PLOS Genetics

Microexons are short alternative exons up to 51 nucleotides long that are highly enriched in neuronal genes. Their dysregulation has been linked to human neurodevelopmental disorders, including autism spectrum disorders. In the nematode Caenorhabditis elegans, global regulation of microexons is also critical for proper development. Here we show that microexon alternative splicing (AS) changes between C. elegans larval and adult stages and that microexon inclusion is differentially regulated among distinct neuronal types. Consistently with previous evidence that C. elegans splicing is regulated in response to environmental stimuli, we found here that specific microexons are modulated upon food availability. Both the inclusion levels of these microexons and the feeding behavior seem to depend on the DNA topology, which may affect transcription dynamics, as revealed by the effects of the topoisomerase I (TOP1) inhibitor, camptothecin (CPT). CPT treatment alters responses related to food availability such as speed reduction and exploration. Furthermore, animals carrying a mutation in the global regulator of microexon splicing prp-40 exhibit altered food preference, independently demonstrating that disruption of microexon AS has important consequences on animal behavior.

Yeast responding to acute stress reallocate cellular resources, in part via the Environmental Stress Response (ESR) that induces stress-defense genes while repressing ribosome-biogenesis and growth genes. The purpose and regulation of coordinated induction and repression is incompletely understood, but both responses are influenced by ESR transcription factors Msn2 and Msn4 (Msn2/4). Here we used single-cell microscopy and transcriptomic analysis to investigate the role of upstream regulator Pde2 in ESR regulation and post-stress fitness. Loss of PDE2 weakened and shortened Msn2 activation following salt stress and produced muted induction of Msn2/4 targets, similar to a msn2{triangleup}msn4{triangleup} strain. In contrast, Pde2 had at most a minor impact on ESR repressor Dot6, yet was important for repression of its targets beyond Msn2/4 influence. Consistent with our recent resource-reallocation model, pde2{triangleup} cells had normal or faster post-stress growth rates, despite weaker activation of the ESR. We discuss implications for ESR regulation and function.

Melanin is a pigment found in the skin and cuticle of animals. Oculocutaneous albinism (OCA) is a group of autosomal recessive disorders defined by reduced melanin in skin and eyes, and is associated with visual defects such as foveal hypoplasia and infantile nystagmus. Sleep disturbance has been documented in children with OCA, and oca2 loss-of-function in cavefish causes constitutive sleep loss, indicating a sleep regulatory function of OCA-associated genes in the visual system. To test potential roles of OCA-associated genes in regulating sleep and vision through evolutionarily conserved mechanisms, we used Drosophila melanogaster, a high-throughput phenotyping system to screen sleep and visual phenotypes for genetic mutants of OCA-associated genes. Among the OCA-associated genes, bidirectional DRSC Integrative Ortholog Prediction Tool identified Drosophila orthologues for OCA2, SLC45A2, SLC24A5 and LRMDA. RNAi-mediated knockdown in developing Drosophila eye tissue identified the OCA2 orthologues hoe1, hoe2, and the SLC45A2 orthologue lovit as candidate gene required for normal sleep. Moreover, hoe1, hoe2 and lovit1 null alleles reduced sleep and circadian rhythmicity, and showed altered photoreceptor neurotransmission. Collectively the data indicate evolutionarily conserved neuronal function of OCA2 and SLC45A2 orthologues that regulates sleep and photoreceptor neurotransmission. Author summaryOculocutaneous albinism (OCA) is a pigmentation disorder of the skin and eyes accompanied by reduced visual acuity and nystagmus. Children with albinism also report sleep disturbance, and the mechanism is unclear. We tested whether genes mutated in albinism regulate sleep in the fruit fly Drosophila melanogaster, an organism that has a divergent melanin synthesis pathway and lacks tyrosinase, the principal pigmentation enzyme in mammals. We screened fly orthologues of seven human OCA-associated genes and identified two that regulate sleep: the OCA2 orthologues hoe1 and hoe2, and the SLC45A2 orthologue lovit. Mutants of these genes show reduced sleep and circadian rhythmicity; electrical recordings show that photoreceptors fail to signal normally to downstream neurons, placing the sleep defect within a defined visual circuit. Because none of the above mutation cause pigmentation defect, our finding shows that OCA2 and SLC45A2 have a neuronal function that is separate from pigment synthesis. Pigment synthesis cells and neurons share a common embryonic origin, which may explain how the same transporter genes came to function in both cell types, and the data are consistent with the proposal that this pleiotropic neuronal function underlies the sleep and vision symptoms in albinism.

The nucleotide diadenosine tetraphosphate (Ap4A) accumulates during stress across organisms and cell types and is widely hypothesized to be an alarmone or second messenger. While Gram-negative bacteria use ApaH-family hydrolases to degrade Ap4A and other dinucleoside tetraphosphates (Ap4Ns), Gram-positive bacteria, including Staphylococcus aureus, use YqeK. Inactivation of Ap4A hydrolases and corresponding Ap4A accumulation cause diverse phenotypic effects in both Gram-negative and Gram-positive bacteria, ranging from increased sensitivity to antimicrobials to reduced virulence. However, the physiological role of YqeK in S. aureus remains uncharacterized. Here, we constructed an isogenic yqeK mutant in S. aureus and showed that {Delta}yqeK was sensitive to nitrosative and organic acid stress. We used a luminescence-based assay to show that {Delta}yqeK had [~]1000-fold higher relative Ap4N levels than wild-type even during unstressed growth, and all phenotypes were restored by complementation. Transcriptomics revealed that {Delta}yqeK exhibited stress-specific dysregulation of translation, nucleotide metabolism, central metabolism, iron acquisition, and stress response genes. In contrast, {Delta}yqeK had few transcriptional differences relative to wild-type during unstressed growth despite the large Ap4N accumulation, suggesting that the effects of Ap4Ns are contingent on the cellular stress state. Unexpectedly, we also found that the entire agr quorum sensing operon and numerous additional virulence genes, including hemolytic toxins, had reduced expression in {Delta}yqeK, correlating with reduced hemolytic activity in the mutant even in the absence of stress. Our data reveal YqeK to be a critical metabolic determinant of S. aureus stress resistance and virulence and position this hydrolase as a promising candidate for anti-virulence drug development. ImportanceS. aureus is a leading cause of antibiotic-resistant bacterial infections worldwide and is resistant to many components of the host immune response. Here, we discovered that deletion of YqeK, an enzyme that degrades a stress-associated nucleotide signaling molecule called Ap4A, rendered S. aureus more susceptible to infection-relevant stress conditions but had little impact on normal growth. Ap4Ns accumulated in the yqeK mutant and caused major stress-specific changes in gene expression, including reduced expression of key virulence genes. This correlated with a reduction in the destruction of red blood cells, a measure of bacterial toxicity toward host cells. Our data suggest that YqeK represents a promising target for new drugs aimed at reducing the virulence of S. aureus.

During meiosis, homologous chromosomes pair to form synaptonemal complexes (SCs) and exchange genetic material through a process known as meiotic recombination. First, programmed DNA double-strand breaks form, followed by the assembly of recombination foci on SCs. These foci mark the sites of recombination intermediates and future crossovers. Distributions of recombination foci along SCs have been studied in many eukaryotes, revealing the interplay between recombination patterns and genome evolution. However, in fish, data on recombination patterns are scarce, and, for the majority of groups, completely absent. Here, we measure the positions of MLH1 foci in 3,504 SCs from 219 male meiotic cells of an African annual killifish Nothobranchius virgatus, a representative of a genus with remarkable karyotype and genome diversity, and present a detailed statistical analysis of its recombination patterns. We found that, in contrast to the several other fish species characterised to date, recombination in N. virgatus occurs across almost entire chromosome arms, excluding (peri)centromeres and telomeres. In the longest SCs, we observed a proximal and a distal peak of the recombination focus frequency and explained the peaks by chromosome pairing dynamics. We also revealed the typical positions of focus pairs, demonstrated interference between foci, with the minimal interfocus distance of 4 m, and described regions of the total recombination suppression near centromeres and telomeres. In sum, our study provides a detailed analysis of recombination patterns in a killifish with a fully acrocentric karyotype and contributes to cytogenomic and statistical methodology for future exploration of meiotic recombination patterns.

Standard genome-wide association studies (GWASs) are vulnerable to confounding factors, including stratification, assortative mating, and dynastic effects. Family studies such as sibling-based GWAS (sib-GWAS) mitigate such confounding and are becoming the tool of choice for teasing apart direct genetic effects--causal effects of ones genotype on ones own phenotype-- from other factors. However, due in part to their smaller sample sizes, sib-GWAS allelic effect estimates are substantially more variable than standard (i.e., population-based) GWAS estimates. The quantification of this uncertainty is essential for many uses of sib-GWAS, including polygenic scoring, causal inference (e.g., Mendelian randomization), disentangling direct from indirect familial effects, and measuring assortative mating. Here, we investigate sources of uncertainty in sib-GWAS allelic effect estimators. We study their impacts on the biases of three uncertainty measurement methods, including two that are commonly used and a new resampling-based approach we propose. We find that heterogeneity in allelic effects or heteroskedasticity across families (e.g., due to variation in genetic backgrounds or environments) can bias existing methods, and that this bias is more severe for small samples and rare variants. In contrast, the resampling-based approach we propose is approximately unbiased under all scenarios we considered. We validate our theoretical predictions, as well as the importance of effect heterogeneity and heteroskedasticity, using simulations and empirical analysis in the UK Biobank. In sum, this study helps understand the sources of uncertainty in family-based genotype-phenotype association studies and provides a robust method to estimate uncertainty.

The spatiotemporal regulation of an actin mesh during Drosophila oogenesis is essential for proper localization of cell polarity determinants that establish the future patterning of the embryo. Here, we reveal an unexpected role for Semaphorin-2a (Sema2a) in actin mesh regulation and oogenesis. Sema2a classically functions as a secreted guidance cue that binds its cognate Plexin-B (PlexB) receptor to establish neural circuits. In contrast, we find that Sema2a is expressed inside the germarium, germline, and follicle cells of the developing ovary. Sema2a mutants possess small ovaries that fail to develop past mid-oogenesis. We demonstrate that Sema2a interacts with Cappuccino (Capu), a key actin nucleator crucial for building the actin mesh in Drosophila oocytes. Sema2a inhibits the actin assembly activity of Capu in vitro. Furthermore, genetic interaction between Sema2a and Capu influences mesh density and disrupts oskar mRNA localization. PlexB mutants, however, exhibit wild-type size ovaries with oskar mRNA localization distinct from Sema2a mutants, confirming the non-canonical role of Sema2a in oogenesis. SummaryThis study reveals a novel interaction between the actin nucleator Cappuccino and the typically secreted neural guidance factor Semaphorin-2a. It is shown that Semaphorin-2a inhibits the actin polymerization activity of Cappuccino in vitro and play an intracellular role in oogenesis.

Meiotic drivers are selfish elements which co-opt gametogenesis to increase their own transmission. Driving alleles may spread in a population even if harmful to overall fitness, requiring the emergence of host suppressors to ameliorate these costs. In some cases, intense co-evolutionary arms races between drivers and their host genomes may occur. These conflicts have been invoked to explain the rapid evolution of karyotypes and reproduction-associated proteins across the tree of life. Despite their evolutionary importance, relatively few meiotic drivers have been well-characterized, in large part due to the difficulties inherent to detecting meiotic drivers, distinguishing them from viability effects, and performing systematic screens. To address these gaps, we present an approach to driver detection at the embryo stage in wild-derived D. melanogaster. By combining fluorescent markers with a method to induce embryonic arrest at a standard developmental stage, we detect transmission of wild-derived alleles as compared to their fluorescently marked homologs in early embryos, before most fitness differences among alleles (which may mimic drive) manifest. We provide proof-of-concept for the approach and identify several areas for future improvement.

The key features of meiosis that enhance evolutionary success compared to mitosis are the processes of recombination and independent assortment during chromosome segregation, which help cells adapt to changing environments. Cohesins play critical roles in both these processes and have evolved specialized paralogs that are essential for meiotic chromosome dynamics. Studies so far have elucidated the roles of these meiotic cohesins but it is still unclear why the original mitotic proteins could not serve these evolved functions. In this study, we identify the mechanistic steps that are lost during meiosis when the mitotic counterparts replace the meiotic cohesins in Schizosaccharomyces pombe. The meiotic cohesin subunit Rec8REC8 has evolved multiple unique features that differentiate it from its mitotic paralog Rad21RAD21. Although ectopic expression of Rad21 in meiosis allows its chromatin enrichment, it fails to support reductional separation of chromosomes, initiation of recombination and protection of cohesion in anaphase I, resulting in catastrophic segregation errors. In contrast, the meiotic cohesin regulatory subunit Rec11STAG3, has only one major function of initiation of recombination, which is expectedly hampered in its absence. We show that although the mitotic paralog Psc3STAG1/2 is highly enriched at the cohesin-rich chromosomal axes, it is unable to recruit the downstream activators required for the induction of double-strand breaks. Our work systematically demonstrates the minimal functions that were necessary for the molecular evolution of these paralogs and explains the mechanisms that led to these adaptations.

Histone lactylation is a recently identified histone post-translational modification (PTM) that links energy metabolism to chromatin regulation. Although histone lactylation has been implicated in transcriptional activation, its function in meiotic chromatin remains unclear. Previously, we identified enrichment of multiple histone lactylation marks within the meiotic karyosome, a highly condensed and transcriptionally repressive chromatin structure formed in Drosophila oocytes. Here, through an RNAi-based screen, we identified the CBP family protein dCBP as a regulator of histone lactylation in the karyosome. Germline-specific knockdown of dCBP preferentially reduced histone lactylation, including H4K8 lactylation, and caused premature disruption of the synaptonemal complex, abnormal egg chamber development with excess nurse cells, reduced egg production, and decreased embryonic viability. Corresponding histone acetylation marks were comparatively less affected than histone lactylation by dCBP knockdown. Together, our findings provide evidence that dCBP-mediated histone lactylation contributes to meiotic chromosome maintenance and suggest a potential link between energy metabolism and meiotic chromatin regulation.

AO_SCPLOWBSTRACTC_SCPLOWThe coordination between DNA damage repair and cell cycle progression is essential to ensure cell survival and organ homeostasis. This is particularly critical during gametogenesis, where germline cells first proliferate and then transition from mitosis to meiosis. Meiotic cells frequently undergo recombination, which itself implies the generation of severe DNA damage in the form of double-strand DNA breaks (DSBs) that ought to be repaired to preserve genome integrity. Here, we identify Drosophila bru1 as an essential factor in the mitotic-to-meiotic transition in the female germline. The RNA-binding protein Bru1 is a translational repressor of multiple targets, including cyclins, and is sharply upregulated at the mitotic-to-meiotic boundary. We show that loss of bru1 disrupts germline development by altering cell cycle regulation, increasing DNA damage and cellular stress, and triggering apoptosis. bru1 mutants display clear signs of accelerated mitotic activity leading to extra divisions in the germline, in agreement with their elevated Cyclin A and B levels. Importantly, slowing cell cycle progression in bru1 mutants via string/cdc25 knockdown decreases DNA damage and cell death. Mechanistically, bru1 regulates mei-W68 transcription, the topoisomerase responsible for DSB production in the germline. Higher Mei-W68 levels induce premature and ectopic DSBs, which persist longer in the mutant germline, indicating defective repair and potentially resulting in p53-mediated apoptosis. Our work classifies bru1 as a safeguard of genome integrity and germline survival during the early stages of Drosophila female gametogenesis. bru1 regulates Mei-W68 levels and DSB formation, and controls the mitotic-to-meiotic transition by influencing cell cycle progression. The existence of bru1 homologues in mammals with established roles in gametogenesis suggests a broader biological relevance of our discoveries.

