Gene conversion in human rearranged immunoglobulin genes

Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V<sub>H</sub> segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V<sub>H</sub> replacements with no addition of untemplated nucleotides at the V<sub>H</sub>–V<sub>H</sub> joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V<sub>H</sub> replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion

Elite opinion and foreign policy in post-communist Russia

Russian elite opinion on matters of foreign policy may be classified as ‘Liberal Westerniser’, ‘Pragmatic Nationalist’ and ‘Fundamentalist Nationalist’, terms that reflect longstanding debates about the country’s relationship with the outside world. An analysis of press statements and election manifestoes together with a programme of elite interviews between 2004 and 2006 suggests a clustering of opinion on a series of strategic issues. Liberal Westernisers seek the closest possible relationship with Europe, and favour eventual membership of the EU and NATO. Pragmatic Nationalists are more inclined to favour practical co-operation, and do not assume an identity of values or interests with the Western countries. Fundamentalist Nationalists place more emphasis on the other former Soviet republics, and on Asia as much as Europe, and see the West as a threat to Russian values as well as to its state interests. Each of these positions, in turn, draws on an identifiable set of domestic constituencies: Liberal Westernisers on the promarket political parties, Pragmatic Nationalists on the presidential administration and defence and security ministries, and Fundamentalist Nationalists on the Orthodox Church and Communists

Disturbance of meromixis in saline Lake Shira (Siberia, Russia): possible reasons and ecosystem response

Saline Lake Shira (Southern Siberia, Russia) was meromictic through the observation period 2002-2015. During the under-ice periods of 2015 and 2016, complete mixing of the water column was recorded for the first time, and hydrogen sulphide temporarily disappeared from the water column of the lake; i.e. in those years the lake turned to holomixis. In the summer of 2015, a sharp increase in chlorophyll a, organic carbon, zooplankton, and phytoflagellates was observed in the lake, which was probably due to the release of nutrients from the monimolimnion. Purple sulfur bacteria completely disappeared from the lake after the first mixing in 2015, and did not reappear despite the restoration of meromixis in 2017. Thus, it was demonstrated that purple sulfur bacteria are sensitive to the weakening of the stratification of Lake Shira. Based on the data of the seasonal monitoring of temperature and salinity profiles over the period 2002-2017, it was presumed that the main cause of deep mixing in 2015 was the weakening of the salinity gradient due to strong wind impact and early ice retreat in the spring of 2014. In addition, it was shown that in previous years a significant contribution to the maintenance of meromixis was made by an additional influx of fresh water, which caused a rise in the lake level in the period 2002-2007. Thus, we identified a relationship between the stratification regime of the lake and the change in its level, which provides valuable information both for the forecast of water quality and for reconstruction of the Holocene climate humidity in this region of Southern Siberia from the sediment cores of Lake Shira

Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome

The spliceosome, a sophisticated molecular machine involved in the removal of intervening sequences from the coding sections of eukaryotic genes, appeared and subsequently evolved rapidly during the early stages of eukaryotic evolution. The last eukaryotic common ancestor (LECA) had both complex spliceosomal machinery and some spliceosomal introns, yet little is known about the early stages of evolution of the spliceosomal apparatus. The Sm/Lsm family of proteins has been suggested as one of the earliest components of the emerging spliceosome and hence provides a first in-depth glimpse into the evolving spliceosomal apparatus. An analysis of 335 Sm and Sm-like genes from 80 species across all three kingdoms of life reveals two significant observations. First, the eukaryotic Sm/Lsm family underwent two rapid waves of duplication with subsequent divergence resulting in 14 distinct genes. Each wave resulted in a more sophisticated spliceosome, reflecting a possible jump in the complexity of the evolving eukaryotic cell. Second, an unusually high degree of conservation in intron positions is observed within individual orthologous Sm/Lsm genes and between some of the Sm/Lsm paralogs. This suggests that functional spliceosomal introns existed before the emergence of the complete Sm/Lsm family of proteins; hence, spliceosomal machinery with considerably fewer components than today's spliceosome was already functional

The Pierre Auger Observatory: Contributions to the 34th International Cosmic Ray Conference (ICRC 2015)

Contributions of the Pierre Auger Collaboration to the 34th International Cosmic Ray Conference, 30 July - 6 August 2015, The Hague, The NetherlandsComment: 24 proceedings, the 34th International Cosmic Ray Conference, 30 July - 6 August 2015, The Hague, The Netherlands; will appear in PoS(ICRC2015

