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Vosseberg J, Stolker D, von der Dunk SHA, Snel B. Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome. Mol Biol Evol 2023; 40:6985000. [PMID: 36631250 PMCID: PMC9887622 DOI: 10.1093/molbev/msad011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.
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Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands,Laboratory of Microbiology, Wageningen University & Research, 6700 EH Wageningen, the Netherlands
| | - Daan Stolker
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Samuel H A von der Dunk
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
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2
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Gao C, Lu S, Zhou R, Ding J, Fan J, Han B, Chen M, Wang B, Cao Y. Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family. BMC Genomics 2022; 23:744. [DOI: 10.1186/s12864-022-08956-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.
Result
Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.
Conclusion
U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.
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3
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Wong DK, Stark MS, Rader SD, Fast NM. Characterization of Pre-mRNA Splicing and Spliceosomal Machinery in Porphyridium purpureum and Evolutionary Implications for Red Algae. J Eukaryot Microbiol 2021; 68:e12844. [PMID: 33569840 DOI: 10.1111/jeu.12844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a highly conserved eukaryotic process, but our understanding of it is limited by a historical focus on well-studied organisms such as humans and yeast. There is considerable diversity in mechanisms and components of pre-mRNA splicing, especially in lineages that have evolved under the pressures of genome reduction. The ancestor of red algae is thought to have undergone genome reduction prior to the lineage's radiation, resulting in overall gene and intron loss in extant groups. Previous studies on the extremophilic red alga Cyanidioschyzon merolae revealed an intron-sparse genome with a highly reduced spliceosome. To determine whether these features applied to other red algae, we investigated multiple aspects of pre-mRNA splicing in the mesophilic red alga Porphyridium purpureum. Through strand-specific RNA-Seq, we observed high levels of intron retention across a large number of its introns, and nearly half of the transcripts for these genes are not spliced at all. We also discovered a relationship between variability of 5' splice site sequences and levels of splicing. To further investigate the connections between intron retention and splicing machinery, we bioinformatically assembled the P. purpureum spliceosome, and biochemically verified the presence of snRNAs. While most other core spliceosomal components are present, our results suggest highly divergent or missing U1 snRNP proteins, despite the presence of an uncharacteristically long U1 snRNA. These unusual aspects highlight the diverse nature of pre-mRNA splicing that can be seen in lesser-studied eukaryotes, raising the importance of investigating fundamental eukaryotic processes outside of model organisms.
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Affiliation(s)
- Donald K Wong
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
| | - Martha S Stark
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
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Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. THE PLANT CELL 2018; 30:1424-1444. [PMID: 29764987 PMCID: PMC6096597 DOI: 10.1105/tpc.18.00177] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/20/2018] [Accepted: 05/10/2018] [Indexed: 05/18/2023]
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four early AS splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE Such factors likely drive cascades of AS of downstream genes that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.
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Affiliation(s)
- Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Allan B James
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Paige E Panter
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heather Knight
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Hugh G Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
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5
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Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. THE PLANT CELL 2018; 30:1424-1444. [PMID: 29764987 DOI: 10.1101/251876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/20/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four early AS splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE Such factors likely drive cascades of AS of downstream genes that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.
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Affiliation(s)
- Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Allan B James
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Paige E Panter
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heather Knight
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Hugh G Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
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Weber G, DeKoster GT, Holton N, Hall KB, Wahl MC. Molecular principles underlying dual RNA specificity in the Drosophila SNF protein. Nat Commun 2018; 9:2220. [PMID: 29880797 PMCID: PMC5992148 DOI: 10.1038/s41467-018-04561-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 05/02/2018] [Indexed: 12/22/2022] Open
Abstract
The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the auxiliary U2A' protein. Here we investigate its functions by crystal structures of SNF alone and bound to U1 stem-loop II, U2A' or U2 stem-loop IV and U2A', SNF dynamics from NMR spectroscopy, and structure-guided mutagenesis in binding studies. We find that different loop-closing base pairs and a nucleotide exchange at the tips of the loops contribute to differential SNF affinity for the RNAs. U2A' immobilizes SNF and RNA residues to restore U2 stem-loop IV binding affinity, while U1 stem-loop II binding does not require such adjustments. Our findings show how U2A' can modulate RNA specificity of SNF without changing SNF conformation or relying on direct RNA contacts.
