Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes.

Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences called internal eliminated sequences (IESs), which have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of 9 Paramecium species (from approximately 100 Mb in Paramecium aurelia species to >1.5 Gb in Paramecium caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single copy in present-day genomes, we identified several families of mobile IESs, including nonautonomous elements acquired via horizontal transfer, which generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.

Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae.

Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant in fitness. Recently, we argued that many adaptive mutations might also be commonly overdominant in fitness. Natural (directional) selection acting on overdominant mutations should drive them into the population but then, instead of bringing them to fixation, should maintain them as balanced polymorphisms via heterozygote advantage. If true, this would make adaptive evolution in sexual diploids differ drastically from that of haploids. The validity of this prediction has not yet been tested experimentally. Here, we performed four replicate evolutionary experiments with diploid yeast populations (Saccharomyces cerevisiae) growing in glucose-limited continuous cultures. We sequenced 24 evolved clones and identified initial adaptive mutations in all four chemostats. The first adaptive mutations in all four chemostats were three copy number variations, all of which proved to be overdominant in fitness. The fact that fitness overdominant mutations were always the first step in independent adaptive walks supports the prediction that heterozygote advantage can arise as a common outcome of directional selection in diploids and demonstrates that overdominance of de novo adaptive mutations in diploids is not rare.

Patterns of variation during adaptation in functionally linked loci.

An understanding of the distribution of natural patterns of genetic variation is relevant to such fundamental biological fields as evolution and development. One recent approach to understanding such patterns has been to focus on the constraints that may arise as a function of the network or pathway context in which genes are embedded. Despite theoretical expectations of higher evolutionary constraint for genes encoding upstream versus downstream enzymes in metabolic pathways, empirical results have varied. Here we combine two complementary models from population genetics and enzyme kinetics to explore genetic variation as a function of pathway position when selection acts on whole-pathway flux. We are able to qualitatively reproduce empirically observed patterns of polymorphism and divergence and suggest that expectations should vary depending on the evolutionary trajectory of a population. Upstream genes are initially more polymorphic and diverge faster after an environmental change, while we see the opposite trend as the population approaches its fitness optimum.

Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics.

Conserved, ultraconserved and other classes of constrained elements (collectively referred as CNEs here), identified by comparative genomics in a wide variety of genomes, are non-randomly distributed across chromosomes. These elements are defined using various degrees of conservation between organisms and several thresholds of minimal length. We here investigate the chromosomal distribution of CNEs by studying the statistical properties of distances between consecutive CNEs. We find widespread power-law-like distributions, i.e. linearity in double logarithmic scale, in the inter-CNE distances, a feature which is connected with fractality and self-similarity. Given that CNEs are often found to be spatially associated with genes, especially with those that regulate developmental processes, we verify by appropriate gene masking that a power-law-like pattern emerges irrespectively of whether elements found close or inside genes are excluded or not. An evolutionary model is put forward for the understanding of these findings that includes segmental or whole genome duplication events and eliminations (loss) of most of the duplicated CNEs. Simulations reproduce the main features of the observed size distributions. Power-law-like patterns in the genomic distributions of CNEs are in accordance with current knowledge about their evolutionary history in several genomes.

Widespread occurrence of power-law distributions in inter-repeat distances shaped by genome dynamics.

Repetitive DNA sequences derived from transposable elements (TE) are distributed in a non-random way, co-clustering with other classes of repeat elements, genes and other genomic components. In a previous work we reported power-law-like size distributions (linearity in log-log scale) in the spatial arrangement of Alu and LINE1 elements in the human genome. Here we investigate the large-scale features of the spatial arrangement of all principal classes of TEs in 14 genomes from phylogenetically distant organisms by studying the size distribution of inter-repeat distances. Power-law-like size distributions are found to be widespread, extending up to several orders of magnitude. In order to understand the emergence of this distributional pattern, we introduce an evolutionary scenario, which includes (i) Insertions of DNA segments (e.g., more recent repeats) into the considered sequence and (ii) Eliminations of members of the studied TE family. In the proposed model we also incorporate the potential for transposition events (characteristic of the DNA transposons' life-cycle) and segmental duplications. Simulations reproduce the main features of the observed size distributions. Furthermore, we investigate the effects of various genomic features on the presence and extent of power-law size distributions including TE class and age, mode of parental TE transmission, GC content, deletion and recombination rates in the studied genomic region, etc. Our observations corroborate the hypothesis that insertions of genomic material and eliminations of repeats are at the basis of power-laws in inter-repeat distances. The existence of these power-laws could facilitate the formation of the recently proposed "fractal globule" for the confined chromatin organization.

Phosphorylation of the arginine/serine repeats of lamin B receptor by SRPK1-insights from molecular dynamics simulations.

