Nat Commun. 2024 Aug 12;15(1):6893. doi: 10.1038/s41467-024-51158-3.

ABSTRACT

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.

PMID:39134553 | DOI:10.1038/s41467-024-51158-3

Nat Commun. 2024 Aug 12;15(1):6906. doi: 10.1038/s41467-024-51189-w.

ABSTRACT

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 (CLAMT1) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.

PMID:39134551 | DOI:10.1038/s41467-024-51189-w

Crit Rev Biotechnol. 2024 Aug 12:1-21. doi: 10.1080/07388551.2024.2383754. Online ahead of print.

ABSTRACT

Natural products have long served as critical raw materials in chemical and pharmaceutical manufacturing, primarily which can provide superior scaffolds or intermediates for drug discovery and development. Over the last century, natural products have contributed to more than a third of therapeutic drug production. However, traditional methods of producing drugs from natural products have become less efficient and more expensive over the past few decades. The combined utilization of genome mining and synthetic biology based on genome sequencing, bioinformatics tools, big data analytics, genetic engineering, metabolic engineering, and systems biology promises to counter this trend. Here, we reviewed recent (2020-2023) examples of genome mining and synthetic biology used to resolve challenges in the production of natural products, such as less variety, poor efficiency, and low yield. Additionally, the emerging efficient tools, design principles, and building strategies of synthetic biology and its application prospects in NPs synthesis have also been discussed.

PMID:39134459 | DOI:10.1080/07388551.2024.2383754

Neurochem Int. 2024 Aug 10:105828. doi: 10.1016/j.neuint.2024.105828. Online ahead of print.

ABSTRACT

Cyclic AMP (cAMP) is an important second messenger in virtually all animal cell types, including astrocytes. In the brain, it modulates energy metabolism, development and synaptic plasticity. Dopamine receptors are G protein-coupled receptors that affect cAMP production by adenylyl cyclases. They are divided into two subgroups, D1-like receptors linked to Gs proteins stimulating cAMP production and D2-like receptors linked to Gi/o proteins inhibiting cAMP production. In the present study, we investigated the effect of dopamine receptor activation on cAMP dynamics in astrocytes of the mouse olfactory bulb, the brain region with the largest population of dopaminergic neurons. Using the genetically encoded cAMP sensor Flamindo2 we visualized changes in the cytosolic cAMP concentration and showed that dopamine application results in a transient increase in cAMP. This cAMP increase could be mimicked by the D1-like receptor agonist A 68930 and was inhibited by the D1-like receptor antagonist SCH 23390, whereas D2-like receptor ligands had no effect on the astrocytic cAMP concentration. Thus, olfactory bulb astrocytes express D1-like receptors that are linked to cAMP production.

PMID:39134121 | DOI:10.1016/j.neuint.2024.105828

Med Res Rev. 2024 Aug 12. doi: 10.1002/med.22071. Online ahead of print.

ABSTRACT

Pyroptosis, a newly characterized type of inflammatory programmed cell death (PCD), is usually triggered by multiple inflammasomes which can recognize different danger or damage-associated molecular patterns (DAMPs), leading to the activation of caspase-1 and the cleavage of gasdermin D (GSDMD). Gasdermin family pore-forming proteins are the executers of pyroptosis and are normally maintained in an inactive state through auto-inhibition. Upon caspases mediated cleavage of gasdermins, the pro-pyroptotic N-terminal fragment is released from the auto-inhibition of C-terminal fragment and oligomerizes, forming pores in the plasma membrane. This results in the secretion of interleukin (IL)-1β, IL-18, and high-mobility group box 1 (HMGB1), generating osmotic swelling and lysis. Current therapeutic approaches including chemotherapy, radiotherapy, molecularly targeted therapy and immunotherapy for lung cancer treatment efficiently force the cancer cells to undergo pyroptosis, which then generates local and systemic antitumor immunity. Thus, pyroptosis is recognized as a new therapeutic regimen for the treatment of lung cancer. In this review, we briefly describe the signaling pathways involved in pyroptosis, and endeavor to discuss the antitumor effects of pyroptosis and its potential application in lung cancer therapy, focusing on the contribution of pyroptosis to microenvironmental reprogramming and evocation of antitumor immune response.

PMID:39132876 | DOI:10.1002/med.22071

Bioinform Adv. 2024 Jul 29;4(1):vbae109. doi: 10.1093/bioadv/vbae109. eCollection 2024.

ABSTRACT

MOTIVATION: In single-cell studies, principal component analysis (PCA) is widely used to reduce the dimensionality of dataset and visualize in 2D or 3D PC plots. Scientists often focus on different clusters within PC plot, overlooking the specific phenomenon, such as horse-shoe-like effect, that may reveal hidden knowledge about underlying biological dataset. This phenomenon remains largely unexplored in single-cell studies.

