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Martinez-Gomez L, Cerdán-Vélez D, Abascal F, Tress ML. Origins and Evolution of Human Tandem Duplicated Exon Substitution Events. Genome Biol Evol 2022; 14:6809199. [PMID: 36346145 PMCID: PMC9741552 DOI: 10.1093/gbe/evac162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022] Open
Abstract
The mutually exclusive splicing of tandem duplicated exons produces protein isoforms that are identical save for a homologous region that allows for the fine tuning of protein function. Tandem duplicated exon substitution events are rare, yet highly important alternative splicing events. Most events are ancient, their isoforms are highly expressed, and they have significantly more pathogenic mutations than other splice events. Here, we analyzed the physicochemical properties and functional roles of the homologous polypeptide regions produced by the 236 tandem duplicated exon substitutions annotated in the human gene set. We find that the most important structural and functional residues in these homologous regions are maintained, and that most changes are conservative rather than drastic. Three quarters of the isoforms produced from tandem duplicated exon substitution events are tissue-specific, particularly in nervous and cardiac tissues, and tandem duplicated exon substitution events are enriched in functional terms related to structures in the brain and skeletal muscle. We find considerable evidence for the convergent evolution of tandem duplicated exon substitution events in vertebrates, arthropods, and nematodes. Twelve human gene families have orthologues with tandem duplicated exon substitution events in both Drosophila melanogaster and Caenorhabditis elegans. Six of these gene families are ion transporters, suggesting that tandem exon duplication in genes that control the flow of ions into the cell has an adaptive benefit. The ancient origins, the strong indications of tissue-specific functions, and the evidence of convergent evolution suggest that these events may have played important roles in the evolution of animal tissues and organs.
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Affiliation(s)
- Laura Martinez-Gomez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Daniel Cerdán-Vélez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Federico Abascal
- Somatic Evolution Group, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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2
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Márquez Y, Mantica F, Cozzuto L, Burguera D, Hermoso-Pulido A, Ponomarenko J, Roy SW, Irimia M. ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Genome Biol 2021; 22:239. [PMID: 34416914 PMCID: PMC8379844 DOI: 10.1186/s13059-021-02441-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).
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Affiliation(s)
- Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Antonio Hermoso-Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Scott W Roy
- San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,ICREA, Barcelona, Spain.
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3
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Martinez Gomez L, Pozo F, Walsh TA, Abascal F, Tress ML. The clinical importance of tandem exon duplication-derived substitutions. Nucleic Acids Res 2021; 49:8232-8246. [PMID: 34302486 PMCID: PMC8373072 DOI: 10.1093/nar/gkab623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023] Open
Abstract
Most coding genes in the human genome are annotated with multiple alternative transcripts. However, clear evidence for the functional relevance of the protein isoforms produced by these alternative transcripts is often hard to find. Alternative isoforms generated from tandem exon duplication-derived substitutions are an exception. These splice events are rare, but have important functional consequences. Here, we have catalogued the 236 tandem exon duplication-derived substitutions annotated in the GENCODE human reference set. We find that more than 90% of the events have a last common ancestor in teleost fish, so are at least 425 million years old, and twenty-one can be traced back to the Bilateria clade. Alternative isoforms generated from tandem exon duplication-derived substitutions also have significantly more clinical impact than other alternative isoforms. Tandem exon duplication-derived substitutions have >25 times as many pathogenic and likely pathogenic mutations as other alternative events. Tandem exon duplication-derived substitutions appear to have vital functional roles in the cell and may have played a prominent part in metazoan evolution.
