Prp8 in a Reduced Spliceosome Lacks a Conserved Toggle that Correlates with Splicing Complexity across Diverse Taxa

Garside, E.L.; Whelan, Thomas A.; Stark, Martha R.; Rader, Stephen D.; Fast, Naomi M.; MacMillan, Andrew M.

doi:10.1016/j.jmb.2019.04.047

Cited by 5 publications

(6 citation statements)

References 55 publications

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“…It contains a 17 amino acid insertion between two adjacent β-strands termed the “Toggle loop” motif ( Schellenberg et al 2013 ; Mayerle et al 2017 ). This loop motif is not conserved in Cm; absence of the 17 amino acid insertion was suggested bioinformatically and confirmed crystallographically ( Garside et al 2019 ). In place of the Toggle loop, the Cm Prp8 RH domain contains a well-ordered type II β-turn that locks the RH domain in the “Closed loop” conformation ( Garside et al 2019 ).…”

Section: Analysis Of Homology Modelsmentioning

confidence: 77%

“…This loop motif is not conserved in Cm; absence of the 17 amino acid insertion was suggested bioinformatically and confirmed crystallographically ( Garside et al 2019 ). In place of the Toggle loop, the Cm Prp8 RH domain contains a well-ordered type II β-turn that locks the RH domain in the “Closed loop” conformation ( Garside et al 2019 ). The Closed loop conformation of the Cm Prp8 RH domain, combined with the absence of the Toggle loop and other regulatory proteins previously discussed, leads us to predict the Cm spliceosome is slow during assembly, transitional, and catalytic stages.…”

Section: Analysis Of Homology Modelsmentioning

confidence: 77%

“…Phylogenetic evidence suggests that the ancestral state of the Cm spliceosome and intron complement was much closer to that of fungi such as S. pombe , that is, the genome contained several thousand introns and a larger spliceosome that included the U1 snRNP ( Hudson et al 2015 ). We have studied pre-mRNA splicing in Cm ( Stark et al 2015 ; Black et al 2016 ; Reimer et al 2017 ; Garside et al 2019 ), and previously reported that it possesses a unique algal spliceosome lacking the entire U1 snRNP and several other splicing and spliceosome assembly proteins ( Table 1 ; Fig. 2 ; Stark et al 2015 ; Reimer et al 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes

Black

Whelan

Garside

et al. 2023

RNA

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Pre-messenger RNA splicing is catalyzed by the spliceosome, a multi-megadalton RNA-protein complex that assembles in a highly-regulated process on each intronic substrate. Most studies of splicing and spliceosomes have been carried out in human or S. cerevisiae model systems. There exists, however, a large diversity of spliceosomes, particularly in organisms with reduced genomes, that suggests a means of analyzing the essential elements of spliceosome assembly and regulation. In this review, we characterize changes in spliceosome composition across phyla, describing those that are most frequently observed and highlighting an analysis of the reduced spliceosome of the red alga Cyanidioschyzon merolae. We used homology modelling to predict what effect splicing protein loss would have on the spliceosome, based on currently available cryo-EM structures. We observe strongly correlated loss of proteins that function in the same process, e.g. in interacting with the U1 snRNP (which is absent in C. merolae), regulation of Brr2, or coupling transcription and splicing. Based on our observations, we predict splicing in C. merolae to be inefficient, inaccurate, and post-transcriptional, consistent with the apparent trend towards its elimination in this lineage. This work highlights the striking flexibility of the splicing pathway and the spliceosome when viewed in the context of eukaryotic diversity.

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Section: Analysis Of Homology Modelsmentioning

confidence: 77%

Section: Analysis Of Homology Modelsmentioning

confidence: 77%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes

Black

Whelan

Garside

et al. 2023

RNA

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“…The Arabidopsis hypomorphic prp8-7 mutation causes a G1820E substitution in a 17-amino-acid extension within the RNase H-like domain of PRP8 (residues 1860–1875 in yeast, which correspond to residues 1812–1827 in Arabidopsis; Supplementary Figure S2 ). Cryo-EM analyses of yeast Prp8 revealed that this protein undergoes conformational rearrangements during pre-mRNA splicing and that the 17-amino-acid region can exist as a β-hairpin or a disordered loop, depending of the splicing step ( 44 ). Some missense prp8 alleles affecting residues of this 17-amino-acid region stabilize the disordered loop conformation, which in turn provides high efficiency but low fidelity to the splicing of pre-mRNAs from reporter constructs.…”

