Origin and evolution of spliceosomal introns

ABSTRACT: Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded 'introns first' held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes. This article was reviewed by I. King Jordan, Manuel Irimia (nominated by Anthony Poole), Tobias Mourier (nominated by Anthony Poole), and Fyodor Kondrashov. For the complete reports, see the Reviewers' Reports section.     

A general model for the evolution of nuclear pre-mRNA introns

We present an overview of the evolution of eukaryotic split gene structure and pre-mRNA splicing mechanisms. We have drawn together several seemingly conflicting ideas and we show that they can all be incorporated in a single unified theory of intron evolution. The resulting model is consistent with the notion that introns, as a class, are very ancient, having originated in the "RNA world"; it also supports the concept that introns may have played a crucial role in the construction of many eukaryotic genes and it accommodates the idea that introns are related to mobile insertion elements. Our conclusion is that introns could have a profound effect on the course of eukaryotic gene evolution, but that the origin and maintenance of intron sequences depends, largely, on natural selection acting on the intron sequences themselves.     

Origin of Spliceosomal Introns and Alternative Splicing

In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.     

On What It is to Fly Can Tell Us Something About What It is to Live

The plurality of definitions of life is often perceived as an unsatisfying situation stemming from still incomplete knowledge about ‘what it is to live’ as well as from the existence of a variety of methods for reaching a definition. For many, such plurality is to be remedied and the search for a unique and fully satisfactory definition of life pursued. In this contribution on the contrary, it is argued that the existence of such a variety of definitions of life undermines the very feasibility of ever reaching a unique unambiguous definition. It is argued that focusing on the definitions of specific types of ‘living systems’—somehow in the same way that one can define specific types of ‘flying systems’—could be more fruitful from a heuristic point of view than looking for ‘the’ right definition of life, and probably more accurate in terms of carving Nature at its joints.     

Critique of ‘Australopithecus afarensis’ as a single species based on dental metrics and morphology

Leonard andHegmon (1987) compare a series of dental metrics of ‘Australopithecus afarensis Johanson, White, andCoppens, 1978’ with criteria for modern apes, to test the hypothesis that ‘A. afarensis’ represents a single species. They also compare the morphology of the lower third premolar. The dental breadth of ‘A. afarensis’ shows a wide range of variation, particularly in the lower third premolar morphology which displays greater variation than in modern apes—yet the study concludes that the single species hypothesis cannot be rejected. The study is flawed by applying criteria for pongids inappropriate for a hominid. When ‘A. afarensis’ is compared with criteria for hominids, the range of variation in dental size, breadth, and third premolar morphology is greater than that in any hominid species. The single species hypothesis is, therefore, once again rejected. Moreover, the name ‘A. afarensis’ is preoccupied byPraeanthropus africanus (Weinert) and must be dropped.     

Boundaries that demarcate structural and functional domains of chromatin

Understanding of how the eukaryotic genome is packaged into chromatin and what the functional consequences of this organization are has begun to emerge recently. The concept of ‘chromatin domains’ — the topologically independent structural unit — is the basis of higher order chromatin organization. The idea that this structural unit may also coincide with the functional unit, offers a useful framework in dissecting the structure-function relationship. Boundaries that define these domains have been identified and several assays have been developed to test themin vivo. We have used genetic means to identify and analyse such boundary elements in the bithorax complex ofDrosophila melanogaster. In this review we discuss chromatin domain boundaries identified in several systems using different means. Although there is no significant sequence conservation among various chromatin domain boundaries, these elements show functional conservation across the species. Finally, we discuss mechanistic aspects of how chromatin domain boundaries may function in organizing and regulating eukaryotic genome.     

A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes

Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6-7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing.     

Statistical characteristics of eukaryotic intron database

A database called eukaryotic intron database (EID) was developed based on the data from GenBank. Studies on the statistical characteristics of EID show that there were 103, 848 genes, 478,484 introns, and 582,332 exons, with an average of 4.61 introns and 5.61 exons per gene. Introns of 40–120 nt in length were abundant in the database. Results of the statistical analysis on the data from nine model species showed that in eukaryotes, higher species do not necessarily have more introns or exons in a gene than lower species. Furthermore, characteristics of EID, such as intron phase, distribution of different splice sites, and the relationship between genome size and intron proportion or intron density, have been studied. __________ Translated from Acta Scientiarum Naturalium Universitatis Sunyatseni, 2005, 44(6): 79–82 [译自: 中山大学学报, 2005, 44(6): 79–82]     

Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast

Correct identification of all introns is necessary to discern the protein-coding potential of a eukaryotic genome. The existence of most of the spliceosomal introns predicted in the genome of Saccharomyces cerevisiae remains unsupported by molecular evidence. We tested the intron predictions for 87 introns predicted to be present in non-ribosomal protein genes, more than a third of all known or suspected introns in the yeast genome. Evidence supporting 61 of these predictions was obtained, 20 predicted intron sequences were not spliced and six predictions identified an intron-containing region but failed to specify the correct splice sites, yielding a successful prediction rate of <80%. Alternative splicing has not been previously described for this organism, and we identified two genes (YKL186C/MTR2 and YML034W) which encode alternatively spliced mRNAs; YKL186C/MTR2 produces at least five different spliced mRNAs. One gene (YGR225W/SPO70) has an intron whose removal is activated during meiosis under control of the MER1 gene. We found eight new introns, suggesting that numerous introns still remain to be discovered. The results show that correct prediction of introns remains a significant barrier to understanding the structure, function and coding capacity of eukaryotic genomes, even in a supposedly simple system like yeast.     

