Hypoxia exposure blunts angiogenic signaling and upregulates the antioxidant system in endothelial cells derived from elephant seals

BACKGROUND

Elephant seals exhibit extreme hypoxemic tolerance derived from repetitive hypoxia/reoxygenation episodes they experience during diving bouts. Real-time assessment of the molecular changes underlying protection against hypoxic injury in seals remains restricted by their at-sea inaccessibility. Hence, we developed a proliferative arterial endothelial cell culture model from elephant seals and used RNA-seq, functional assays, and confocal microscopy to assess the molecular response to prolonged hypoxia.

RESULTS

Seal and human endothelial cells exposed to 1% O2 for up to 6 h respond differently to acute and prolonged hypoxia. Seal cells decouple stabilization of the hypoxia-sensitive transcriptional regulator HIF-1α from angiogenic signaling. Rapid upregulation of genes involved in glutathione (GSH) metabolism supports the maintenance of GSH pools, and intracellular succinate increases in seal but not human cells. High maximal and spare respiratory capacity in seal cells after hypoxia exposure occurs in concert with increasing mitochondrial branch length and independent from major changes in extracellular acidification rate, suggesting that seal cells recover oxidative metabolism without significant glycolytic dependency after hypoxia exposure.

CONCLUSIONS

We found that the glutathione antioxidant system is upregulated in seal endothelial cells during hypoxia, while this system remains static in comparable human cells. Furthermore, we found that in contrast to human cells, hypoxia exposure rapidly activates HIF-1 in seal cells, but this response is decoupled from the canonical angiogenesis pathway. These results highlight the unique mechanisms that confer extraordinary tolerance to limited oxygen availability in a champion diving mammal.

Insights into mammalian TE diversity through the curation of 248 genome assemblies

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

Horizontal transfer of transposable elements is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of transposable elements at what appears to be a high rate compared to other mammals. We investigated the occurrence of horizontally transferred DNA transposons involving bats. We found over 200 putative horizontally transferred elements within bats; sixteen transposons were shared across distantly related mammalian clades and two other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.

Identification of viral RNA sequences in vampire bats (Desmodus rotundus) from central Mexico

Bats are important reservoirs of viral entities that cause diverse economical and health problems in several sectors. The purpose of this study was to determine the prevalence of the rabies virus in vampire bats. We also tested for 3 other zoonotic viruses in the collected tissue. We captured 45 vampire bats (Desmodus rotundus), which were measured and  sexed under standard parameters. We followed an RT-PCR reaction to amplify the viral products of four virus types: chikungunya (CHIKV), dengue (DENV), rabies (RABV) and Zika virus (ZIKV) from cerebral tissue. We obtained an amplicon of 100 bp for ZIKV in 2 samples, representing a prevalence of 4.4%. An amplicon of 581 bp for RABV was observed in 9 individuals, which is equivalent to 20% of our sample. We obtained 4 different haplotypes for RABV and a single haplotype for ZIKV. We did not record the presence of DENV and CHIKV. We corroborated the presence of the family Rhabdoviridae in the vampire bat and recorded the presence of ZIKV for the first time in this bat species.

Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality

Bat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past ~40 million years. Each also exhibits its own target site preferences (sometimes shared with other TEs) that impact where they are likely to insert when mobilizing. Therefore, bats provide a great resource for understanding the diversity of TE insertion patterns. To gain insight into how these diverse TEs impact genome structure, we performed comparative spatial analyses between different TE classes and genomic features, including genic regions and CpG islands. Our results showed a depletion of all TEs in the coding sequence and revealed patterns of species- and element-specific attraction in the transcript. Trends of attraction in the distance tests also suggested significant TE activity in regions adjacent to genes. In particular, the enrichment of small, non-autonomous TE insertions in introns and near coding regions supports the hypothesis that the genomic distribution of TEs is the product of a balance of the TE insertion preference in open chromatin regions and the purifying selection against TEs within genes.

Transcriptomic analysis elucidates evolution of the major histocompatibility complex class I in neotropical bats

The Order Chiroptera comprises more than 1,400 species, each with its evolutionary history and under unique selective pressures, among which are the host–pathogen interactions. Bats have coped with complex interactions with a broad spectrum of microbes throughout their evolutionary history, prompting the development of unique adaptations that allow them to co-exist with microbes with pathogenic potential more efficiently than other nonadapted species. In this sense, an extraordinary immune system with unique adaptations has been hypothesized in bats. To explore this, we focused on the major histocompatibility complex (MHC), which plays a crucial role in pathogen recognition and presentation to T cells to trigger the adaptive immune response. We analyzed MHC class I transcripts in five species, each from different families of New World bats. From RNA-seq data, we assembled a partial region of the MHC-I comprising the α1 and α2 domains, which are responsible for peptide binding and recognition. We described five putative functional variants, two of which have two independent insertions at the α2 domain. Our results suggest that this insertion appeared after the divergence of the order Chiroptera and may have an adaptive function in the defense against intracellular pathogens, providing evidence of positive selection and trans-specific polymorphism on the peptide-binding sites.

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats

High-throughput RNA sequencing is a powerful tool that allows us to perform gene prediction and analyze tissue-specific overexpression of genes, but also at species level comparisons can be performed, although in a more restricted manner. In the present study complete liver transcriptomes of five tropical bat species were De novo assembled and annotated. Highly expressed genes in the five species were involved in glycolysis and lipid metabolism pathways. Cross-species differential expression analysis was conducted using single copy orthologues shared across the five species. Between 22 and 29 orthologs were upregulated for each species. We detected upregulated expression in Artibeus jamaicensis genes related to fructose metabolism pathway. Such findings can be correlated with A. jamaicensis dietary habits, as it was the unique frugivorous species included. This is the first report of transcriptome assembly by RNA-seq in these species, except for A. jamaicensis and as far as our knowledge is the first cross-species comparisons of transcriptomes and gene expression in tropical bats.

Genetic Variation at Exon 2 of the MHC Class II DQB Locus in Blue Whale (Balaenoptera musculus) from the Gulf of California

The genes of the Major Histocompatibility Complex (MHC) play an important role in the vertebrate immune response and are among the most polymorphic genes known in vertebrates. In some marine mammals, MHC genes have been shown to be characterized by low levels of polymorphism compared to terrestrial taxa; this reduction in variation is often explained as a result of lower pathogen pressures in marine habitats. To determine if this same reduction in variation applies to the migratory population of blue whales (Balaenoptera musculus) that occurs in the Gulf of California, we genotyped a 172 bp fragment of exon 2 of the MHC Class II DQB locus for 80 members of this population. Twenty-two putatively functional DQB allotypes were identified, all of which were homologous with DQB sequences from other cetacean species. Up to 5 putative alleles per individual were identified, suggesting that gene duplication has occurred at this locus. Rates of non-synonymous to synonymous substitutions (ω) and maximum likelihood analyses of models of nucleotide variation provided potential evidence of ongoing positive selection at this exon. Phylogenetic analyses of DQB alleles from B. musculus and 16 other species of cetaceans revealed trans-specific conservation of MHC variants, suggesting that selection has acted on this locus over prolonged periods of time. Collectively our findings reveal that immunogenic variation in blue whales is comparable to that in terrestrial mammals, thereby providing no evidence that marine taxa are subject to reduced pathogen-induced selective pressures.