Surprisingly high number of Twintrons in vertebrates

Twintrons represent a special intronic arrangement in which introns of two different types occupy the same gene position. Consequently, alternative splicing of these introns requires two different spliceosomes competing for the same RNA molecule. So far, only two twintrons have been described in insects. Surprisingly, we discovered several such arrangements in vertebrate genomes, which are quite conserved throughout the lineages. Reviewers: This article was reviewed by Fyodor Kondrashow and Eugene Koonin.

Amoebozoa possess lineage-specific globin gene repertoires gained by individual horizontal gene transfers

The Amoebozoa represent a clade of unicellular amoeboid organisms that display a wide variety of lifestyles, including free-living and parasitic species. For example, the social amoeba Dictyostelium discoideum has the ability to aggregate into a multicellular fruiting body upon starvation, while the pathogenic amoeba Entamoeba histolytica is a parasite of humans. Globins are small heme proteins that are present in almost all extant organisms. Although several genomes of amoebozoan species have been sequenced, little is known about the phyletic distribution of globin genes within this phylum. Only two flavohemoglobins (FHbs) of D. discoideum have been reported and characterized previously while the genomes of Entamoeba species are apparently devoid of globin genes. We investigated eleven amoebozoan species for the presence of globin genes by genomic and phylogenetic in silico analyses. Additional FHb genes were identified in the genomes of four social amoebas and the true slime mold Physarum polycephalum. Moreover, a single-domain globin (SDFgb) of Hartmannella vermiformis, as well as two truncated hemoglobins (trHbs) of Acanthamoeba castellanii were identified. Phylogenetic evidence suggests that these globin genes were independently acquired via horizontal gene transfer from some ancestral bacteria. Furthermore, the phylogenetic tree of amoebozoan FHbs indicates that they do not share a common ancestry and that a transfer of FHbs from bacteria to amoeba occurred multiple times

Comparative genomics of neuroglobin reveals its early origins.

Neuroglobin (Ngb) is a hexacoordinated globin expressed mainly in the central and peripheral nervous system of vertebrates. Although several hypotheses have been put forward regarding the role of neuroglobin, its definite function remains uncertain. Ngb appears to have a neuro-protective role enhancing cell viability under hypoxia and other types of oxidative stress. Ngb is phylogenetically ancient and has a substitution rate nearly four times lower than that of other vertebrate globins, e.g. hemoglobin. Despite its high sequence conservation among vertebrates Ngb seems to be elusive in invertebrates.We determined candidate orthologs in invertebrates and identified a globin of the placozoan Trichoplax adhaerens that is most likely orthologous to vertebrate Ngb and confirmed the orthologous relationship of the polymeric globin of the sea urchin Strongylocentrotus purpuratus to Ngb. The putative orthologous globin genes are located next to genes orthologous to vertebrate POMT2 similarly to localization of vertebrate Ngb. The shared syntenic position of the globins from Trichoplax, the sea urchin and of vertebrate Ngb strongly suggests that they are orthologous. A search for conserved transcription factor binding sites (TFBSs) in the promoter regions of the Ngb genes of different vertebrates via phylogenetic footprinting revealed several TFBSs, which may contribute to the specific expression of Ngb, whereas a comparative analysis with myoglobin revealed several common TFBSs, suggestive of regulatory mechanisms common to globin genes.Identification of the placozoan and echinoderm genes orthologous to vertebrate neuroglobin strongly supports the hypothesis of the early evolutionary origin of this globin, as it shows that neuroglobin was already present in the placozoan-bilaterian last common ancestor. Computational determination of the transcription factor binding sites repertoire provides on the one hand a set of transcriptional factors that are responsible for the specific expression of the Ngb genes and on the other hand a set of factors potentially controlling expression of a couple of different globin genes

Emergence and Evolution of ERM Proteins and Merlin in Metazoans

Ezrin, radixin, moesin, and merlin are cytoskeletal proteins, whose functions are specific to metazoans. They participate in cell cortex rearrangement, including cell–cell contact formation, and play an important role in cancer progression. Here, we have performed a comprehensive phylogenetic analysis of the proteins spanning 87 species. The results describe a possible mechanism for the protein family origin in the root of Metazoa, paralogs diversification in vertebrates, and acquisition of novel functions, including tumor suppression. In addition, a merlin paralog, present in most vertebrates but lost in mammals, has been described here for the first time. We have also highlighted a set of amino acid variations within the conserved motifs as the candidates for determining physiological differences between ERM paralogs

Life cycle adapted upstream open reading frames (uORFs) in 'Trypanosoma congolense': A post-transcriptional approach to accurate gene regulation

The presented work explores the regulatory influence of upstream open reading frames (uORFs) on gene expression in Trypanosoma congolense. More than 31,000 uORFs in total were identified and characterized here. We found evidence for the uORFs’ appearance in the transcriptome to be correlated with proteomic expression data, clearly indicating their repressive potential in T. congolense, which has to rely on post-transcriptional gene expression regulation due to its unique genomic organization. Our data show that uORF’s translation repressive potential does not only correlate with elemental sequence features such as length, position and quantity, but involves more subtle components, in particular the codon and amino acid profiles. This corresponds with the popular mechanistic model of a ribosome shedding initiation factors during the translation of a uORF, which can prevent reinitiation at the downstream start codon of the actual protein-coding sequence, due to the former extensive consumption of crucial translation components. We suggest that uORFs with uncommon codon and amino acid usage can slow down the translation elongation process in T. congolense, systematically deplete the limited factors, and restrict downstream reinitiation, setting up a bottleneck for subsequent translation of the protein-coding sequence. Additionally we conclude that uORFs dynamically influence the T. congolense life cycle. We found evidence that transition to epimastigote form could be supported by gain of uORFs due to alternative trans-splicing, which down-regulate housekeeping genes’ expression and render the trypanosome in a metabolically reduced state of endurance

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

Most genomes are populated by hundreds of thousands of sequences originated from mobile elements. On the one hand, these sequences present a real challenge in the process of genome analysis and annotation. On the other hand, they are very interesting biological subjects involved in many cellular processes. Here we present an overview of transposable elements biodiversity, and we discuss different approaches to transposable elements detection and analyses

Predicted motifs and possible corresponding transcription factors found via phylogenetic footprinting.

<p>Predicted motifs and possible corresponding transcription factors found via phylogenetic footprinting.</p

Distribution of missense mutations over the coding sequences of Teleostei fishes.

<p>The ancestral sequence of Tetrapoda and Teleostei was used as a reference. The sum of nonsynonymous substitutions was calculated for each 30 nucleotides.</p

Schematic representation of the coding exon structure of selected vertebrate Ngbs and several invertebrate globins.

<p>The coding exons and the corresponding protein alignments are printed in red and blue, respectively. Black lines indicate introns. Vertebrate Ngb genes consist of four highly conserved coding exons and three introns at positions B12.2, E11.0 and G7.0. The globins from <i>Ciona intestinalis</i> also possess a central intron at position E10.2. However, this intron is not orthologous to the central intron in Ngb genes. Abbreviations are explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047972#pone.0047972.s005" target="_blank">Table S1</a>.</p