A putative antiviral role of plant cytidine deaminases

[EN] Background: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade. Host cytidine deaminases (e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis. By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity. To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation. The model plant Arabidopsis thaliana genome encodes nine cytidine deaminases (AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Methods: Here we tested the effects of expression of AtCDAs on the pararetrovirus Cauliflower mosaic virus (CaMV). Two different experiments were carried out. First, we transiently overexpressed each one of the nine A. thaliana AtCDA genes in Nicotiana bigelovii plants infected with CaMV, and characterized the resulting mutational spectra, comparing them with those generated under normal conditions. Secondly, we created A. thaliana transgenic plants expressing an artificial microRNA designed to knock-out the expression of up to six AtCDA genes. This and control plants were then infected with CaMV. Virus accumulation and mutational spectra where characterized in both types of plants. Results: We have shown that the A. thaliana AtCDA1 gene product exerts a mutagenic activity, significantly increasing the number of G to A mutations in vivo, with a concomitant reduction in the amount of CaMV genomes accumulated. Furthermore, the magnitude of this mutagenic effect on CaMV accumulation is positively correlated with the level of AtCDA1 mRNA expression in the plant. Conclusions: Our results suggest that deamination of viral genomes may also work as an antiviral mechanism in plants.This work was supported by the former Spanish Ministerio de Ciencia e Innovación-FEDER grant BFU2009-06993 to SFE. JMC was supported by the CSIC JAE-doc program/Fondo Social Europeo. AG-P was supported by a grant for Scientific and Technical Activities and by grant P10-CVI-65651, both from Junta de Andalucía.Martín, S.; Cuevas, J.; Grande-Perez, A.; Elena Fito, SF. (2017). A putative antiviral role of plant cytidine deaminases. F1000Research. 1-14. https://doi.org/10.12688/f1000research.11111.2S11

Intron Evolution: Testing Hypotheses of Intron Evolution Using the Phylogenomics of Tetraspanins

BACKGROUND: Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life. METHODOLOGY/PRINCIPAL FINDINGS: We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three additional ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel introns in combination with the ancestral introns 1 to 6, define three basic tetraspanin gene structures which have been conserved throughout the animal kingdom. Our phylogenomic approach also allows the estimation of the time at which the introns of the 33 human tetraspanin paralogs appeared, which in many cases coincides with the concomitant acquisition of new introns. On the other hand, we observed that new introns (introns other than 1-6, 4a, b and c) were not randomly inserted into the tetraspanin gene structure. The region of tetraspanin genes corresponding to the small extracellular loop (SEL) accounts for only 10.5% of the total sequence length but had 46% of the new animal intron insertions. CONCLUSIONS/SIGNIFICANCE: Our results indicate that tests of intron evolution are strengthened by the phylogenomic approach with specific gene families like tetraspanins. These tests add to our understanding of genomic innovation coupled to major evolutionary divergence events, functional constraints and the timing of the appearance of evolutionary novelty

Width of Gene Expression Profile Drives Alternative Splicing

Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection

Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences

The mechanism by which protein-coding portions of eukaryotic genes came to be separated by long non-coding stretches of DNA, and the purpose for this perplexing arrangement, have remained unresolved fundamental biological problems for three decades. We report here a plausible solution to this problem based on analysis of open reading frame (ORF) length constraints in the genomes of nine diverse species. If primordial nucleic acid sequences were random in sequence, functional proteins that are innately long would not be encoded due to the frequent occurrence of stop codons. The best possible way that a long protein-coding sequence could have been derived was by evolving a split-structure from the random DNA (or RNA) sequence. Results of the systematic analyses of nine complete genome sequences presented here suggests that perhaps the major underlying structural features of split-genes have evolved due to the indigenous occurrence of split protein-coding genes in primordial random nucleotide sequence. The results also suggest that intron-rich genes containing short exons may have been the original form of genes intrinsically occurring in random DNA, and that intron-poor genes containing long exons were perhaps derived from the original intron-rich genes

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function

<p>Abstract</p> <p>Background</p> <p>Plants contain numerous <it>Su(var)3-9 </it>homologues (<it>SUVH</it>) and related (<it>SUVR</it>) genes, some of which await functional characterization. Although there have been studies on the evolution of plant <it>Su(var)3-9 SET </it>genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation.</p> <p>Results</p> <p>Putative orthologs of plant Su(var)3-9 SET protein sequences were retrieved from major representatives of land plants. A novel clustering that included most members analyzed, henceforth referred to as core <it>Su(var)3-9 </it>homologues and related (<it>cSUVHR</it>) gene clade, was identified as well as all orthologous groups previously identified. Our analysis showed that plant Su(var)3-9 SET proteins possessed a variety of domain organizations, and can be classified into five types and ten subtypes. Plant <it>Su(var)3-9 SET </it>genes also exhibit a wide range of gene structures among different paralogs within a family, even in the regions encoding conserved PreSET and SET domains. We also found that the majority of SUVH members were intronless and formed three subclades within the SUVH clade.</p> <p>Conclusions</p> <p>A detailed phylogenetic analysis of the plant <it>Su(var)3-9 SET g</it>enes was performed. A novel deep phylogenetic relationship including most plant <it>Su(var)3-9 SET </it>genes was identified. Additional domains such as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial PreSET/SET/PostSET domain organization. At least three classes of gene structures had been formed before the divergence of <it>Physcomitrella patens </it>(moss) from other land plants. One or multiple retroposition events might have occurred among <it>SUVH </it>genes with the donor genes leading to the V-2 orthologous group. The structural differences among evolutionary groups of plant <it>Su(var)3-9 SET </it>genes with different functions were described, contributing to the design of further experimental studies.</p