Georgy Smyshlyaev

Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination.

Background: Tyrosine recombinases perform site-specific genetic recombination in bacteria and archaea. They safeguard genome integrity by resolving chromosome multimers, as well as mobilize transposons, phages and integrons, driving dissemination of genetic traits and antibiotic resistance. Despite their abundance and genetic impact, tyrosine recombinase diversity and evolution has not been thoroughly characterized, which greatly hampers their functional classification. Results: Here, we conducted a comprehensive search and comparative analysis of diverse tyrosine recombinases from bacterial, archaeal and phage genomes. We characterized their major phylogenetic groups and show that recombinases of integrons and insertion sequences are closely related to the chromosomal Xer proteins, while integrases of integrative and conjugative elements (ICEs) and phages are more distant. We find that proteins in distinct phylogenetic groups share specific structural features and have characteristic taxonomic distribution. We further trace tyrosine recombinase evolution and propose that phage and ICE integrases originated by acquisition of an N-terminal arm-binding domain. Based on this phylogeny, we classify numerous known ICEs and predict new ones. Conclusions: This work provides a new resource for comparative analysis and functional annotation of tyrosine recombinases. We reconstitute protein evolution and show that adaptation for a role in gene transfer involved acquisition of a specific protein domain, which allows precise regulation of excision and integration.

Ty3/Gypsy long terminals repeat (LTR) retrotransposons are structurally and phylogenetically close to retroviruses. Two notable structural differences between these groups of genetic elements are 1) the presence in retroviruses of an additional envelope gene, env, which mediates infection, and 2) a specific dual ribonuclease H (RNH) domain encoded by the retroviral pol gene. However, similar to retroviruses, many Ty3/Gypsy LTR retrotransposons harbor additional env-like genes, promoting concepts of the infective mode of these retrotransposons. Here, we provide a further line of evidence of similarity between retroviruses and some Ty3/Gypsy LTR retrotransposons. We identify that, together with their additional genes, plant Ty3/Gypsy LTR retrotransposons of the Tat group have a second RNH, as do retroviruses. Most importantly, we show that the resulting dual RNHs of Tat LTR retrotransposons and retroviruses emerged independently, providing strong evidence for their convergent evolution. The convergent resemblance of Tat LTR retrotransposons and retroviruses may indicate similar selection pressures acting on these diverse groups of elements and reveal potential evolutionary constraints on their structure. We speculate that dual RNH is required to accelerate retrotransposon evolution through increased rates of strand transfer events and subsequent recombination events.

The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.

Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons.

Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.

Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.

At present, only fragmentary data about the biodiversity and structural features of L1 retrotransposons of angiosperms related to individual elements from few genomes are available. There is no clear cladistic classification of transposable elements of this family. Structural data on elements from particular groups of angiosperm L1 retrotransposons are also scarce. For these reasons, a comprehensive structural and phylogenetic analysis of L1 retrotransposons in angiosperms has been undertaken. We have compiled information on 19 genomes of angiosperm species that was available in databases and discerned three clades of L1 elements on the base of the phylogeny of the conserved reverse transcriptase region and on their structural organization. It is demonstrated that the emergence of new protein types that form the ribonucleoprotein particles of the retrotransposons and the acquisition of RNH protein-encoding regions by several elements were crucial steps in the formation of new L1 retrotransposon types.

Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta) suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes.