Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes

Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation–decentralized innovation–hierarchical import model that accounts for the emergence of eukaryotic complexity.

The Use of Biologic Wound Healing Agents in Cheek Reconstruction

The unique requirements of reconstructing cheek defects, often with its proximity to the mobile elements of the face including the lip and the eyelid, have been met very handily with the directed and thoughtful use of biologic wound healing agents. One of the key advantages of these agents is their ability to provide coverage in patients with multiple comorbid conditions for the mobile elements of the cheek where the cervicofacial advancement flap is contraindicated due to its anesthetic requirement. The biologic agents are also highly successful coverage options for patients who have limited skin laxity to provide for proper skin closure using the standard cheek closure techniques with local flaps. In addition, these agents provide an ability to provide stable wound closure with minimal wound care while waiting for the excisional biopsy results to be finalized. This article describes the unique indications for biologic wound agents, including preservation of lip and eyelid mobile element anatomy without retraction from a local flap, which has not been previously described.

Giant Starship elements mobilize accessory genes in fungal genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a novel group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize 4 additional Starships whose past and ongoing activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first known agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

Hierarchical length and sequence preferences establish a single major piRNA 3'-end

PIWI-interacting RNAs (piRNAs) guard germline genomes against the deleterious action of retroviruses and other mobile genetic elements. How piRNAs faithfully discriminate between self and non-self to restrict all mobile elements while sparing essential genes remains a key outstanding question in genome biology. PiRNAs use extensive base-pairing to recognize their targets and variable 3'ends could change the specificity and efficacy of piRNA silencing. Here, we identify conserved rules that ensure the generation of a single major piRNA 3'end in flies and mice. Our data suggest that the PIWI proteins initially define a short interval on pre-piRNAs that grants access to the ZUC-processor complex. Within this Goldilocks zone, the preference of the ZUC-processor to cut in front of a Uridine determines the ultimate processing site. We observe a mouse-specific roadblock that relocates the Goldilocks zone and generates an opportunity for consecutive trimming by PNLDC1. Our data reveal a conserved hierarchy between length and sequence preferences that controls the piRNA sequence space. The unanticipated precision of 3'end formation bolsters the emerging understanding that the functional piRNA sequence space is tightly controlled to ensure effective defense.

A bistable orthogonal prokaryotic differentiation system underlying development of conjugative transfer competence

The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that stands model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. The ICE only transfers from a small fraction of cells in a population, which we uncover here, results from a dedicated transfer competence program imposed by the ICE. Transfer competence is orthogonally maintained in individual cells in which it is activated, making them the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.

Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients

Mesial temporal lobe epilepsy (MTLE) is the most common form of epilepsy, and temporal lobe epilepsy patients with hippocampal sclerosis (TLE-HS) show worse drug treatment effects and prognosis. TLE has been shown to have a genetic component, but its genetic research has been mostly limited to coding sequences of genes with known association to epilepsy. Representing a major component of the genome, mobile elements (MEs) are believed to contribute to the genetic etiology of epilepsy despite limited research. We analyzed publicly available human RNA-seq-based transcriptome data to determine the role of mobile elements in epilepsy by performing de novo transcriptome assembly, followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts), to compare their frequency across different sample groups. Significantly higher levels of ME-transcripts in hippocampal tissues of epileptic patients, particularly in TLE-HS, were observed. Among ME classes, short interspersed nuclear elements (SINEs) were shown to be the most frequent contributor to ME-transcripts, followed by long interspersed nuclear elements (LINEs) and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences. For protein coding genes, ME sequences were mostly found in the 3′-UTR regions, with a significant portion also in the coding sequences (CDSs), leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for the mRNA splicing process and an apparent bias in epileptic transcriptomes toward neural- and epilepsy-associated genes. The findings of this study suggest that abnormal splicing involving MEs, leading to loss of functions in critical genes, plays a role in epilepsy, particularly in TLE-HS, thus providing a novel insight into the molecular mechanisms underlying epileptogenesis.