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Affiliation(s)
- Laura Martinez Gomez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Thomas A Walsh
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.,Eukaryotic Annotation Team, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA. UK
| | - Federico Abascal
- Somatic Evolution Group, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
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4
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Karyoevolution inPotamorhina(Cope, 1878) (Ostariophysi, Curimatidae): Using Repetitive DNA for the Elucidation of Genome Organization. Zebrafish 2016; 13:118-31. [DOI: 10.1089/zeb.2015.1187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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5
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Chen FC, Pan CL, Lin HY. Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs. Evol Bioinform Online 2014; 10:219-28. [PMID: 25574121 PMCID: PMC4264600 DOI: 10.4137/ebo.s20772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) have been suggested as playing important roles in human gene regulation. The majority of annotated human lincRNAs include multiple exons and are alternatively spliced. However, the connections between alternative RNA splicing (AS) and the functions/regulations of lincRNAs have remained elusive. In this study, we compared the sequence evolution and biological features between single-exonic lincRNAs and multi-exonic lincRNAs (SELs and MELs, respectively) that were present only in the hominoids (hominoid-specific) or conserved in primates (primate-conserved). The MEL exons were further classified into alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs) for evolutionary analyses. Our results indicate that SELs and MELs differed significantly from each other. Firstly, in hominoid-specific lincRNAs, MELs (both CSEs and ASEs) evolved slightly more rapidly than SELs, which evolved approximately at the neutral rate. In primate-conserved lincRNAs, SELs and ASEs evolved slightly more slowly than CSEs and neutral sequences. The evolutionary path of hominid-specific lincRNAs thus seemed to have diverged from that of their more ancestral counterparts. Secondly, both of the exons and transcripts of SELs were significantly longer than those of MELs, and this was probably because SEL transcripts were more resistant to RNA splicing than MELs. Thirdly, SELs were physically closer to coding genes than MELs. Fourthly, SELs were more widely expressed in human tissues than MELs. These results suggested that SELs and MELs represented two biologically distinct groups of genes. In addition, the SEL-MEL and ASE-CSE differences implied that splicing might be important for the functionality or regulations of lincRNAs in primates.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan. ; Department of Biological Science and Technology, National Chiao-Tung University, Taiwan. ; Department of Dentistry, China Medical University, Taiwan
| | - Chia-Lin Pan
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan
| | - Hsuan-Yu Lin
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan
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6
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Kuroyanagi H, Takei S, Suzuki Y. Comprehensive analysis of mutually exclusive alternative splicing in C. elegans. WORM 2014; 3:e28459. [PMID: 25254147 PMCID: PMC4165533 DOI: 10.4161/worm.28459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/28/2014] [Accepted: 03/06/2014] [Indexed: 12/03/2022]
Abstract
Mutually exclusive selection of one exon in a cluster of exons is a rare form of alternative pre-mRNA splicing, yet suggests strict regulation. However, the repertoires of regulation mechanisms for the mutually exclusive (ME) splicing in vivo are still unknown. Here, we experimentally explore putative ME exons in C. elegans to demonstrate that 29 ME exon clusters in 27 genes are actually selected in a mutually exclusive manner. Twenty-two of the clusters consist of homologous ME exons. Five clusters have too short intervening introns to be excised between the ME exons. Fidelity of ME splicing relies at least in part on nonsense-mediated mRNA decay for 14 clusters. These results thus characterize all the repertoires of ME splicing in this organism.
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Affiliation(s)
- Hidehito Kuroyanagi
- Laboratory of Gene Expression; Medical Research Institute; Tokyo Medical and Dental University; Bunkyo-ku, Tokyo, Japan
| | - Satomi Takei
- Laboratory of Gene Expression; Medical Research Institute; Tokyo Medical and Dental University; Bunkyo-ku, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Science; University of Tokyo; Kashiwa, Chiba, Japan
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Barua B. Periodicities designed in the tropomyosin sequence and structure define its functions. BIOARCHITECTURE 2013; 3:51-6. [PMID: 23887197 DOI: 10.4161/bioa.25616] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Tropomyosin is an actin binding protein that regulates actin filament dynamics and its interactions with actin binding proteins such as myosin, tropomodulin, formin, Arp2/3 and ADF-cofilin in most eukaryotic cells. Tropomyosin is the prototypical two-chained, α-helical coiled coil protein that associates end-to-end and binds to both sides of the actin filament. Each tropomyosin molecule spans four to seven actin monomers in the filament, depending on the size of the tropomyosin. Tropomyosins have a periodic heptad repeat sequence that is characteristic of coiled coil proteins as well as additional periodicities required for its interaction with the actin filament, where each periodic repeat interacts with one actin molecule. This review addresses the role of periodic features of the Tm molecule in carrying out its universal functions of binding to the actin filament and its regulation and the specific features that may determine the isoform specificity of tropomyosins.
