PLoS Genetics最新文献

Identifying genes associated with rare diseases remains challenging due to the scarcity of patients and the limited statistical power of traditional association methods. Here, we introduce PERADIGM ( Phenotype Embedding similarity-based RAre DIsease Gene Mapping), a novel framework that leverages natural language processing techniques to integrate comprehensive phenotype information from electronic health records for rare disease gene discovery. PERADIGM employs an embedding model to capture relationships between ICD-10 codes, providing a nuanced representation of individual phenotypes. By utilizing patient similarity scores, it enhances the identification of candidate genes associated with disease-specific phenotypes, surpassing conventional methods that rely on binary disease status. We applied PERADIGM to the UK Biobank dataset for three rare diseases: autosomal dominant polycystic kidney disease (ADPKD), Marfan syndrome, and neurofibromatosis type 1 (NF1). PERADIGM identified additional candidate genes associated with ADPKD-related and Marfan syndrome-related phenotypes, some of which are supported by existing literature, and demonstrated enhanced signal detection for NF1-specific phenotypes beyond traditional methods. Our findings demonstrate the potential of PERADIGM to identify genes associated with rare diseases and related phenotypes by incorporating phenotype embeddings and patient similarity, providing a powerful tool for precision medicine and a deeper understanding of rare disease genetics and clinical manifestations.

Phenotypic variation is essential for the selection of new traits of interest. Structural variants, consisting of deletions, duplications, inversions, and translocations, have greater potential for phenotypic consequences than single nucleotide variants. Pan-genome studies have highlighted the importance of structural variation in the evolution and selection of novel traits. Here, we describe a simple method to induce structural variation in plants. We demonstrate that a short period of growth on the topoisomerase II inhibitor etoposide induces heritable structural variation and altered phenotypes in Arabidopsis thaliana at high frequency. Using long-read sequencing and genetic analyses, we identified deletions and inversions underlying semi-dominant and recessive phenotypes. This method requires minimal resources, is potentially applicable to any plant species, and can replace irradiation as a source of induced large-effect structural variation.

Morphological phenotype and gene expression differences are observed between genetically identical plants grown in the same environment. While we now have a good understanding of the source and consequences of transcriptional differences observed between cells, our knowledge is still very limited regarding variability between multicellular organisms. We characterised this variability using the high-affinity nitrate transporter gene NRT2.1 as a model for high inter-individual transcriptional variability. Thanks to a combination of live imaging and transcriptomics, we show that the differences in expression of this gene between plants are established in young seedlings and maintained for up to three weeks. However, the expression level of NRT2.1 in plants does not permit predicting its expression in the next generation. Our results also indicate that these expression differences could have phenotypic consequences on root growth and nitrate uptake mediated by NRT2.1. Finally, we observed enriched photosynthesis-related functions among genes whose expression correlates with NRT2.1 in individual seedlings. Our study thus demonstrates that a global coordination of the genes involved in the carbon/nitrogen (C/N) balance in plants is established in young seedlings, at different levels in each plant, and maintained over time. Our results also highlight the fact that not all transcriptional regulators of NRT2.1 were identified, and propose UNE10 as a transcription factor for further study focused on its possible involvement in this pathway. This work shows that thanks to single-plant analysis of gene expression, we can gain new knowledge on the mechanisms behind a phenotype of interest that is normally masked in studies performed on pooled plants.

Ethanol is a fermentation product widely used as a fuel and chemical precursor in various applications. However, its accumulation imposes severe stress on the microbial producer, leading to significant production losses. To address this, improving a strain's ethanol tolerance is considered an effective strategy to enhance production. In our previous research, we conducted an adaptive evolution experiment with Escherichia coli growing under gradually increasing concentrations of ethanol, which gave rise to multiple hypertolerant populations. Based on the genomic mutational data, we demonstrated in this work that adaptive alleles in the EnvZ-OmpR two-component system drive the development of ethanol tolerance in E. coli. Specifically, when a single leucine was substituted for a proline residue within the periplasmic domain using CRISPR, the mutated EnvZ osmosensor caused a significant increase in ethanol tolerance. Through promoter fusion assays, we showed that this particular mutation stabilizes EnvZ in a kinase-dominating state, which reprograms signal transduction involving its cognate OmpR response regulator. Whole-genome proteomics analysis revealed that this altered signaling pathway predominantly maintains outer membrane stability by upregulating global porin levels and attenuating ferric uptake and metabolism in the tolerant envZ*L116P mutant. Moreover, we demonstrated that the hypertolerant envZ*L116P allele also promotes ethanol productivity in fermentation, providing valuable insights for enhancing industrial ethanol production.

Exocrine glands have evolved several times independently in Coleoptera to produce defensive chemical compounds with repellent, antimicrobial, or toxic effects. Research on such glands had focused on morphological or chemical ecology methods. However, modern genetic approaches were missing to better understand this biological process. With the rise of the red flour beetle, Tribolium castaneum, as a model for studies of development and pest biology, molecular genetic tools are now available to also study the safe generation of toxic compounds in defensive stink glands. Using the RNA-interference-based, genome-wide, phenotypic screen "iBeetle" and the re-analysis of gland-specific transcriptomics based on a significantly improved genome annotation, we could identify 490 genes being involved in odoriferous stink gland function. In the iBeetle screen, 247 genes were identified, of which we present here 178 genes identified during iBeetle's 3rd phase, while the transcriptomics analyses identified 249 genes, with six genes being identified in both functional genomics approaches. Of these 490 genes, only about 40% of these genes have molecularly characterized homologs in the vinegar fly, while for 213 genes no fly homologs were recognized and for 13 genes no gene ontology at all was identified. This highlights the importance of genome-wide gene identification in tissues that have not been previously analyzed to recognize potentially new gene functions. Gene ontology analysis revealed "SNARE interactions in vesicular transport", "Lysosome", "Pancreatic secretion", and "MAPK signaling pathway - fly" as key pathways. Additionally, many of the genes are encoding enzymes, transcription factors, transporters, or are involved in membrane trafficking. As the phenoloxidase responsible for generating the toxic para-benzoquinones in the stink glands of the beetle, we could identify laccase2, which is expressed in the last secretory cell in contact with the cuticle-lined vesicular organelle, where the toxic compounds are safely produced before being released into the gland reservoir.