The expanded evolutionary synthesis—a response to Godfrey-Smith,Haig, and West-Eberhard

In responding to three reviews of Evolution in Four Dimensions (Jablonka and Lamb, 2005, MIT Press), we briefly consider the historical background to the present genecentred view of evolution, especially the way in which Weismann’s theories have influenced it, and discuss the origins of the notion of epigenetic inheritance. We reaffirm our belief that all types of hereditary information—genetic, epigenetic, behavioural and cultural—have contributed to evolutionary change, and outline recent evidence, mainly from epigenetic studies, that suggests that non-DNA heritable variations are not rare and can be quite stable. We describe ways in which such variations may have influenced evolution. The approach we take leads to broader definitions of terms such as ‘units of heredity’, ‘units of evolution’, and ‘units of selection’, and we maintain that ‘information’ can be a useful concept if it is defined in terms of its effects on the receiver. Although we agree that evolutionary theory is not undergoing a Kuhnian revolution, the incorporation of new data and ideas about hereditary variation, and about the role of development in generating it, is leading to a version of Darwinism that is very different from the gene-centred one that dominated evolutionary thinking in the second half of the twentieth century.     

A structural analysis of the group II intron active site and implications for the spliceosome

Group II introns are self-splicing, mobile genetic elements that have fundamentally influenced the organization of terrestrial genomes. These large ribozymes remain important for gene expression in almost all forms of bacteria and eukaryotes and they are believed to share a common ancestry with the eukaryotic spliceosome that is required for processing all nuclear pre-mRNAs. The three-dimensional structure of a group IIC intron was recently determined by X-ray crystallography, making it possible to visualize the active site and the elaborate network of tertiary interactions that stabilize the molecule. Here we describe the molecular features of the active site in detail and evaluate their correspondence with prior biochemical, genetic, and phylogenetic analyses on group II introns. In addition, we evaluate the structural significance of RNA motifs within the intron core, such as the major-groove triple helix and the domain 5 bulge. Having combined what is known about the group II intron core, we then compare it with known structural features of U6 snRNA in the eukaryotic spliceosome. This analysis leads to a set of predictions for the molecular structure of the spliceosomal active site.     

The estimation of productivity and yield of linseed (<Emphasis Type="Italic">Linum usitatissimum</Emphasis> L.) using the growth analysis

In three year field experiments (2001 – 2003) the growth, yield and productivity of 8 flax cultivars were compared. Cultivars ‘AC Linora’, ‘Flanders’, ‘Linola™ 947’, ‘Norlin’ and ‘Omega’ were obtained from Canada, ‘Barbara’ and ‘Hungarian Gold’ from Hungary and ‘Opal’ from Poland. Apart from the estimation of the yield of aboveground parts dry matter and seed yield the determinations of the primary index value of growth analysis were done and on their basis the indices LAI, LAD, RGR, CGR and HI were calculated. The obtained yield results of the examined flax cultivars show significant genotypic — environmental relationships pertaining to the dynamics of dry matter accumulation and the amount of seed yield. Meteorological conditions in the successive years significantly influenced the particular phases of growth and development of cultivars and the factor which increased the amount of dry matter was the air temperature during the period of plant emergence — budding. During the vegetative season with a large amount of rainfall the average seed yield was about 40 % lower than compared with a year of average precipitation and a warm second part of the second period of flax vegetation. Among the analyzed cultivars a stable yield in all the years was characteristic for cultivars ‘Flanders’, ‘Barbara’ and ‘AC Linora’ (that cultivar, however, during a wet year yielded at a low level). The assimilation leaf surface of the linseed quickly increased during the period from budding to flowering and the accumulation of dry matter of the aboveground parts lasted up to the green maturity. In the successive years of the experiment there were observed significant (linear or logarithmic regressions) relationship between the yield of dry matter and the indices of growth analysis. The biggest values of the CGR indicator were observed for the period from budding to flowering. The maintaining of a high CGR value after plant flowering in the year with a favourable course of climatic parameters was beneficial for a better yield of all flax cultivars. The low values of the RGR index after flowering of cultivar ‘Hungarian Gold’ and ‘Opal’ strictly corresponded to their low yield of seed and straw biomass.     