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Affiliation(s)
- Bipasha Barua
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Piscataway, NJ, USA.
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8
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Cañestro C, Albalat R, Irimia M, Garcia-Fernàndez J. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 2013; 24:83-94. [DOI: 10.1016/j.semcdb.2012.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
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9
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Su Z, Gu X. Revisit on the evolutionary relationship between alternative splicing and gene duplication. Gene 2012; 504:102-6. [PMID: 22621894 DOI: 10.1016/j.gene.2012.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/18/2012] [Accepted: 05/07/2012] [Indexed: 11/19/2022]
Abstract
Gene duplications and alternative splicing (AS) isoforms are two widespread types of genetic variations that can facilitate diversification of protein function. A number of studies claimed that after gene duplication, two AS isoforms with differential functions can be 'fixed', respectively, in each of the duplicate copies. This simple 'functional-sharing' hypothesis was recently challenged by Roux and Robinson-Rechavi (2011). Instead, they proposed a more sophisticated hypothesis, invoking that less alternative splicing genes tend to be duplicated more frequently, and single-copy genes are younger than duplicate genes, or the 'duplicability-age' hypothesis for short. In this letter, we show that all these genome-wide analyses of AS isoforms actually did not provide clear-cut evidence to nullify the basic idea of functional-sharing hypothesis. After updating our understanding of genome-wide alternative splicing, duplicability and CNV (copy number variation), we argue that the foundation of the duplicability-age hypothesis remains to be justified carefully. Finally, we suggest that a better approach to resolving this controversy is the correspondence analysis of indels (insertions and deletions) between duplicate genes to the genomic exon-intron structure, which can be used to experimentally test the effect of functional-sharing hypothesis.
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Affiliation(s)
- Zhixi Su
- MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
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10
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Armitage SAO, Freiburg RY, Kurtz J, Bravo IG. The evolution of Dscam genes across the arthropods. BMC Evol Biol 2012; 12:53. [PMID: 22500922 PMCID: PMC3364881 DOI: 10.1186/1471-2148-12-53] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 04/13/2012] [Indexed: 11/05/2023] Open
Abstract
BACKGROUND One way of creating phenotypic diversity is through alternative splicing of precursor mRNAs. A gene that has evolved a hypervariable form is Down syndrome cell adhesion molecule (Dscam-hv), which in Drosophila melanogaster can produce thousands of isoforms via mutually exclusive alternative splicing. The extracellular region of this protein is encoded by three variable exon clusters, each containing multiple exon variants. The protein is vital for neuronal wiring where the extreme variability at the somatic level is required for axonal guidance, and it plays a role in immunity where the variability has been hypothesised to relate to recognition of different antigens. Dscam-hv has been found across the Pancrustacea. Additionally, three paralogous non-hypervariable Dscam-like genes have also been described for D. melanogaster. Here we took a bioinformatics approach, building profile Hidden Markov Models to search across species for putative orthologs to the Dscam genes and for hypervariable alternatively spliced exons, and inferring the phylogenetic relationships among them. Our aims were to examine whether Dscam orthologs exist outside the Bilateria, whether the origin of Dscam-hv could lie outside the Pancrustacea, when the Dscam-like orthologs arose, how many alternatively spliced exons of each exon cluster were present in the most common recent ancestor, and how these clusters evolved. RESULTS Our results suggest that the origin of Dscam genes may lie after the split between the Cnidaria and the Bilateria and supports the hypothesis that Dscam-hv originated in the common ancestor of the Pancrustacea. Our phylogeny of Dscam gene family members shows six well-supported clades: five containing Dscam-like genes and one containing all the Dscam-hv genes, a seventh clade contains arachnid putative Dscam genes. Furthermore, the exon clusters appear to have experienced different evolutionary histories. CONCLUSIONS Dscam genes have undergone independent duplication events in the insects and in an arachnid genome, which adds to the more well-known tandem duplications that have taken place within Dscam-hv genes. Therefore, two forms of gene expansion seem to be active within this gene family. The evolutionary history of this dynamic gene family will be further unfolded as genomes of species from more disparate groups become available.