[This corrects the article DOI: 10.1371/journal.pgen.1011799.].

Reproduction and immunity are energy intensive processes that often compete for resources, leading to trade-offs across species. Lipid metabolism integrates these processes, particularly during stressful conditions such as pathogenic infections, yet the underlying molecular mechanisms remain poorly understood. TCER-1, the C. elegans homolog of mammalian TCERG1, suppresses immunity and promotes fertility, especially upon maternal infection. Here, we show that TCER-1 coordinates this balance by regulating two conserved lysosomal lipases, lipl-1 and lipl-2. Using transcriptomic, lipidomic, and molecular-genetic analyses, we demonstrate that both lipases mediate infection-induced lipid remodeling but with distinct outcomes: lipl-1 promotes immunity, whereas, lipl-2 does not. LIPL-1 catalyzes the accumulation of specific ceramide species, including Cer 17:1;O2/24:0, whose supplementation rescues the immunity phenotypes of tcer-1;lipl-1 mutants and enhances post-infection survival of wild-type animals. Both lipases influence fertility with lipl-2 playing a key role in maintaining embryonic-eggshell integrity during maternal infection and aging. Remarkably, expression of human lysosomal acid lipase (hLAL/LIPA), the ortholog of 'lipl' genes, restores immunity defects triggered by lipl-1 loss and enhances immune resilience but does not significantly ameliorate the fertility defects. Together, these findings reveal distinct roles for lipl-1 and lipl-2 in modulating lipid species that link immune defense, reproductive fitness and healthspan through a potentially conserved mechanism.

The cryptochrome-photolyase family, a highly conserved set of flavoproteins, mediates many direct and indirect responses to sunlight. While the photolyases are light-dependent enzymes which catalyze photoreactivation repair of UV-induced DNA damage, the cryptochromes serve as circadian clock components and photoreceptors. Do DNA repair and circadian clock functions overlap in these flavoproteins? While 6-4 photolyase (6-4phr) is well-documented to repair UV-induced 6-4 photoproducts, we demonstrate that loss of 6-4phr function in fish cells and fin clips significantly attenuates circadian rhythms of period gene expression. Importantly, 6-4phr represses, as well as activates transcription directed by E-box and D-box enhancer elements respectively. Furthermore, we document physical interaction between 6-4phr and Clock1/Bmal1 at multiple domains which interferes with Clock1-Bmal1 heterodimerization. In addition, 6-4phr interacts with the D-box binding transcription factor, Tef. Thus, we reveal significant overlap between DNA repair and circadian clock functions in 6-4phr.

Enteroendocrine cells (EECs) of the intestinal epithelium are major regulators of metabolism and energy homeostasis. This is mainly due to their expression and secretion of enteroendocrine peptides (EEPs). These peptides serve as hormones that control many aspects of metabolic homeostasis including feeding behavior, intestinal contractions, and utilization of energy stores. Regulation of EEP production and release depends largely on EEC-exclusive G protein-coupled receptors (GPCRs) that sense nutrient levels. Here we report the characterization of a GPCR expressed principally in EECs, which we have named GulpR due to its role in the response to nutrient stress. We show that GulpR regulates transcription of the EEP Tachykinin (Tk) and that both GulpR and Tk are essential for the transcriptional response that promotes survival of nutrient limitation. Oral infection with V. cholerae also activates expression of GulpR, Tk, and lipid mobilization genes. However, Tk does not play a role in regulation of lipid mobilization genes during infection and does not impact survival. Our findings identify a role for GulpR and Tk in survival during starvation and suggest that, although starvation and infection result in significant mobilization of energy stores, the signal transduction systems that regulate the metabolic response to each are distinct.

DNA:RNA hybrids are unusual structures found throughout the genomes of many species, including yeast and mammals. While DNA:RNA hybrids may promote various cellular functions, persistent hybrids lead to double strand breaks, resulting in genomic instability. DNA:RNA hybrid formation and removal are therefore highly regulated, including by enzymes that either degrade or unwind RNA from the hybrid. Meiosis is the specialized cell division that creates haploid gametes for sexual reproduction. Previous work in yeast and mammals showed that elimination of DNA:RNA hybrids by RNase H facilitates meiotic recombination. This work demonstrates that the conserved Sen1 DNA/RNA helicase functions during three temporally distinct processes during yeast meiosis. First, SEN1 allows meiosis-specific genes to be expressed at the proper time to allow entry into meiosis. Second, SEN1 prevents the accumulation of hybrids during premeiotic DNA replication. Third, SEN1 promotes the repair of programmed meiotic double strand breaks that are necessary to form crossovers between homologous chromosomes to allow their proper segregation at the first meiotic division. Given the evolutionary conservation of Sen1 with its mammalian counterpart, Senataxin, studies of Sen1 function in yeast are likely to be informative about the regulation of DNA:RNA hybrids during human meiosis as well.