Most species are geographically structured, leaving characteristic signatures in neutral regions of the genome. These signatures can be distorted when neutral regions are linked to deleterious mutations. In such regions, purifying selection can reduce genetic diversity through Background Selection (BGS) or, for recessive mutations, increase diversity through Associative Overdominance (AOD). While the effect of BGS and AOD are well characterized in panmictic populations, their effects remain largely unexplored in structured populations. Here, we investigated an Isolation with Migration model using forward simulations across a range of migration, selection, dominance, and recombination parameters. We first used a genotype-based approach to quantify the effects of deleterious mutations on standard summary statistics ({pi}, dxy, FST, DAFi). We then showed that an Ancestral Recombination Graph-based (ARG) approach, tracking tree sequences from a sample of one diploid per deme, recovers the same patterns while directly relating genetic variation to the underlying coalescent processes. When recombination is sufficiently low, we found a BGS-driven regime for weakly codominant mutations, characterized by lower diversity and increased genetic differentiation (FST). For recessive mutations, we first identified an AOD-driven regime, characterized by increased diversity and lower FST values followed by a transition to a subsequent BGS-driven regime. Genealogies were similarly impacted by deleterious mutations: BGS shrunk coalescent times and produced a shift towards lineage sorting topologies, while AOD stretched coalescent times and produced a shift toward incomplete lineage-sorting topologies. These patterns were weakened by gene flow, with FST and topologies remaining close to expected under neutrality, while diversity and coalescence times remained robust to demography. Our results provide clear evidence of BGS, AOD, and of their transition in a structured model with gene flow. Importantly, these processes leave distinct and interpretable signatures on gene trees, highlighting the potential of ARG-based approaches for inferring linked selection and dominance in structured populations. Author summaryCharacterizing how demography and selection jointly shape genomic variation is a central question in population genetics. As deleterious mutations reduce fitness, they are continuously removed from populations by purifying selection. Through linkage, this affects nearby regions of the genome, leaving signatures of selection on linked neutral genetic diversity. While these effects are well understood in random mating populations, much less is known in structured populations. Specifically, the occurrence of Background Selection (BGS), which reduces diversity, and Associative Overdominance (AOD), which increases diversity, remains underexplored. Here, we used simulations to investigate how deleterious mutations shape genomic variation in a structured two-population isolation with migration model. By combining standard population genetic analyses with a genealogical approach based on Ancestral Recombination Graphs (ARGs), we showed that BGS and AOD leave distinct and interpretable signatures on common summary statistics and the underlying genealogies. We identified clear signatures of BGS and AOD when recombination was low and revealed a transition from AOD to BGS for recessive mutations, as the strength of selection increased. Our results highlight the importance of jointly considering demography and linked selection when interpreting genomic data and demonstrate the potential of ARGs to jointly infer demography, selection, and dominance from genomic data.

LD Score Regression (LDSC) is a prominent method, which estimates whole-genome SNP heritability from summary statistics via the slope of a linear regression of GWAS test statistics corresponding to a trait of interest against LD scores. It was claimed by the LDSC authors that the free intercept in the regression accounts for confounding bias such as population stratification. In this study, we argue that the intercept in LDSC must be fixed to 1 for accurate SNP heritability estimation. We show both theoretically and with simulations that the estimated intercept does not accurately capture population stratification effects, and that it adversely affects the accuracy of the heritability estimate introducing bias and increasing variance. Fixing the intercept to 1 eliminates bias and reduces variance when no population stratification is present. On the other hand, under population stratification, LDSC is biased with both the free and the fixed intercept. Additionally, we show that estimated standard errors in LDSC are underestimated, potentially leading to false-positives in downstream GWAS analyses.

Interoceptive paraneurons are neuron-like cells located within internal epithelial cell surfaces that sense internal stimuli to evoke specific behavioral or physiological responses. The elucidation of terminal differentiation programs of paraneurons is expected to provide insights into how epithelial cells acquire neuron-like feature during development and possibly also over evolutionary time. We define here transcriptional programs that control the terminal differentiation of an interoceptive paraneuron class in the nematode C. elegans, called uv1. The uv1 cells sense mechanosensory inputs in the uterus and signal via the HSN neurons to modulate egg-laying behavior. We show that like in canonical neurons, the neuron-like secretory features of uv1 are controlled by a combination of CUT homeobox genes, while the combinatorial terminal gene battery that defines the unique functional features of uv1 is jointly controlled by a combination of at least three transcription factors, a LIM homeodomain (LIN-11), a SoxD (EGL-13) and a Pax family (EGL-38) protein. These factors act in a terminal selector-type manner to jointly co-regulate the many distinct uv1-paraneuron specific molecular features, such as sensory receptors, neuromodulatory receptors and neuropeptides, as well as uv1s tyraminergic identity. Our findings demonstrate notable similarities in the dichotomous architecture of gene regulatory programs of neurons and paraneurons.

