Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome

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

The rise of complex life: Tracing the origins of the eukaryotic cell

Compared with prokaryotes, eukaryotic cells are tremendously complex. Eukaryotic cells are larger, contain more genetic material, have an elaborate endomembrane system and operate a dynamic cytoskeleton. The last eukaryotic common ancestor (LECA) very likely already had this typical eukaryotic organisation. The large gap between prokaryotic and eukaryotic complexity because of the lack of evolutionary intermediates makes the emergence of eukaryotes from prokaryotes (eukaryogenesis) one of the greatest evolutionary enigmas and the topic of a lively scientific debate. Many scenarios have been proposed on the order of events during this transition but empirical data supporting a specific scenario are scarce. The research described in this thesis contributes various novel data. I have reconstructed proto-eukaryotic genetic innovations to illuminate the intermediate stages that resulted in the first complex, eukaryotic cells. To perform these reconstructions, I applied both large-scale phylogenomic and small-scale phylogenetic methods to a diverse set of eukaryotes and prokaryotes. Firstly, I focus on the gene duplications that occurred during the transition. We reconstructed and characterised these proto-eukaryotic duplications. Genes that were inherited form the archaeal ancestor were duplicated frequently while relatively few duplications occurred in endosymbiont-derived and metabolic genes. By analysing the branch lengths in phylogenetic trees, we obtained relative time estimates for the duplication events, mitochondrial endosymbiosis and horizontal gene transfers from other prokaryotes. Proteins that build the complex eukaryotic cell, such as the endomembrane system and cytoskeleton, resulted from early duplications, in contrast with the late duplication of regulatory proteins. According to our time estimates, mitochondrial endosymbiosis probably took place between the two duplication waves. Subsequently, the abovementioned duplication data have been combined with the inferred presence of shared intron positions between paralogs to trace the spread of introns through the proto-eukaryotic genome. We detected many intron positions that were shared between proto-eukaryotic paralogs. We argued that most of these shared introns originated from intron insertions before the duplication event. This implies that introns had spread early in eukaryogenesis. Introns are removed from pre-mRNA molecules by the spliceosome, one of the most complex molecular machines that originated during eukaryogenesis. We inferred the evolutionary histories of the different spliceosomal proteins in LECA using phylogenetic trees and intron analyses. Both the introns and the core of the spliceosomal machinery originated from self-splicing group II introns. Proteins that were added to this spliceosomal core primarily had a ribosome-related function. Numerous gene duplications shaped the spliceosome into a highly complex machinery in LECA. The many shared introns between spliceosomal paralogs indicate that introns were widespread through the proto-eukaryotic genome before most spliceosomal complexity originated. Finally, I discuss the implications of our findings on the distinct scenarios for the origin of eukaryotic complexity. I point to potential directions for future research and highlight promising development that may affect our views on eukaryogenesis

Domestication of self-splicing introns during eukaryogenesis : the rise of the complex spliceosomal machinery

ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences. REVIEWERS: This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Vivek Anantharaman

Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery

Abstract ᅟ The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences. Reviewers This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Vivek Anantharaman

The spread of the first introns in proto-eukaryotic paralogs

Spliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20–35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were wide spread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established

Draft Genome Sequence of "Candidatus Moanabacter tarae," Representing a Novel Marine Verrucomicrobial Lineage

The Tara Oceans Consortium has published various metagenomes of marine environmental samples. Here, we report a contig of 2.6 Mbp from the assembly of a sample collected near the Marquesas Islands in the Pacific Ocean, covering a nearly complete novel verrucomicrobial genome. We propose the name "Candidates Moanabacter tarae" for the corresponding bacterium

The rise of complex life: Tracing the origins of the eukaryotic cell

Compared with prokaryotes, eukaryotic cells are tremendously complex. Eukaryotic cells are larger, contain more genetic material, have an elaborate endomembrane system and operate a dynamic cytoskeleton. The last eukaryotic common ancestor (LECA) very likely already had this typical eukaryotic organisation. The large gap between prokaryotic and eukaryotic complexity because of the lack of evolutionary intermediates makes the emergence of eukaryotes from prokaryotes (eukaryogenesis) one of the greatest evolutionary enigmas and the topic of a lively scientific debate. Many scenarios have been proposed on the order of events during this transition but empirical data supporting a specific scenario are scarce. The research described in this thesis contributes various novel data. I have reconstructed proto-eukaryotic genetic innovations to illuminate the intermediate stages that resulted in the first complex, eukaryotic cells. To perform these reconstructions, I applied both large-scale phylogenomic and small-scale phylogenetic methods to a diverse set of eukaryotes and prokaryotes. Firstly, I focus on the gene duplications that occurred during the transition. We reconstructed and characterised these proto-eukaryotic duplications. Genes that were inherited form the archaeal ancestor were duplicated frequently while relatively few duplications occurred in endosymbiont-derived and metabolic genes. By analysing the branch lengths in phylogenetic trees, we obtained relative time estimates for the duplication events, mitochondrial endosymbiosis and horizontal gene transfers from other prokaryotes. Proteins that build the complex eukaryotic cell, such as the endomembrane system and cytoskeleton, resulted from early duplications, in contrast with the late duplication of regulatory proteins. According to our time estimates, mitochondrial endosymbiosis probably took place between the two duplication waves. Subsequently, the abovementioned duplication data have been combined with the inferred presence of shared intron positions between paralogs to trace the spread of introns through the proto-eukaryotic genome. We detected many intron positions that were shared between proto-eukaryotic paralogs. We argued that most of these shared introns originated from intron insertions before the duplication event. This implies that introns had spread early in eukaryogenesis. Introns are removed from pre-mRNA molecules by the spliceosome, one of the most complex molecular machines that originated during eukaryogenesis. We inferred the evolutionary histories of the different spliceosomal proteins in LECA using phylogenetic trees and intron analyses. Both the introns and the core of the spliceosomal machinery originated from self-splicing group II introns. Proteins that were added to this spliceosomal core primarily had a ribosome-related function. Numerous gene duplications shaped the spliceosome into a highly complex machinery in LECA. The many shared introns between spliceosomal paralogs indicate that introns were widespread through the proto-eukaryotic genome before most spliceosomal complexity originated. Finally, I discuss the implications of our findings on the distinct scenarios for the origin of eukaryotic complexity. I point to potential directions for future research and highlight promising development that may affect our views on eukaryogenesis

alphaproteobacteria_mitochondria_untreated.aln

Concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared

alphamito24.otherMitoTaxa.concat.stattrim.aln

Stationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, a more diverse set of mitochondria has been selected. See associated publication for technical details on how this alignment was prepared