BACKGROUND: Arginine/serine (RS) repeats are found in several proteins in metazoans with a wide variety of functions, many of which are regulated by SR protein kinase 1 (SRPK1)-mediated phosphorylation. Lamin B receptor (LBR) is such a protein implicated in chromatin anchorage to the nuclear envelope. METHODS: Molecular dynamics simulations were used to investigate the conformation of two LBR peptides containing four (human-) and five (turkey-orthologue) consecutive RS dipeptides, in their unphosphorylated and phosphorylated forms and of a conserved peptide, in isolation and in complex with SRPK1. GST pull-down assays were employed to study LBR interactions. RESULTS: Unphosphorylated RS repeats adopt short, transient helical conformations, whereas serine phosphorylation induces Arginine-claw-like structures. The SRSRSRSPGR peptide, overlapping with the LBR RS repeats, docks into the known, acidic docking groove of SRPK1, in an extended conformation. Phosphorylation by SRPK1 is necessary for the association of LBR with histone H3. CONCLUSIONS: The C-terminal region of the LBR RS domain constitutes a recognition platform for SRPK1, which uses the same recognition mechanism for LBR as for substrates with long RS domains. This docking may promote unfolding of the RS repeats destined to be phosphorylated. Phosphorylation induces Arginine-claw-like conformations, irrespective of the RS-repeat length, that may facilitate interactions with basic partners. GENERAL SIGNIFICANCE: Our results shed light on the conformational preferences of an important class of repeats before and after their phosphorylation and support the idea that even short RS domains may be constituents of recognition platforms for SRPK1, thus adding to knowledge towards a full understanding of their phosphorylation mechanism.

Heterozygote advantage as a natural consequence of adaptation in diploids.

Molecular adaptation is typically assumed to proceed by sequential fixation of beneficial mutations. In diploids, this picture presupposes that for most adaptive mutations, the homozygotes have a higher fitness than the heterozygotes. Here, we show that contrary to this expectation, a substantial proportion of adaptive mutations should display heterozygote advantage. This feature of adaptation in diploids emerges naturally from the primary importance of the fitness of heterozygotes for the invasion of new adaptive mutations. We formalize this result in the framework of Fisher's influential geometric model of adaptation. We find that in diploids, adaptation should often proceed through a succession of short-lived balanced states that maintain substantially higher levels of phenotypic and fitness variation in the population compared with classic adaptive walks. In fast-changing environments, this variation produces a diversity advantage that allows diploids to remain better adapted compared with haploids despite the disadvantage associated with the presence of unfit homozygotes. The short-lived balanced states arising during adaptive walks should be mostly invisible to current scans for long-term balancing selection. Instead, they should leave signatures of incomplete selective sweeps, which do appear to be common in many species. Our results also raise the possibility that balancing selection, as a natural consequence of frequent adaptation, might play a more prominent role among the forces maintaining genetic variation than is commonly recognized.

Power-laws in the genomic distribution of coding segments in several organisms: an evolutionary trace of segmental duplications, possible paleopolyploidy and gene loss.

Large-scale features of the spatial arrangement of protein-coding segments (PCS) are investigated by means of the inter-PCS spacers' size distributions, which have been found to follow power-laws. Linearity in double-logarithmic scale extends to several orders of magnitude in the genomes of organisms as disparate as mammals, insects and plants. This feature is also present in the most compact eukaryotic genomes and in half of the examined bacteria, despite their very limited non-coding space. We have tried to determine the sequence of events in the course of genomes' evolution which may account for the formation of the observed size distributions. The proposed mechanism essentially includes two types of events: (i) segmental duplications (and possibly paleopolyploidy), and (ii) the subsequent loss of most of the duplicated genes. It is shown by computer simulations that the formulated scenario generates power-law-like inter-PCS spacers' size distributions, which remain robust for a variety of parameter choices, even if insertion of external sequences, such as viruses or proliferating retroelements is included. Moreover, power-laws are preserved after most of the non-coding DNA has been removed, thus explaining the finding of this pattern in genomes as compact as that of Takifugu rubripes.

Gromita: a fully integrated graphical user interface to gromacs 4.

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

Alu and LINE1 distributions in the human chromosomes: evidence of global genomic organization expressed in the form of power laws.

Spatial distribution and clustering of repetitive elements are extensively studied during the last years, as well as their colocalization with other genomic components. Here we investigate the large-scale features of Alu and LINE1 spatial arrangement in the human genome by studying the size distribution of interrepeat distances. In most cases, we have found power-law size distributions extending in several orders of magnitude. We have also studied the correlations of the extent of the power law (linear region in double-logarithmic scale) and of the corresponding exponent (slope) with other genomic properties. A model has been formulated to explain the formation of the observed power laws. According to the model, 2 kinds of events occur repetitively in evolutionary time: random insertion of several types of intruding sequences and occasional loss of repeats belonging to the initial population due to "elimination" events. This simple mechanism is shown to reproduce the observed power-law size distributions and is compatible with our present knowledge on the dynamics of repeat proliferation in the genome.