A greater genetic susceptibility has been proposed as an explanation of the greater rates of cardiovascular and metabolic disease in South Asian relative to European populations. We first demonstrate that after accounting for technical artefacts the genetic effects for related traits are largely consistent between ancestral groups, which downplays the role of GxG or GxE interactions driving differential prevalence. If higher genetic susceptibility in South Asians is due to selective pressures acting through adiposity-related traits in the evolutionary past, signatures of selection should be evident at loci associated with cardiometabolic disease and other causally related traits (e.g. fat distribution). We tested for enrichment of several selection statistics (FST, XP-EHH and XP-nSL) at loci associated with a range of traits related to cardiometabolic disease, in comparison to a null distribution of linkage disequilibrium (LD) score and minor allele frequency (MAF) matched SNPs. Loci associated with a subset of these traits (Type 2 diabetes mellitus, trunk fat percentage, body fat percentage and trunk fat mass) exhibited enrichment for FST, consistent with a moderate adaptive explanation for their cross-population differentiation. In contrast, none of the studied traits were enriched for haplotype-based statistics, indicative that cross population genetic divergence is unlikely to have been driven by recent selective sweeps but has rather likely arisen from either ancient selection or recent polygenic selection acting on standing variation.

Loop extrusion has been clearly shown to be insufficient as a mechanism to explain TAD formation, leaving a large gap in our understanding of how the specificity of TAD boundary interactions and inter-TAD chromosomal interactions are determined. Many TAD binding proteins have been implicated in boundary interactions, including the gypsy transposon boundary binding protein Su(Hw). How these proteins generate the often specific and orientation-dependent boundary interactions that underpin chromosomal architecture is largely unknown. Here, we investigate the role of the single Su(Hw) binding site located in each of the boundaries that flank the Drosophila eve locus, homie and nhomie. We show that Su(Hw), which binds hundreds of sites throughout the Drosophila genome, plays a large role in the highly selective and orientation-specific interactions of homie and nhomie. Despite its outsized role in the binding strength and stability of these interactions, other boundary binding proteins are implicated as the primary determinants of the specificity of the interactions. These studies provide an important example of the need to more fully investigate how strength and specificity of TAD boundary interactions are separately encoded in this important class of genome architectural elements.

The circadian clock is a highly conserved evolutionary advantage which allows organisms to anticipate regular changes in daily environmental conditions. Clocks from fungi to mammals rely on a transcription-translation feedback loop (TTFL) mechanism. Phosphorylation is understood to be a critical regulatory step for maintaining the period of the circadian clock and feedback loop closure. The role of kinases in the Neurospora clock has been examined extensively; however, phosphatases have not been systematically interrogated. By re-examining the Neurospora genome using current informatic tools we identified the 30 genes previously identified as encoding protein phosphatases as well as 13 novel genes, and we assessed the function of the core circadian clock in 39 non-essential phosphatases using a real-time luciferase reporter. We observed both period lengthening and shortening effects, which are not restricted to a single phosphatase family or fold. All but one deletion mutant maintained a rhythmic core clock. In addition, we observed a new temperature compensation defect in the previously studied knockout of phosphatase pph-4, the result of nutritional growth conditions.

