The Enterprise,a massive transposon carrying Spok meiotic drive genes

The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.

Transposable elements (TEs) are major agents of change in eukaryotic genomes. Their ability to selfishly parasitize their host replication machinery has large impacts on both genome size and on gene regulation (Chénais et al. 2012). In extreme cases, TEs can contribute up to 85% of genomic content (Schnable et al. 2009), and expansion and reduction of TEs can result in rapid changes in both genome size and architecture (Haas et al. 2009; Möller and Stukenbrock 2017; Talla et al. 2017). Generally, TEs have small sizes (∼50–12,000 bp) and accomplish these large-scale changes through their sheer number. For example, there are ∼1.1 million Alu elements in the human genome, which have had a large impact on genome evolution (Jurka 2004; Bennett et al. 2008). The largest known cases among Class I retrotransposons are long terminal repeat (LTR) elements that can be as large as 30 kb, but among Class II DNA transposons, Mavericks/Polintons are known to grow as large as 40 kb through the capture of additional open reading frames (ORFs) (Arkhipova and Yushenova 2019). Recently, a behemoth TE named Teratorn was described in teleost fish; it can be up to 182 kb in length, dwarfing all other known TEs. Teratorn has achieved this impressive size by fusing a piggyBac DNA transposon with a herpesvirus, thereby blurring the line between TEs and viruses (Inoue et al. 2017, 2018). Truly massive transposons may be lurking in the depths of many eukaryotic genomes, but the limitations of short-read genome sequencing technologies and the lack of population-level high-quality assemblies may make them difficult to identify.The Spok block is a large genomic feature that was first identified thanks to the presence of the spore killing (Spok) genes in species from the genus Podospora (Grognet et al. 2014; Vogan et al. 2019). The Spoks are selfish genetic elements that bias their transmission to the next generation in a process known as meiotic drive. Here, drive occurs by inducing the death of spores that do not inherit them, through a single protein that operates as both a toxin and an antidote (Grognet et al. 2014; Vogan et al. 2019). The first Spok gene described, Spok1, was discovered in Podospora comata (Grognet et al. 2014). In P. anserina, the homologous gene Spok2 is found at high population frequencies, whereas two other genes of the Spok family, Spok3 and Spok4, are at low to intermediate frequencies (Vogan et al. 2019). Unlike Spok1 and Spok2, however, Spok3 and Spok4 are always associated with a large genomic region (the Spok block). The Spok block can be located at different chromosomal locations in different individuals but is never found more than once in natural strains. The number of Spok genes and the location of the Spok block (which carries Spok3, Spok4, or both) define the overall meiotic driver behavior of a given genome, which can be classified into the so-called Podospora spore killers or Psks (van der Gaag et al. 2000; Vogan et al. 2019). The Spok block stands out not only because of its size, typically around 150 kb, but also because there is otherwise high genome collinearity among strains of P. anserina and with the related species P. comata and P. pauciseta (Vogan et al. 2019).The fact that the Spok block is found at unique genomic positions between otherwise highly similar strains is of prime interest as each novel Spok block position creates a unique meiotic drive type (Psk) due to the intricacies of meiosis in Podospora (Vogan et al. 2019). We therefore set out to determine the mechanism through which the Spok block relocates throughout the genome. Additionally, we annotated the gene content of the various Spok blocks to describe their composition and understand what represents the minimal component of the Spok block. Lastly, we conducted fitness assays to investigate whether the presence of the Spok block imparts any detrimental effects upon the host.     

The protein product of the het-s heterokaryon incompatibility gene of the fungus Podospora anserina behaves as a prion analog