Section: Resultsmentioning

confidence: 99%

Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites

Cabezas-Fuster

Micol-Ponce

Fontcuberta-Cervera

et al. 2022

Nucleic Acids Research

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Efficient splicing requires a balance between high-fidelity splice-site (SS) selection and speed. In Saccharomyces cerevisiae, Pre-mRNA processing factor 8 (Prp8) helps to balance precise SS selection and rapid, efficient intron excision and exon joining. argonaute1-52 (ago1-52) and incurvata13 (icu13) are hypomorphic alleles of the Arabidopsis thaliana genes ARGONAUTE1 (AGO1) and AUXIN RESISTANT6 (AXR6) that harbor point mutations creating a novel 3′SS and 5′SS, respectively. The spliceosome recognizes these novel SSs, as well as the intact genuine SSs, producing a mixture of wild-type and aberrant mature mRNAs. Here, we characterized five novel mutant alleles of PRP8 (one of the two Arabidopsis co-orthologs of yeast Prp8), naming these alleles morphology of ago1-52 suppressed5 (mas5). In the mas5-1 background, the spliceosome preferentially recognizes the intact genuine 3′SS of ago1-52 and 5′SS of icu13. Since point mutations that damage genuine SSs make the spliceosome prone to recognizing cryptic SSs, we also tested alleles of four genes carrying damaged genuine SSs, finding that mas5-1 did not suppress their missplicing. The mas5-1 and mas5-3 mutations represent a novel class of missplicing suppressors that increase splicing fidelity by hampering the use of novel SSs, but do not alter general pre-mRNA splicing.

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“…Due to its simple cellular ultrastructure and genome organisation, C. merolae has been used as a model organism to study the evolution and molecular mechanisms of the cell cycle, cell signalling, and circadian rhythm processes (Miyagishima and Tanaka, 2021). It is also becoming an important model organism for the study of the evolution and mechanism of pre-mRNA splicing (Stark et al, 2015; Black et al, 2016; Reimer et al, 2017; Garside et al, 2019). More recently, much attention has been devoted to deciphering the molecular mechanisms of photoadaptation in this extremophile, specifically by dissecting the structure and function of the photosynthetic molecular machinery that is closely related to that of other eukaryotic phototrophs, albeit with significant exceptions.…”

Section: Introductionmentioning

confidence: 99%

Molecular mechanisms of long-term light adaptation of an extremophilic alga Cyanidioschyzon merolae

Abram

Kaňa

Olofsson

et al. 2022

Preprint

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Oxygenic phototrophs have evolved a remarkable plethora of strategies to react to changes in light intensity and spectral range, which allows them to thrive in a wide range of environmental conditions. Varying light quality and quantity influences the balance between solar energy capture and utilisation in photosynthesis, affecting concomitantly the downstream processes of central carbon and nitrogen metabolism as well as cellular growth and division. Here, we performed a comprehensive analysis of the mechanisms of long-term photoacclimation of an extremophilic red alga Cyanidioschyzon merolae that grows in sulphuric hot springs at high temperatures and low pH. By using spectroscopic, confocal fluorescence microscopy, photosynthetic performance measurements and global transcriptome analyses, we identified several molecular mechanisms underlying the long-term adaptation of this acido-thermophilic red alga to varying light intensity and spectral quality. These include: (1) remodelling of the functional antenna size of both photosystems; (2) rearrangement of the PSB/PSII/PSI microdomains within thylakoids; (3) modulation of the photosynthetic performance parameters, especially at the level of non-photochemical quenching, and (4) transcriptional regulation of photosynthesis and its regulatory components as well as downstream metabolic pathways related to ROS detoxification, cell/organelle division, and central carbon and nitrogen metabolism. Such an intricate network of interplay between light-driven reactions and downstream metabolic pathways provides the necessary basis for maintaining the highest photosynthetic performance under light-limiting conditions.

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Prp8 in a Reduced Spliceosome Lacks a Conserved Toggle that Correlates with Splicing Complexity across Diverse Taxa

Cited by 5 publications

References 55 publications

Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes

Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes

Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites

Molecular mechanisms of long-term light adaptation of an extremophilic alga Cyanidioschyzon merolae

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