Tuning the cochlea: wave-mediated positive feedback between cells

Frequency analysis by the mammalian cochlea is traditionally thought to occur via a hydrodynamically coupled ‘travelling wave’ along the basilar membrane. A persistent difficulty with this picture is how sharp tuning can emerge. This paper proposes, and models, a supplementary or alternative mechanism: it supposes that the cochlea analyses sound by setting up standing waves between parallel rows of outer hair cells. In this scheme, multiple cells mutually interact through positive feedback of wave-borne energy. Analytical modelling and numerical evaluation presented here demonstrate that this can provide narrow-band frequency analysis. Graded cochlear tuning will then rely on the distance between rows becoming greater as distance from the base increases (as exhibited by the actual cochlea) and on the wave’s phase velocity becoming slower. In effect, tuning is now a case of varying the feedback delay between the rows, and a prime candidate for a wave exhibiting suitably graded phase velocity—a short-wavelength ‘squirting wave’—is identified and used in the modelling. In this way, resonance between rows could supply both amplification and high Q, characteristics underlying the ‘cochlear amplifier’—the device whose action has long been evident to auditory science but whose anatomical basis and mode of operation are still obscure.     

The origin of RNA interference: Adaptive or neutral evolution?

The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability.

Where does RNA interference come from? This Essay describes a new step-by-step evolutionary model of how RNA interference might have originated in early eukaryotes through neutral events from the molecular machinery present in prokaryotes.     

Explanations in search of observations

The paper explores how, in economics and biology, theoretical models are used as explanatory devices. It focuses on a modelling strategy by which, instead of starting with an unexplained regularity in the world, the modeller begins by creating a credible model world. The model world exhibits a regularity, induced by a mechanism in that world. The modeller concludes that there may be a part of the real world in which a similar regularity occurs and that, were that the case, the model would offer an explanation. Little concrete guidance is given about where such a regularity might be found. Three modelling exercises in evolutionary game theory—one from economics and two from biology—are used as case studies. Two of these (one from each discipline) exemplify ‘explanation in search of observation’. The third goes a step further, analysing a regularity in a model world and treating it as informative about the real world, but without saying anything about real phenomena. The paper argues that if the relation between the model and real worlds is understood in terms of similarity, and if modelling is understood as an ongoing discovery process rather than as the demonstration of empirical truths, there can be value in creating explanations before finding the regularities that are to be explained.     

Warm temperature accelerates short photoperiod-induced growth cessation and dormancy induction in hybrid poplar (Populus × spp.)

There is increasing evidence that temperature, in addition to photoperiod, may be an important factor regulating bud dormancy. The impact of temperature during growth cessation, dormancy development, and subsequent cold acclimation was examined in four hybrid poplar clones with contrasting acclimation patterns: ‘Okanese’—EARLY, ‘Walker’—INT1, ‘Katepwa’—INT2, and ‘Prairie Sky’—LATE. Four day–night temperature treatments (13.5/8.5, 18.5/13.5, 23.5/8.5, and 18.5/3.5°C) were applied during a 60-day induction period to reflect current and predicted future annual variation in autumn temperature for Saskatoon, SK. Warm night temperature (18.5/13.5°C) strongly accelerated growth cessation, dormancy development, and cold acclimation in all four clones. Day temperature had the opposite effect of night temperature. Day and night temperatures appeared to act antagonistically against each other during growth cessation and subsequent dormancy development and cold acclimation. Growth cessation, dormancy development, and cold acclimation in EARLY and LATE were less affected by induction temperature than INT1 and INT2 suggesting that genotypic variations exist in response to temperature. Separating specific phenological stages and the impact by temperature on each clone revealed the complexity of fall phenological changes and their interaction with temperature. Most importantly, future changes in temperature may affect time to growth cessation, subsequently altering the depth of dormancy and cold hardiness in hybrid poplar.     

Effects of NaCl stress on germination, antioxidant responses, and proline content in two rice cultivars

We investigated the physiological and biochemical bases for salt tolerance in two rice (Oryza sativa L.) cultivars — relatively salt-tolerant ‘Dongjin’ and salt-sensitive ‘Kumnam’. Salinized hydroponic cultures were studied at the germination and seedling stages. NaCI inhibited germination more severely in ‘Kumnam’ than in ‘Dongjin’. Increasing the salt concentration also deterred growth to a larger extent in the former. Moreover, the leaves of ‘Kumnam’ exhibited greater increases in lipid peroxidation and Na⁺ accumulation than those of ‘Dongjin’ under stress. The activities of constitutive and salt-induced superoxide dismutase (SOD, EC 1.15.1.1) and ascorbate peroxidase (AP, EC 1.11.1.11) were also higher in ‘Kumnam’, while only catalase (CAT, EC 1.11.1.6) activity was slightly higher in stressed plants of ‘Dongjin’. The positive correlation between leaf proline levels and NaCI concentration was more evident in ‘Kumnam’. However, ‘Dongjin’ seeds, which had higher germinability in the presence of NaCI, also contained more proline. These results suggest that the higher salt tolerance in ‘Dongjin’ seedlings could be ascribed to their lower NaCI accumulations in the leaves. This presumably is due to reductions in the uptake or transport rates of saline ions to the shoots from the roots. Finally, we believe that the higher germination rate by ‘Dongjin’ is caused by its higher seed proline content.