The het-s locus of Podospora anserina is a heterokaryon incompatibility locus. The coexpression of the antagonistic het-s and het-S alleles triggers a lethal reaction that prevents the formation of viable heterokaryons. Strains that contain the het-s allele can display two different phenotypes, [Het-s] or [Het-s*], according to their reactivity in incompatibility. The detection in these phenotypically distinct strains of a protein expressed from the het-s gene indicates that the difference in reactivity depends on a posttranslational difference between two forms of the polypeptide encoded by the het-s gene. This posttranslational modification does not affect the electrophoretic mobility of the protein in SDS/PAGE. Several results suggest a similarity of behavior between the protein encoded by the het-s gene and prions. The [Het-s] character can propagate in [Het-s*] strains as an infectious agent, producing a [Het-s*] → [Het-s] transition, independently of protein synthesis. Expression of the [Het-s] character requires a functional het-s gene. The protein present in [Het-s] strains is more resistant to proteinase K than that present in [Het-s*] mycelium. Furthermore, overexpression of the het-s gene increases the frequency of the transition from [Het-s*] to [Het-s]. We propose that this transition is the consequence of a self-propagating conformational modification of the protein mediated by the formation of complexes between the two different forms of the polypeptide.     

Thermal niches of planktonic foraminifera are static throughout glacial–interglacial climate change

Abiotic niche lability reduces extinction risk by allowing species to adapt to changing environmental conditions in situ. In contrast, species with static niches must keep pace with the velocity of climate change as they track suitable habitat. The rate and frequency of niche lability have been studied on human timescales (months to decades) and geological timescales (millions of years), but lability on intermediate timescales (millennia) remains largely uninvestigated. Here, we quantified abiotic niche lability at 8-ka resolution across the last 700 ka of glacial–interglacial climate fluctuations, using the exceptionally well-known fossil record of planktonic foraminifera coupled with Atmosphere–Ocean Global Climate Model reconstructions of paleoclimate. We tracked foraminiferal niches through time along the univariate axis of mean annual temperature, measured both at the sea surface and at species’ depth habitats. Species’ temperature preferences were uncoupled from the global temperature regime, undermining a hypothesis of local adaptation to changing environmental conditions. Furthermore, intraspecific niches were equally similar through time, regardless of climate change magnitude on short timescales (8 ka) and across contrasts of glacial and interglacial extremes. Evolutionary trait models fitted to time series of occupied temperature values supported widespread niche stasis above randomly wandering or directional change. Ecotype explained little variation in species-level differences in niche lability after accounting for evolutionary relatedness. Together, these results suggest that warming and ocean acidification over the next hundreds to thousands of years could redistribute and reduce populations of foraminifera and other calcifying plankton, which are primary components of marine food webs and biogeochemical cycles.

Abiotic niche dynamics determine patterns of community composition over space and regulate trajectories of diversity over time (1). Both niche lability (2, 3) and conservatism (1, 4) have been proposed to spur speciation, and abiotic niche lability has been associated with ecological invasions (5–7) and with reduced risk of extinction during times of climate change (8). Thus, a deeper understanding of species’ propensity for niche stasis versus lability could improve predictions of biodiversity restructuring in response to anthropogenic climate change (9).Stasis in species’ abiotic niches through time has been documented in empirical research, but most such studies have been limited to ecological niche modeling on decadal scales (reviewed in ref. 10) or paleoecological examination on 10⁶ to 10⁷ y scales (5, 11, 12). Since empirical rates of niche change are scarce and difficult to acquire, many studies merely assume that niche evolution occurs at a constant rate along branches of a phylogeny (2, 3, 6, 7). Niche dynamics at intermediate timescales of centuries to millennia are particularly poorly documented (10), and studies at this meso scale have been restricted to terrestrial systems (e.g., refs. 13–15) or to comparisons between the present day and the single historical time step of the Last Glacial Maximum, ∼21 ka (16–20). Quantifying the rate and relative frequency of niche change in marine species over timescales of 10² to 10⁵ years is important, however, because species will adapt or go extinct in response to anthropogenic ocean changes over this timescale (21).Here, we investigated climatic niche lability from the rich sedimentary archive of global planktonic foraminifera across the last 700 ka of glacial–interglacial cycles at 8-ka resolution. Planktonic foraminifera (Protista) construct “shells” (tests) of calcite, thereby sequestering carbon and recording an isotopic signature of past ocean conditions. Tests readily accumulate over large expanses of the seafloor. Consequently, the fossil record of foraminifera—arguably “the best fossil record on Earth” (22)—affords an exceptionally high-resolution view into past species distributions. This detailed record fuels studies of biostratigraphy, paleoclimatology, and paleoecology (20, 22–25). Moreover, the complete species diversity of planktonic foraminifera has been described for the Plio–Pleistocene, with good agreement between morphological and molecular phylogenies (22, 25–27). Although some have speculated that foraminifera competitively exclude each other (24), recent work found that planktonic foraminifera species seldom restrict each other’s distributions (28). Presumably, therefore, species occupy the full envelope of existing environmental conditions within their tolerance limits, and geographic distributions are determined almost entirely by physical ocean conditions.We developed five analyses to investigate the degree of abiotic niche lability in foraminifera. All methods examined the univariate niche axis of temperature, which is the single most important explanatory variable in regard to geographic distributions of foraminifera (20, 29–32) and is a climate-related stressor and extinction driver for diverse marine fauna across timescales (33, 34). The adaptive potential of thermal niches has been taken as a key determinant of global community structure and genetic connectance in plankton (35). Primary productivity and other environmental variables, however, may also structure abiotic niches of plankton (36). Our suite of analyses quantified whether and by how much planktonic foraminiferal niches shifted along a temperature axis. First, we correlated time series of species’ thermal optima with global temperature to determine whether species tracked suitable habitat or experienced environmental fluctuations in situ. We then quantified species’ niche dissimilarity between pairs of time bins—either tracking niches across bin boundaries or contrasting niches at climatic extremes of glacial maxima and interglacial thermal peaks. To characterize niche change we applied trait evolution models to time series of temperatures at occupied sites. Lastly, we explored variation in intraspecific niche lability among ecotypes while accounting for phylogenetic relatedness. SI Appendix, Table S1 lists the response variable and sample size for each analysis.     