Emergence of the cfr gene in Vibrio diabolicus of seafood origin

The emergence and transmission of multidrug resistance gene cfr incur great public health concerns worldwide. Recently, Gram-negative pathogens were found to carry cfr by various mobile elements. Here, we investigated a cfr -positive Vibrio diabolicus by phenotyping and genomic analysis, and found cfr in a translocatable structure (IS 26 - hp - cfr -IS 26 ) among the MDR region in pNV27-cfr-208K, an emerging MDR plasmid in Vibrio species. This study highlights the necessity of surveillance of cfr in bacteria of diverse origins.

Landscape, Soil, Lithology, Climate and Permafrost Control on Dissolved Carbon, Major and Trace Elements in the Ob River, Western Siberia

In order to foresee possible changes in the elementary composition of Arctic river waters, complex studies with extensive spatial coverage, including gradients in climate and landscape parameters, are needed. Here, we used the unique position of the Ob River, draining through the vast partially frozen peatlands of the western Siberia Lowland and encompassing a sizable gradient of climate, permafrost, vegetation, soils and Quaternary deposits, to assess a snap-shot (8–23 July 2016) concentration of all major and trace elements in the main stem (~3000 km transect from the Tom River confluence in the south to Salekhard in the north) and its 11 tributaries. During the studied period, corresponding to the end of the spring flood-summer baseflow, there was a systematic decrease, from the south to the north, of Dissolved Inorganic Carbon (DIC), Specific Conductivity, Ca and some labile trace elements (Mo, W and U). In contrast, Dissolved Organic Carbon (DOC), Fe, P, divalent metals (Mn, Ni, Cu, Co and Pb) and low mobile trace elements (Y, Nb, REEs, Ti, Zr, Hf and Th) sizably increased their concentration northward. The observed latitudinal pattern in element concentrations can be explained by progressive disconnection of groundwaters from the main river and its tributaries due to a northward increase in the permafrost coverage. A northward increase in bog versus forest coverage and an increase in DOC and Fe export enhanced the mobilization of insoluble, low mobile elements which were present in organo-ferric colloids (1 kDa—0.45 µm), as confirmed by an in-situ dialysis size fractionation procedure. The chemical composition of the sampled mainstream and tributaries demonstrated significant (p < 0.01) control of latitude of the sampling point; permafrost coverage; proportion of bogs, lakes and floodplain coverage and lacustrine and fluvio-glacial Quaternary deposits of the watershed. This impact was mostly pronounced on DOC, Fe, P, divalent metals (Mn, Co, Ni, Cu and Pb), Rb and low mobile lithogenic trace elements (Al, Ti, Cr, Y, Zr, Nb, REEs, Hf and Th). The pH and concentrations of soluble, highly mobile elements (DIC, SO4, Ca, Sr, Ba, Mo, Sb, W and U) positively correlated with the proportion of forest, loesses, eluvial, eolian, and fluvial Quaternary deposits on the watershed. Consistent with these correlations, a Principal Component Analysis demonstrated two main factors explaining the variability of major and trace element concentration in the Ob River main stem and tributaries. The DOC, Fe, divalent metals and trivalent and tetravalent trace elements were presumably controlled by a northward increase in permafrost, floodplain, bogs, lakes and lacustrine deposits on the watersheds. The DIC and labile alkaline-earth metals, oxyanions (Mo, Sb and W) and U were impacted by southward-dominating forest coverage, loesses and eluvial and fertile soils. Assuming that climate warming in the WSL will lead to a northward shift of the forest and permafrost boundaries, a “substituting space for time” approach predicts a future increase in the concentration of DIC and labile major and trace elements and a decrease of the transport of DOC and low soluble trace metals in the form of colloids in the main stem of the Ob River. Overall, seasonally-resolved transect studies of large riverine systems of western Siberia are needed to assess the hydrochemical response of this environmentally-important territory to on-going climate change.