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Affiliation(s)
- Sophie AO Armitage
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany
| | - Rebecca Y Freiburg
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany
| | - Ignacio G Bravo
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany
- Unit of Infections and Cancer, Catalan Institute of Oncology (ICO), Gran Via de L' Hospitalet, 199, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
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Abstract
The recent explosion of genome sequences from all major phylogenetic groups has unveiled an unexpected wealth of cases of recurrent evolution of strikingly similar genomic features in different lineages. Here, we review the diverse known types of recurrent evolution in eukaryotic genomes, with a special focus on metazoans, ranging from reductive genome evolution to origins of splice-leader trans-splicing, from tandem exon duplications to gene family expansions. We first propose a general classification scheme for evolutionary recurrence at the genomic level, based on the type of driving force-mutation or selection-and the environmental and genomic circumstances underlying these forces. We then discuss various cases of recurrent genomic evolution under this scheme. Finally, we provide a broader context for repeated genomic evolution, including the unique relationship of genomic recurrence with the genotype-phenotype map, and the ways in which the study of recurrent genomic evolution can be used to understand fundamental evolutionary processes.
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Affiliation(s)
- Ignacio Maeso
- Department of Zoology, University of Oxford, United Kingdom
| | - Scott William Roy
- Department of Biology, Stanford University
- Department of Biology, San Francisco State University
| | - Manuel Irimia
- Department of Biology, Stanford University
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Canada
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12
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Severing EI, van Dijk ADJ, Morabito G, Busscher-Lange J, Immink RGH, van Ham RCHJ. Predicting the impact of alternative splicing on plant MADS domain protein function. PLoS One 2012; 7:e30524. [PMID: 22295091 PMCID: PMC3266260 DOI: 10.1371/journal.pone.0030524] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 12/18/2011] [Indexed: 11/18/2022] Open
Abstract
Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1-3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins.
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Affiliation(s)
- Edouard I. Severing
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
| | - Giuseppa Morabito
- Plant Developmental Systems, Plant Research International, Wageningen, The Netherlands
| | | | - Richard G. H. Immink
- Centre for BioSystems Genomics, Wageningen, The Netherlands
- Plant Developmental Systems, Plant Research International, Wageningen, The Netherlands
| | - Roeland C. H. J. van Ham
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands
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Chen TW, Wu TH, Ng WV, Lin WC. Interrogation of alternative splicing events in duplicated genes during evolution. BMC Genomics 2011; 12 Suppl 3:S16. [PMID: 22369477 PMCID: PMC3333175 DOI: 10.1186/1471-2164-12-s3-s16] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background Gene duplication provides resources for developing novel genes and new functions while retaining the original functions. In addition, alternative splicing could increase the complexity of expression at the transcriptome and proteome level without increasing the number of gene copy in the genome. Duplication and alternative splicing are thought to work together to provide the diverse functions or expression patterns for eukaryotes. Previously, it was believed that duplication and alternative splicing were negatively correlated and probably interchangeable. Results We look into the relationship between occurrence of alternative splicing and duplication at different time after duplication events. We found duplication and alternative splicing were indeed inversely correlated if only recently duplicated genes were considered, but they became positively correlated when we took those ancient duplications into account. Specifically, for slightly or moderately duplicated genes with gene families containing 2 - 7 paralogs, genes were more likely to evolve alternative splicing and had on average a greater number of alternative splicing isoforms after long-term evolution compared to singleton genes. On the other hand, those large gene families (contain at least 8 paralogs) had a lower proportion of alternative splicing, and fewer alternative splicing isoforms on average even when ancient duplicated genes were taken into consideration. We also found these duplicated genes having alternative splicing were under tighter evolutionary constraints compared to those having no alternative splicing, and had an enrichment of genes that participate in molecular transducer activities. Conclusions We studied the association between occurrences of alternative splicing and gene duplication. Our results implicate that there are key differences in functions and evolutionary constraints among singleton genes or duplicated genes with or without alternative splicing incidences. It implies that the gene duplication and alternative splicing may have different functional significance in the evolution of speciation diversity.
