Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin.

Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.

LTR Retroelements and Bird Adaptation to Arid Environments.

TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth's dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments.

Transcriptional Contribution of Transposable Elements in Relation to Salinity Conditions in Teleosts and Silencing Mechanisms Involved.

Fish are an interesting taxon comprising species adapted to a wide range of environments. In this work, we analyzed the transcriptional contribution of transposable elements (TEs) in the gill transcriptomes of three fish species exposed to different salinity conditions. We considered the giant marbled eel Anguilla marmorata and the chum salmon Oncorhynchus keta, both diadromous, and the marine medaka Oryzias melastigma, an euryhaline organism sensu stricto. Our analyses revealed an interesting activity of TEs in the case of juvenile eels, commonly adapted to salty water, when exposed to brackish and freshwater conditions. Moreover, the expression assessment of genes involved in TE silencing mechanisms (six in heterochromatin formation, fourteen known to be part of the nucleosome remodeling deacetylase (NuRD) complex, and four of the Argonaute subfamily) unveiled that they are active. Finally, our results evidenced for the first time a krüppel-associated box (KRAB)-like domain specific to actinopterygians that, together with TRIM33, might allow the functioning of NuRD complex also in fish species. The possible interaction between these two proteins was supported by structural prediction analyses.

Transposable Element Tissue-Specific Response to Temperature Stress in the Stenothermal Fish Puntius tetrazona.

Ray-finned fish represent a very interesting group of vertebrates comprising a variety of organisms living in different aquatic environments worldwide. In the case of stenothermal fish, thermal fluctuations are poorly tolerated, thus ambient temperature represents a critical factor. In this paper, we considered the tiger barb Puntius tetrazona, a freshwater fish belonging to the family Cyprinidae, living at 21-28 °C. We analyzed the available RNA-Seq data obtained from specimens exposed at 27 °C and 13 °C to investigate the transcriptional activity of transposable elements (TEs) and genes encoding for proteins involved in their silencing in the brain, gill, and liver. TEs are one of the tools generating genetic variability that underlies biological evolution, useful for organisms to adapt to environmental changes. Our findings highlighted a different response of TEs in the three analyzed tissues. While in the brain and gill, no variation in TE transcriptional activity was observed, a remarkable increase at 13 °C was recorded in the liver. Moreover, the transcriptional analysis of genes encoding proteins involved in TE silencing such as heterochromatin formation, the NuRD complex, and the RISC complex (e.g., AGO and GW182 proteins) highlighted their activity in the hepatic tissue. Overall, our findings suggested that this tissue is a target organ for this kind of stress, since TE activation might regulate the expression of stress-induced genes, leading to a better response of the organism to temperature changes. Therefore, this view corroborates once again the idea of a potential role of TEs in organism rapid adaptation, hence representing a promising molecular tool for species resilience.

Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome.

Caudata is an order of amphibians with great variation in genome size, which can reach enormous dimensions in salamanders. In this work, we analysed the activity of transposable elements (TEs) in the transcriptomes obtained from female and male gonads of the Chinese fire-bellied newt, Cynops orientalis, a species with a genome about 12-fold larger than the human genome. We also compared these data with genomes of two basal sarcopterygians, coelacanth and lungfish. In the newt our findings highlighted a major impact of non-LTR retroelements and a greater total TE activity compared to the lungfish Protopterus annectens, an organism also characterized by a giant genome. This difference in TE activity might be due to the presence of young copies in newt in agreement also with the increase in the genome size, an event that occurred independently and later than lungfish. Moreover, the activity of 33 target genes encoding proteins involved in the TE host silencing mechanisms, such as Ago/Piwi and NuRD complex, was evaluated and compared between the three species analysed. These data revealed high transcriptional levels of the target genes in both newt and lungfish and confirmed the activity of NuRD complex genes in adults. Finally, phylogenetic analyses performed on PRDM9 and TRIM28 allowed increasing knowledge about the evolution of these two key genes of the NuRD complex silencing mechanism in vertebrates. Our results confirmed that the gigantism of the newt genomes may be attributed to the activity and accumulation of TEs.

Contribution of Drugs Interfering with Protein and Cell Wall Synthesis to the Persistence of Pseudomonas aeruginosa Biofilms: An In Vitro Model.

The occurrence of Pseudomonas aeruginosa (PA) persisters, including viable but non-culturable (VBNC) forms, subpopulations of tolerant cells that can survive high antibiotic doses, is the main reason for PA lung infections failed eradication and recurrence in Cystic Fibrosis (CF) patients, subjected to life-long, cyclic antibiotic treatments. In this paper, we investigated the role of subinhibitory concentrations of different anti-pseudomonas antibiotics in the maintenance of persistent (including VBNC) PA cells in in vitro biofilms. Persisters were firstly selected by exposure to high doses of antibiotics and their abundance over time evaluated, using a combination of cultural, qPCR and flow cytometry assays. Two engineered GFP-producing PA strains were used. The obtained results demonstrated a major involvement of tobramycin and bacterial cell wall-targeting antibiotics in the resilience to starvation of VBNC forms, while the presence of ciprofloxacin and ceftazidime/avibactam lead to their complete loss. Moreover, a positive correlation between tobramycin exposure, biofilm production and c-di-GMP levels was observed. The presented data could allow a deeper understanding of bacterial population dynamics during the treatment of recurrent PA infections and provide a reliable evaluation of the real efficacy of the antibiotic treatments against the bacterial population within the CF lung.

Transposable Elements and Teleost Migratory Behaviour.

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

Mobile Elements in Ray-Finned Fish Genomes.

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.