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Schaefke B, Sun W, Li YS, Fang L, Chen W. The evolution of posttranscriptional regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1485. [PMID: 29851258 DOI: 10.1002/wrna.1485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Abstract
"DNA makes RNA makes protein." After transcription, mRNAs undergo a series of intertwining processes to be finally translated into functional proteins. The "posttranscriptional" regulation (PTR) provides cells an extended option to fine-tune their proteomes. To meet the demands of complex organism development and the appropriate response to environmental stimuli, every step in these processes needs to be finely regulated. Moreover, changes in these regulatory processes are important driving forces underlying the evolution of phenotypic differences across different species. The major PTR mechanisms discussed in this review include the regulation of splicing, polyadenylation, decay, and translation. For alternative splicing and polyadenylation, we mainly discuss their evolutionary dynamics and the genetic changes underlying the regulatory differences in cis-elements versus trans-factors. For mRNA decay and translation, which, together with transcription, determine the cellular RNA or protein abundance, we focus our discussion on how their divergence coordinates with transcriptional changes to shape the evolution of gene expression. Then to highlight the importance of PTR in the evolution of higher complexity, we focus on their roles in two major phenomena during eukaryotic evolution: the evolution of multicellularity and the division of labor between different cell types and tissues; and the emergence of diverse, often highly specialized individual phenotypes, especially those concerning behavior in eusocial insects. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution Translation > Translation Regulation RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California San Francisco, San Francisco
| | - Yi-Sheng Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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2
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Cormier A, Avia K, Sterck L, Derrien T, Wucher V, Andres G, Monsoor M, Godfroy O, Lipinska A, Perrineau MM, Van De Peer Y, Hitte C, Corre E, Coelho SM, Cock JM. Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. THE NEW PHYTOLOGIST 2017; 214:219-232. [PMID: 27870061 DOI: 10.1111/nph.14321] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/08/2016] [Indexed: 05/28/2023]
Abstract
The genome of the filamentous brown alga Ectocarpus was the first to be completely sequenced from within the brown algal group and has served as a key reference genome both for this lineage and for the stramenopiles. We present a complete structural and functional reannotation of the Ectocarpus genome. The large-scale assembly of the Ectocarpus genome was significantly improved and genome-wide gene re-annotation using extensive RNA-seq data improved the structure of 11 108 existing protein-coding genes and added 2030 new loci. A genome-wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus. A large number of previously undescribed noncoding genes were identified and annotated, including 717 loci that produce long noncoding RNAs. Conservation of lncRNAs between Ectocarpus and another brown alga, the kelp Saccharina japonica, suggests that at least a proportion of these loci serve a function. Finally, a large collection of single nucleotide polymorphism-based markers was developed for genetic analyses. These resources are available through an updated and improved genome database. This study significantly improves the utility of the Ectocarpus genome as a high-quality reference for the study of many important aspects of brown algal biology and as a reference for genomic analyses across the stramenopiles.
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Affiliation(s)
- Alexandre Cormier
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Komlan Avia
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium
| | | | | | - Gwendoline Andres
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Misharl Monsoor
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Olivier Godfroy
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Agnieszka Lipinska
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Marie-Mathilde Perrineau
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yves Van De Peer
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, 0028, Pretoria, South Africa
| | | | - Erwan Corre
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Susana M Coelho
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - J Mark Cock
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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Luthringer R, Lipinska AP, Roze D, Cormier A, Macaisne N, Peters AF, Cock JM, Coelho SM. The Pseudoautosomal Regions of the U/V Sex Chromosomes of the Brown Alga Ectocarpus Exhibit Unusual Features. Mol Biol Evol 2015; 32:2973-85. [PMID: 26248564 PMCID: PMC4610043 DOI: 10.1093/molbev/msv173] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The recombining regions of sex chromosomes (pseudoautosomal regions, PARs) are predicted to exhibit unusual features due to their being genetically linked to the nonrecombining, sex-determining region. This phenomenon is expected to occur in both diploid (XY, ZW) and haploid (UV) sexual systems, with slightly different consequences for UV sexual systems because of the absence of masking during the haploid phase (when sex is expressed) and because there is no homozygous sex in these systems. Despite a considerable amount of theoretical work on PAR genetics and evolution, these genomic regions have remained poorly characterized empirically. We show here that although the PARs of the U/V sex chromosomes of the brown alga Ectocarpus recombine at a similar rate to autosomal regions of the genome, they exhibit many genomic features typical of nonrecombining regions. The PARs were enriched in clusters of genes that are preferentially, and often exclusively, expressed during the sporophyte generation of the life cycle, and many of these genes appear to have evolved since the Ectocarpales diverged from other brown algal lineages. A modeling-based approach was used to investigate possible evolutionary mechanisms underlying this enrichment in sporophyte-biased genes. Our results are consistent with the evolution of the PAR in haploid systems being influenced by differential selection pressures in males and females acting on alleles that are advantageous during the sporophyte generation of the life cycle.