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Affiliation(s)
- Ting-Wen Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
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14
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Oguchi Y, Ishizuka J, Hitchcock-DeGregori SE, Ishiwata S, Kawai M. The role of tropomyosin domains in cooperative activation of the actin-myosin interaction. J Mol Biol 2011; 414:667-80. [PMID: 22041451 DOI: 10.1016/j.jmb.2011.10.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 12/15/2022]
Abstract
To establish α-tropomyosin (Tm)'s structure-function relationships in cooperative regulation of muscle contraction, thin filaments were reconstituted with a variety of Tm mutants (Δ2Tm, Δ3Tm, Δ6Tm, P2sTm, P3sTm, P2P3sTm, P1P5Tm, and wtTm), and force and sliding velocity of the thin filament were studied using an in vitro motility assay. In the case of deletion mutants, Δ indicates which of the quasi-equivalent repeats in Tm was deleted. In the case of period (P) mutants, an Ala cluster was introduced into the indicated period to strengthen the Tm-actin interaction. In P1P5Tm, the N-terminal half of period 5 was substituted with that of period 1 to test the quasi-equivalence of these two Tm periods. The reconstitution included bovine cardiac troponin. Deletion studies revealed that period 3 is important for the positive cooperative effect of Tm on actin filament regulation and that period 2 also contributes to this effect at low ionic strength, but to a lesser degree. Furthermore, Tm with one extra Ala cluster at period 2 (P2s) or period 3 (P3s) did not increase force or velocity, whereas Tm with two extra Ala clusters (P2P3s) increased both force and velocity, demonstrating interaction between these periods. Most mutants did not move in the absence of Ca(2+). Notable exceptions were Δ6Tm and P1P5Tm, which moved near at the full velocity, but with reduced force, which indicate impaired relaxation. These results are consistent with the mechanism that the Tm-actin interaction cooperatively affects actin to result in generation of greater force and velocity.
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Affiliation(s)
- Yusuke Oguchi
- Department of Physics, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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15
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CHIODIN MARTA, ACHATZ JOHANNESG, WANNINGER ANDREAS, MARTINEZ PEDRO. Molecular architecture of muscles in an acoel and its evolutionary implications. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:427-39. [PMID: 21538843 PMCID: PMC3501712 DOI: 10.1002/jez.b.21416] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 03/12/2011] [Accepted: 04/01/2011] [Indexed: 12/14/2022]
Abstract
We have characterized the homologs of an actin, a troponin I, and a tropomyosin gene in the acoel Symsagittifera roscoffensis. These genes are expressed in muscles and most likely coexpressed in at least a subset of them. In addition, and for the first time for Acoela, we have produced a species-specific muscular marker, an antibody against the tropomyosin protein. We have followed tropomyosin gene and protein expression during postembryonic development and during the posterior regeneration of amputated adults, showing that preexisting muscle fibers contribute to the wound closure. The three genes characterized in this study interact in the striated muscles of vertebrates and invertebrates, where troponin I and tropomyosin are key regulators of the contraction of the sarcomere. S. roscoffensis and all other acoels so far described have only smooth muscles, but the molecular architecture of these is the same as that of striated fibers of other bilaterians. Given the proposed basal position of acoels within the Bilateria, we suggest that sarcomeric muscles arose from a smooth muscle type, which had the molecular repertoire of striated musculature already in place. We discuss this model in a broad comparative perspective.
