing of the 5' splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3' exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C* complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.
Subject(s)
Cryoelectron Microscopy , Exons , RNA Splicing , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/metabolism , Spliceosomes/metabolism , Spliceosomes/ultrastructure , Adenosine/metabolism , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/ultrastructure , Biocatalysis , Catalytic Domain , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/ultrastructure , DEAD-box RNA Helicases/chemistry , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/ultrastructure , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/ultrastructure , Exons/genetics , Protein Binding , Protein Domains , RNA Helicases/metabolism , RNA Helicases/ultrastructure , RNA Splice Sites/genetics , RNA Splicing Factors/chemistry , RNA Splicing Factors/metabolism , RNA Splicing Factors/ultrastructure , RNA, Small Nuclear/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/ultrastructure , Ribonuclease H/chemistry , Ribonucleoprotein, U4-U6 Small Nuclear/metabolism , Ribonucleoprotein, U4-U6 Small Nuclear/ultrastructure , Ribonucleoprotein, U5 Small Nuclear/metabolism , Ribonucleoprotein, U5 Small Nuclear/ultrastructure , Ribonucleoproteins, Small Nuclear/metabolism , Ribonucleoproteins, Small Nuclear/ultrastructure , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/ultrastructure , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/ultrastructure , Spliceosomes/chemistryABSTRACT
Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.
Subject(s)
Cryoelectron Microscopy , RNA Splicing , Spliceosomes/metabolism , Spliceosomes/ultrastructure , Adenosine/metabolism , Base Sequence , Biocatalysis , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/ultrastructure , DEAD-box RNA Helicases/chemistry , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/ultrastructure , Exons/genetics , Humans , Introns/genetics , Models, Molecular , Movement , Protein Domains , RNA Splicing Factors/chemistry , RNA Splicing Factors/metabolism , RNA Splicing Factors/ultrastructure , RNA Stability , RNA, Messenger/chemistry , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/ultrastructure , Ribonuclease H/chemistry , Ribonuclease H/metabolism , Ribonucleoproteins, Small Nuclear/chemistry , Ribonucleoproteins, Small Nuclear/metabolism , Ribonucleoproteins, Small Nuclear/ultrastructure , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/enzymology , Spliceosomes/chemistryABSTRACT
Each cycle of precursor messenger RNA (pre-mRNA) splicing comprises two sequential reactions, first freeing the 5' exon and generating an intron lariat-3' exon and then ligating the two exons and releasing the intron lariat. The second reaction is executed by the step II catalytically activated spliceosome (known as the C* complex). Here, we present the cryo-electron microscopy structure of a C* complex from Saccharomyces cerevisiae at an average resolution of 4.0 angstroms. Compared with the preceding spliceosomal complex (C complex), the lariat junction has been translocated by 15 to 20 angstroms to vacate space for the incoming 3'-exon sequences. The step I splicing factors Cwc25 and Yju2 have been dissociated from the active site. Two catalytic motifs from Prp8 (the 1585 loop and the ß finger of the ribonuclease H-like domain), along with the step II splicing factors Prp17 and Prp18 and other surrounding proteins, are poised to assist the second transesterification. These structural features, together with those reported for other spliceosomal complexes, yield a near-complete mechanistic picture on the splicing cycle.