RESULTS: In this study, we investigated into the horse-shoe-like effect in PC plots using simulated and real scRNA-seq datasets. We systematically explain horse-shoe-like phenomenon from various inter-related perspectives. Initially, we establish an intuitive understanding with the help of simulated datasets. Then, we generalized the acquired knowledge on real biological scRNA-seq data. Experimental results provide logical explanations and understanding for the appearance of horse-shoe-like effect in PC plots. Furthermore, we identify a potential problem with a well-known theory of 'distance saturation property' attributed to induce horse-shoe phenomenon. Finally, we analyse a mathematical model for horse-shoe effect that suggests trigonometric solutions to estimated eigenvectors. We observe significant resemblance after comparing the results of mathematical model with simulated and real scRNA-seq datasets.

AVAILABILITY AND IMPLEMENTATION: The code for reproducing the results of this study is available at: https://github.com/najeebullahshah/PCA-Horse-Shoe.

PMID:39132288 | PMC:PMC11316618 | DOI:10.1093/bioadv/vbae109

J Pharm Anal. 2024 Jul;14(7):100944. doi: 10.1016/j.jpha.2024.01.012. Epub 2024 Feb 3.

ABSTRACT

Evaluating toxicity and decoding the underlying mechanisms of active compounds are crucial for drug development. In this study, we present an innovative, integrated approach that combines air flow-assisted desorption electrospray ionization mass spectrometry imaging (AFADESI-MSI), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and spatial metabolomics to comprehensively investigate the nephrotoxicity and underlying mechanisms of nitidine chloride (NC), a promising anti-tumor drug candidate. Our quantitive AFADESI-MSI analysis unveiled the region specific of accumulation of NC in the kidney, particularly within the inner cortex (IC) region, following single and repeated dose of NC. High spatial resolution ToF-SIMS analysis further allowed us to precisely map the localization of NC within the renal tubule. Employing spatial metabolomics based on AFADESI-MSI, we identified over 70 discriminating endogenous metabolites associated with chronic NC exposure. These findings suggest the renal tubule as the primary target of NC toxicity and implicate renal transporters (organic cation transporters, multidrug and toxin extrusion, and organic cation transporter 2 (OCT2)), metabolic enzymes (protein arginine N-methyltransferase (PRMT) and nitric oxide synthase), mitochondria, oxidative stress, and inflammation in NC-induced nephrotoxicity. This study offers novel insights into NC-induced renal damage, representing a crucial step towards devising strategies to mitigate renal damage caused by this compound.

PMID:39131801 | PMC:PMC11314895 | DOI:10.1016/j.jpha.2024.01.012

J Parasitol Res. 2024 Aug 3;2024:1858154. doi: 10.1155/2024/1858154. eCollection 2024.

ABSTRACT

Background: The aim of this study was to assess the anthelmintic activity of Lannea kerstingii and Ficus thonningii, on a nematode model, to promote their use in the Cameroonian pharmacopoeia for the treatment of helminthiases. Methods: One nematode was used, Heligmosomoides polygyrus. First, the effect of the extracts on the eggs and larval stages (L1, L2, and L3) of H. polygyrus was evaluated, 100 μL of extract and 100 μL of parasite suspension (containing 50 eggs) were mixed in a 96-well microplate. The 96-well microplate was incubated for 20 h at 25°C in the WMicroTracker which measures the motility of the worms at various concentrations. Finally, docking studies were conducted by using the Glide module in Schrodinger Maestro. Results: The ethanolic extract of L. kerstingii with the half maximal inhibitory concentration (IC50) of 0.1371 mg/mL produced a higher ovicidal effect than the effect produced by other extracts of these plants. However, with an IC50 of 0.31 mg/mL, the aqueous extract of F. thonningii showed the greatest effect on the L2 stage. The aqueous and ethanolic extracts of L. kerstingii and F. thonningii inhibited the development of the L3 larvae of H. polygyrus with a better effect for the ethanolic extracts. Conclusion: The use of L. kerstingii and F. thonningii for the treatment of helminthiasis has been proved in vitro and in silico by this research. However, more research is required, especially on the acute toxicity and in vivo anthelmintic efficacy to validate this scientific investigation.

PMID:39131749 | PMC:PMC11316912 | DOI:10.1155/2024/1858154

Bio Protoc. 2024 Aug 5;14(15):e5042. doi: 10.21769/BioProtoc.5042. eCollection 2024 Aug 5.

ABSTRACT

The liver is an essential organ that is involved in the metabolism, synthesis, and secretion of serum proteins and detoxification of xenobiotic compounds and alcohol. Studies on liver diseases have largely relied on cancer-derived cell lines that have proven to be inferior due to the lack of drug-metabolising enzymes. Primary human hepatocytes are considered the gold-standard for evaluating drug metabolism. However, several factors such as lack of donors, high cost of cells, and loss of polarity of the cells have limited their widescale adoption and utility. Stem cells have emerged as an alternative source for liver cells that could be utilised for studying liver diseases, developmental biology, toxicology testing, and regenerative medicine. In this article, we describe in detail an optimised protocol for the generation of multicellular 3D liver organoids composed of hepatocytes, stellate cells, and Kupffer cells as a tractable robust model of the liver. Key features • Optimising a protocol for generating multicellular 3D liver organoids from induced pluripotent stem cells. Graphical overview.

PMID:39131195 | PMC:PMC11309960 | DOI:10.21769/BioProtoc.5042

ArXiv [Preprint]. 2024 Aug 1:arXiv:2408.00942v1.