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Affiliation(s)
- MARTA CHIODIN
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
| | | | - ANDREAS WANNINGER
- Department of Evolutionary Biology, Section of Morphology, University of Vienna, Vienna, Austria
| | - PEDRO MARTINEZ
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, Barcelona, Spain
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Irimia M, Maeso I, Burguera D, Hidalgo-Sánchez M, Puelles L, Roy SW, Garcia-Fernàndez J, Ferran JL. Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures. Genome Biol Evol 2011; 3:551-64. [PMID: 21680890 PMCID: PMC3140891 DOI: 10.1093/gbe/evr056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Organisms show striking differences in genome structure; however, the functional implications and fundamental forces that govern these differences remain obscure. The intron–exon organization of nuclear genes is involved in a particularly large variety of structures and functional roles. We performed a 22-species study of Meis/hth genes, intron-rich homeodomain-containing transcription factors involved in a wide range of developmental processes. Our study revealed three surprising results that suggest important and very different functions for Meis intron–exon structures. First, we find unexpected conservation across species of intron positions and lengths along most of the Meis locus. This contrasts with the high degree of structural divergence found in genome-wide studies and may attest to conserved regulatory elements residing within these conserved introns. Second, we find very different evolutionary histories for the 5′ and 3′ regions of the gene. The 5′-most 10 exons, which encode the highly conserved Meis domain and homeodomain, show striking conservation. By contrast, the 3′ of the gene, which encodes several domains implicated in transcriptional activation and response to cell signaling, shows a remarkably active evolutionary history, with diverse isoforms and frequent creation and loss of new exons and splice sites. This region-specific diversity suggests evolutionary “tinkering,” with alternative splicing allowing for more subtle regulation of protein function. Third, we find a large number of cases of convergent evolution in the 3′ region, including 1) parallel losses of ancestral coding sequence, 2) parallel gains of external and internal splice sites, and 3) recurrent truncation of C-terminal coding regions. These results attest to the importance of locus-specific splicing functions in differences in structural evolution across genes, as well as to commonalities of forces shaping the evolution of individual genes along different lineages.
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Affiliation(s)
- Manuel Irimia
- Department of Genetics, School of Biology, University of Barcelona, Barcelona, Spain.
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Evolutionarily conserved surface residues constitute actin binding sites of tropomyosin. Proc Natl Acad Sci U S A 2011; 108:10150-5. [PMID: 21642532 DOI: 10.1073/pnas.1101221108] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Tropomyosin (Tm) is a two-chained, α-helical coiled-coil protein that associates end-to-end to form a continuous strand along actin filaments and regulates the functions and stability of actin in eukaryotic muscle and nonmuscle cells. Mutations in Tm cause skeletal and cardiac myopathies. We applied a neoteric molecular evolution approach to gain insight into the fundamental unresolved question of what makes the Tm coiled coil an actin binding protein. We carried out a phylogenetic analysis of 70 coding sequences of Tm genes from 26 animal species, from cnidarians to chordates, and evaluated the substitution rates (ω) at individual codons to identify conserved sites. The most conserved residues at surface b, c, f heptad repeat positions were mutated in rat striated muscle αTm and expressed in Escherichia coli. Each mutant had 3-4 sites mutated to Ala within the first half or the second half of periods 2-6. Actin affinity and thermodynamic stability were determined in vitro. Mutations in the first half of periods 2, 4, and 5 resulted in the largest reduction in actin affinity (> 4-fold), indicating these mutations include residues in actin-binding sites. Mutations in the second half of the periods had a ≤ 2-fold effect on affinity indicating these residues may be involved in other conserved regulatory functions. The structural relevance of these results was assessed by constructing molecular models for the actin-Tm filament. Molecular evolution analysis is a general approach that may be used to identify potential binding sites of a protein for a conserved protein.