Sexual transmission of the [Het-S] prion leads to meiotic drive in Podospora anserina

In the filamentous fungus Podospora anserina, two phenomena are associated with polymorphism at the het-s locus, vegetative incompatibility and ascospore abortion. Two het-s alleles occur naturally, het-s and het-S. The het-s encoded protein is a prion propagating as a self-perpetuating amyloid aggregate. When prion-infected [Het-s] hyphae fuse with [Het-S] hyphae, the resulting heterokaryotic cells necrotize. [Het-s] and [Het-S] strains are sexually compatible. When, however, a female [Het-s] crosses with [Het-S], a significant percentage of het-S spores abort, in a way similar to spore killing in Neurospora and Podospora. We report here that sexual transmission of the [Het-s] prion after nonisogamous mating in the reproductive cycle of Podospora is responsible for the killing of het-S spores. Progeny of crosses between isogenic strains with distinct wild-type or introduced, ectopic het-s/S alleles were cytologically and genetically analyzed. The effect of het-s/S overexpression, ectopic het-s/S expression, absence of het-s expression, loss of [Het-s] prion infection, and the distribution patterns of HET-s/S-GFP proteins were categorized during meiosis and ascospore formation. This study unveiled a het-S spore-killing system that is governed by dosage of and interaction between the [Het-s] prion and the HET-S protein. Due to this property of the [Het-s] prion, the het-s allele acts as a meiotic drive element favoring maintenance of the prion-forming allele in natural populations.     

Aging elevates basal adenosine monophosphate-activated protein kinase (AMPK) activity and eliminates hypoxic activation of AMPK in mouse liver

Despite the central role of adenosine monophosphate-activated protein kinase (AMPK) in the cellular stress response, it is unknown whether age-related changes in AMPK activity play a role in the diminished stress tolerance that is characteristic of aging. To address this question, we determined in the mouse liver how normal aging affects 1) basal AMPK activity, and 2) the degree to which AMPK activity is increased by in vivo hypoxia. We found that the basal activity of AMPK alpha1, but not alpha2, was higher in livers from 24-month-old mice compared to those from 5-month-old mice. Furthermore, while hypoxia elevated AMPK alpha1 and alpha2 activities in livers from 5-month-old mice, hypoxia failed to increase the activity of either isoform of AMPK in 24-month-old mice. These findings suggest that age-associated changes in hepatic AMPK activity may play a role in the physiological changes that occur in the liver with normal aging.