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Affiliation(s)
- Rémy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Denis Roze
- UMI 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUCCh, UACH, Station Biologique de Roscoff, Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Macaisne
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
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Wu X, Hurst LD. Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associated cis-Motifs. Mol Biol Evol 2015; 32:1847-61. [PMID: 25771198 PMCID: PMC4476162 DOI: 10.1093/molbev/msv069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The nearly neutral theory predicts that small effective population size provides the conditions for weakened selection. This is postulated to explain why our genome is more “bloated” than that of, for example, yeast, ours having large introns and large intergene spacer. If a bloated genome is also an error prone genome might it, however, be the case that selection for error-mitigating properties is stronger in our genome? We examine this notion using splicing as an exemplar, not least because large introns can predispose to noisy splicing. We thus ask whether, owing to genomic decay, selection for splice error-control mechanisms is stronger, not weaker, in species with large introns and small populations. In humans much information defining splice sites is in cis-exonic motifs, most notably exonic splice enhancers (ESEs). These act as splice-error control elements. Here then we ask whether within and between-species intron size is a predictor of the commonality of exonic cis-splicing motifs. We show that, as predicted, the proportion of synonymous sites that are ESE-associated and under selection in humans is weakly positively correlated with the size of the flanking intron. In a phylogenetically controlled framework, we observe, also as expected, that mean intron size is both predicted by Ne.μ and is a good predictor of cis-motif usage across species, this usage coevolving with splice site definition. Unexpectedly, however, across taxa intron density is a better predictor of cis-motif usage than intron size. We propose that selection for splice-related motifs is driven by a need to avoid decoy splice sites that will be more common in genes with many and large introns. That intron number and density predict ESE usage within human genes is consistent with this, as is the finding of intragenic heterogeneity in ESE density. As intronic content and splice site usage across species is also well predicted by Ne.μ, the result also suggests an unusual circumstance in which selection (for cis-modifiers of splicing) might be stronger when population sizes are smaller, as here splicing is noisier, resulting in a greater need to control error-prone splicing.
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Affiliation(s)
- XianMing Wu
- Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
| | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
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The relative ages of eukaryotes and akaryotes. J Mol Evol 2014; 79:228-39. [PMID: 25179144 DOI: 10.1007/s00239-014-9643-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022]
Abstract
The Last Eukaryote Common Ancestor (LECA) appears to have the genetics required for meiosis, mitosis, nucleus and nuclear substructures, an exon/intron gene structure, spliceosomes, many centres of DNA replication, etc. (and including mitochondria). Most of these features are not generally explained by models for the origin of the Eukaryotic cell based on the fusion of an Archeon and a Bacterium. We find that the term 'prokaryote' is ambiguous and the non-phylogenetic term akaryote should be used in its place because we do not yet know the direction of evolution between eukaryotes and akaryotes. We use the term 'protoeukaryote' for the hypothetical stem group ancestral eukaryote that took up a bacterium as an endosymbiont that formed the mitochondrion. It is easier to make detailed models with a eukaryote to an akaryote transition, rather than vice versa. So we really are at a phylogenetic impasse in not being confident about the direction of change between eukaryotes and akaryotes.
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