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Sánchez-Guardado LÓ, Irimia M, Sánchez-Arrones L, Burguera D, Rodríguez-Gallardo L, Garcia-Fernández J, Puelles L, Ferran JL, Hidalgo-Sánchez M. Distinct and redundant expression and transcriptional diversity of MEIS gene paralogs during chicken development. Dev Dyn 2011; 240:1475-92. [PMID: 21465619 DOI: 10.1002/dvdy.22621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2011] [Indexed: 01/20/2023] Open
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Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain. Proc Natl Acad Sci U S A 2011; 108:5319-24. [PMID: 21389270 DOI: 10.1073/pnas.1012333108] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel organismal structures in metazoans are often undergirded by complex gene regulatory networks; as such, understanding the emergence of new structures through evolution requires reconstructing the series of evolutionary steps leading to these underlying networks. Here, we reconstruct the step-by-step assembly of the vertebrate splicing network regulated by Nova, a splicing factor that modulates alternative splicing in the vertebrate central nervous system by binding to clusters of YCAY motifs on pre-RNA transcripts. Transfection of human HEK293T cells with Nova orthologs indicated vertebrate-like splicing regulatory activity in bilaterian invertebrates, thus Nova acquired the ability to bind YCAY clusters and perform vertebrate-like splicing modulation at least before the last common ancestor of bilaterians. In situ hybridization studies in several species showed that Nova expression became restricted to CNS later on, during chordate evolution. Finally, comparative genomics studies revealed a diverse history for Nova-regulated exons, with target exons arising through both de novo exon creation and acquisition of YCAY motifs by preexisting exons throughout chordate and vertebrate history. In addition, we find that tissue-specific Nova expression patterns emerged independently in other lineages, suggesting independent assembly of tissue-specific regulatory networks.
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Developmental expression of high molecular weight tropomyosin isoforms in Mesocestoides corti. Mol Biochem Parasitol 2010; 175:181-91. [PMID: 21093500 DOI: 10.1016/j.molbiopara.2010.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/05/2010] [Accepted: 11/08/2010] [Indexed: 12/12/2022]
Abstract
Tropomyosins are a family of actin-binding proteins with diverse roles in actin filament function. One of the best characterized roles is the regulation of muscle contraction. Tropomyosin isoforms can be generated from different genes, and from alternative promoters and alternative splicing from the same gene. In this work, we have isolated sequences for tropomyosin isoforms from the cestode Mesocestoides corti, and searched for tropomyosin genes and isoforms in other flatworms. Two genes are conserved in the cestodes M. corti and Echinococcus multilocularis, and in the trematode Schistosoma mansoni. Both genes have the same structure, and each gene gives rise to at least two different isoforms, a high molecular weight (HMW) and a low molecular weight (LMW) one. Because most exons are duplicated and spliced in a mutually exclusive fashion, isoforms from one gene only share one exon and are highly divergent. The gene duplication preceded the divergence of neodermatans and the planarian Schmidtea mediterranea. Further duplications occurred in Schmidtea, coupled to the selective loss of duplicated exons, resulting in genes that only code for HMW or LMW isoforms. A polyclonal antibody raised against a HMW tropomyosin from Echinococcus granulosus was demonstrated to specifically recognize HMW tropomyosin isoforms of M. corti, and used to study their expression during segmentation. HMW tropomyosins are expressed in muscle layers, with very low or absent levels in other tissues. No expression of HMW tropomyosins is present in early or late genital primordia, and expression only begins once muscle fibers develop in the genital ducts. Therefore, HMW tropomyosins are markers for the development of muscles during the final differentiation of genital primordia.
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