Ribosome biogenesis is a highly coordinated pathway that involves the assembly of ribosomal RNAs (rRNAs) with ribosomal proteins (r-proteins) to generate functional ribosomal subunits (r-subunits). The Saccharomyces cerevisiae (yeast) large 60S r-subunit consists of three rRNA molecules and 46 r-proteins. The contributions of nearly all r-proteins of the yeast large r-subunit have been characterized; however, a few non-essential proteins remain poorly understood. Although non-essential, human eL22 has been identified as a key player in p53 regulation during ribosomal stress and as a highly mutated target in cancers. Despite this function, the role of eL22 in ribosome maturation is still ill-defined. In this study, we characterized yeast eL22 r-protein. Our results show that eL22 assembles into intermediate nucleolar pre-60S ribosomal particles. Loss of eL22 impairs cell growth and reduces 60S r-subunit accumulation, phenotypes that are exacerbated at low temperatures. Analysis of pre-rRNA processing by pulse-chase labeling, northern blot hybridization, and primer extension reveals a defect in 27S pre-rRNA maturation, specifically at the level of 27SB pre-rRNA processing. Consequently, nuclear export of eL22-deficient pre-60S particles is mildly impaired. Furthermore, we identify genetic interactions between eL22 and neighboring r-proteins, eL38 and eL31. We conclude that eL22 assembly is required for optimal pre-60S maturation during middle nucleolar stages, particularly at low temperatures, a function likely supported by the cooperative action of other r-proteins associated with common elements of 25S rRNA. HighlightsO_LIWe have studied the role of r-protein eL22 in yeast ribosome assembly. C_LIO_LIeL22 is required for 60S ribosomal subunit production. C_LIO_LIThe absence of eL22 is critical at low temperatures. C_LIO_LIeL22 is important for 27SB pre-rRNA processing and nuclear export of pre-ribosomes. C_LIO_LIeL22 functionally interacts with r-proteins eL38 and eL31 in domain III of 25S rRNA. C_LI

Fertilization is the process in which two specialized cells, the sperm and egg, interact, adhere, and fuse their membranes. This occurs in all sexually reproducing organisms. Several transmembrane and secreted proteins have been shown to be required for fertilization. Genetic mutations can alter these proteins and disrupt fertilization, leading to reduced or no offspring. When fertilization-specific sperm proteins are mutated, sperm production, motility, and activation are unaffected, but the sperm lose the ability to successfully fertilize an egg. In this study, we report on the sperm-specific protein SPE-40/FAM187, which is a single-pass transmembrane protein with an immunoglobulin-like domain. When spe-40 is mutated in C. elegans the animals are severely sub-fertile due to a sperm-specific defect. All the characteristics of the sperm that we have evaluated in the mutant are normal, yet sperm lacking SPE-40 do not fertilize. SPE-40 has orthologs in other species, including humans. Thus, we have established a role for SPE-40/FAM187 in fertilization that suggests it represents a conserved component of the fertilization synapse.

Phosphatidylinositol (4,5) bisphosphate (PI(4,5)P2) plays important roles in development, signaling, intracellular trafficking and regulation throughout the nervous system. Using selective and combined gene ablation strategies, we have determined the roles of this lipid and the kinase isoforms of the PIP5KI family primarily responsible for its synthesis in mouse retina. In rod cells, PI(4,5)P2 localizes predominantly to the plasma membrane of inner and outer segments and is enriched in membranes near the synaptic termini. Disruption of the gene encoding the {gamma} PIP5KI isoform, Pip5k1c, throughout the developing retina, using Cre expression driven by a Six3 transcription factor-dependent promoter, yields dramatic, but not complete, loss of the protein, with no apparent effects on morphology or function through the first 3-4 months after birth. Slowly progressing photoreceptor degeneration is observed at later ages. Complete loss of the {gamma} isoform in rods, driven by the rhodopsin promoter-based iCre75 transgene, leads to no obvious developmental defects, but results in an earlier-onset rod degeneration. Germ-line ablation of neither the Pip5k1a nor the Pip5k1b gene leads to any observable morphological defects. Homozygous Pip5k1a ablation leads to functional defects in photoreceptors as revealed by reduced a-wave and b-wave amplitudes in the electroretinograms. On the background of rod-specific Pip5k1c ablation, Pip5k1a deficiency greatly accelerates retinal degeneration. These results reveal a complex interplay among PIP5KI isoforms in ensuring proper photoreceptor function and health, with apparent partial redundancy in fulfilling their critical functions. They underscore the important role of PI(4,5)P2 in neuronal signaling and homeostasis. Significance StatementPhosphatidylinositol(4,5)P2, PI(4,5)P2, plays essential roles in nervous system development and function, but its roles in retina have been unknown. This study combines biochemistry, mouse genetics, light- and electron microscopy to reveal both specific and redundant functions for PIP2 formed by different kinase isoforms in the mammalian retina. It has implications for retinal function, disease and therapy, and for the broader field of phosphoinositide regulation.