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Affiliation(s)
- Gert Weber
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195, Berlin, Germany. .,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489, Berlin, Germany.
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri, 63110, USA
| | - Nicole Holton
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195, Berlin, Germany
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri, 63110, USA.
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195, Berlin, Germany. .,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489, Berlin, Germany.
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Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. PLoS One 2016; 11:e0167877. [PMID: 27930710 PMCID: PMC5145212 DOI: 10.1371/journal.pone.0167877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/22/2016] [Indexed: 12/03/2022] Open
Abstract
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application. Here we present a novel method for the immunoprecipitation of mRNAs and ncRNAs, Urb—RNA immunoprecipitation (Urb-RIP). This method employs the RRM1 domain of the “resurrected” snRNA-binding protein Urb to enrich messages containing a stem-loop tag. Unlike techniques which employ the MS2 protein, which require large repeats of the MS2 binding element, Urb-RIP requires only one stem-loop. This method routinely provides over ~100-fold enrichment of tagged messages. Using this technique we have shown enrichment of tagged mRNAs and lncRNAs as well as miRNAs and RNA-binding proteins bound to those messages. We have confirmed, using Urb-RIP, interaction between RNA PolIII transcribed lncRNA BC200 and polyA binding protein.
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Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes. Genetica 2016; 144:487-96. [PMID: 27450547 DOI: 10.1007/s10709-016-9918-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/15/2016] [Indexed: 10/21/2022]
Abstract
Although the mechanism of pre-mRNA splicing has been well characterized, the evolution of spliceosomal proteins is poorly understood. The U1A/U2B″/SNF family (hereafter referred to as the SNF family) of RNA binding spliceosomal proteins participates in both the U1 and U2 small interacting nuclear ribonucleoproteins (snRNPs). The highly constrained nature of this system has inhibited an analysis of co-evolutionary trends between the proteins and their RNA binding targets. Here we report accelerated sequence evolution in the SNF protein family in Phylum Nematoda, which has allowed an analysis of protein:RNA co-evolution. In a comparison of SNF genes from ecdysozoan species, we found a correlation between trans-splicing species (nematodes) and increased phylogenetic branch lengths of the SNF protein family, with respect to their sister clade Arthropoda. In particular, we found that nematodes (~70-80 % of pre-mRNAs are trans-spliced) have experienced higher rates of SNF sequence evolution than arthropods (predominantly cis-spliced) at both the nucleotide and amino acid levels. Interestingly, this increased evolutionary rate correlates with the reliance on trans-splicing by nematodes, which would alter the role of the SNF family of spliceosomal proteins. We mapped amino acid substitutions to functionally important regions of the SNF protein, specifically to sites that are predicted to disrupt protein:RNA and protein:protein interactions. Finally, we investigated SNF's RNA targets: the U1 and U2 snRNAs. Both are more divergent in nematodes than arthropods, suggesting the RNAs have co-evolved with SNF in order to maintain the necessarily high affinity interaction that has been characterized in other species.
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Williams SG, Hall KB. Binding affinity and cooperativity control U2B″/snRNA/U2A' RNP formation. Biochemistry 2014; 53:3727-37. [PMID: 24866816 PMCID: PMC4067145 DOI: 10.1021/bi500438e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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The U1A and U2B″ proteins
are components of the U1 and U2
snRNPs, respectively, where they bind to snRNA stemloops. While localization
of U1A and U2B″ to their respective snRNP is a well-known phenomenon,
binding of U2B″ to U2 snRNA is typically thought to be accompanied
by the U2A′ protein. The molecular mechanisms that lead to
formation of the RNA/U2B″/U2A′ complex and its localization
to the U2 snRNP are investigated here, using a combination of in vitro RNA–protein and protein–protein fluorescence
and isothermal titration calorimetry binding experiments. We find
that U2A′ protein binds to U2B″ with nanomolar affinity
but binds to U1A with only micromolar affinity. In addition, there
is RNA-dependent cooperativity (linkage) between protein–protein
and protein–RNA binding. The unique combination of tight binding
and cooperativity ensures that the U2A′/U2B″ complex
is partitioned only to the U2 snRNP.
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Affiliation(s)
- Sandra G Williams
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School , St. Louis, Missouri 63110, United States
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