ABSTRACT

Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes. Whereas most systems biology models focus on the structure or dynamics of specific subsystems in controlled conditions, compositional systems biology aims to connect such models into integrative multiscale simulations. This emphasizes the space between models--a compositional perspective asks what variables should be exposed through a submodel's interface? How do coupled models connect and translate across scales? How can we connect domain-specific models across biological and physical research areas to drive the synthesis of new knowledge? What is required of software that integrates diverse datasets and submodels into unified multiscale simulations? How can the resulting integrative models be accessed, flexibly recombined into new forms, and iteratively refined by a community of researchers? This essay offers a high-level overview of the key components for compositional systems biology, including: 1) a conceptual framework and corresponding graphical framework to represent interfaces, composition patterns, and orchestration patterns; 2) standardized composition schemas that offer consistent formats for composable data types and models, fostering robust infrastructure for a registry of simulation modules that can be flexibly assembled; 3) a foundational set of biological templates--schemas for cellular and molecular interfaces, which can be filled with detailed submodels and datasets, and are designed to integrate knowledge that sheds light on the molecular emergence of cells; and 4) scientific collaboration facilitated by user-friendly interfaces for connecting researchers with datasets and models, and which allows a community of researchers to effectively build integrative multiscale models of cellular systems.

PMID:39130201 | PMC:PMC11312625

Sens Diagn. 2024 Jul 11;3(8):1310-1318. doi: 10.1039/d4sd00081a. eCollection 2024 Aug 8.

ABSTRACT

MicroRNAs (miRNAs) are short (about 18-24 nucleotides) non-coding RNAs and have emerged as potential biomarkers for various diseases, including cancers. Due to their short lengths, the specificity often becomes an issue in conventional amplification-based methods. Next-generation sequencing techniques could be an alternative, but the long analysis time and expensive costs make them less suitable for routine clinical diagnosis. Therefore, it is essential to develop a rapid, selective, and accurate miRNA detection assay using a simple, affordable system. In this work, we report a CRISPR/Cas13a-based miRNA biosensing using point-of-care dark-field (DF) imaging. We utilized magnetic-gold nanoparticle (MGNPs) complexes as signal probes, which consist of 200 nm-sized magnetic beads and 60 nm-sized gold nanoparticles (AuNPs) linked by DNA hybridization. Once the CRISPR/Cas13a system recognized the target miRNAs (miR-21-5p), the activated Cas13a cleaved the bridge linker containing RNA sequences, releasing 60 nm-AuNPs detected and quantified by a portable DF imaging system. The combination of CRISPR/Cas13a, MGNPs, and DF imaging demonstrated amplification-free detection of miR-21-5p within 30 min at a detection limit of 500 attomoles (25 pM) and with single-base specificity. The CRISPR/Cas13a-assisted MGNP-DF assay achieved rapid, selective, and accurate detection of miRNAs with simple equipment, thus providing a potential application for cancer diagnosis.

PMID:39129860 | PMC:PMC11308380 | DOI:10.1039/d4sd00081a

Front Plant Sci. 2024 Jul 26;15:1419796. doi: 10.3389/fpls.2024.1419796. eCollection 2024.

ABSTRACT

Forage maize is a versatile crop extensively utilized for animal nutrition in agriculture and holds promise as a valuable resource for the production of fermentable sugars in the biorefinery sector. Within this context, the carbohydrate fraction of the lignocellulosic biomass undergoes deconstruction during ruminal digestion and the saccharification process. However, the cell wall's natural resistance towards enzymatic degradation poses a significant challenge during both processes. This so-called biomass recalcitrance is primarily attributed to the presence of lignin and ferulates in the cell walls. Consequently, maize varieties with a reduced lignin or ferulate content or an altered lignin composition can have important beneficial effects on cell wall digestibility. Considerable efforts in genetic improvement have been dedicated towards enhancing cell wall digestibility, benefiting agriculture, the biorefinery sector and the environment. In part I of this paper, we review conventional and advanced breeding methods used in the genetic improvement of maize germplasm. In part II, we zoom in on maize mutants with altered lignin for improved digestibility and biomass processing.

PMID:39129761 | PMC:PMC11310149 | DOI:10.3389/fpls.2024.1419796

Mol Oncol. 2024 Aug 11. doi: 10.1002/1878-0261.13717. Online ahead of print.

ABSTRACT

Dysregulation of epidermal growth factor receptor (EGFR) is one of the most common mechanisms associated with the pathogenesis of various cancers. Mitogen-inducible gene 6 [MIG6; also known as ERBB receptor feedback inhibitor 1 (ERRFI1)], identified as a feedback inhibitor of EGFR, negatively regulates EGFR by directly inhibiting its kinase activity and facilitating its internalization, subsequently leading to degradation. Despite its proposed role as an EGFR-dependent tumor suppressor, the functional consequences and clinical relevance in cancer etiology remain incompletely understood. Here, we identify that the stoichiometric balance between MIG6 and EGFR is crucial in promoting EGFR-dependent oncogenic growth in various experimental model systems. In addition, a subset of ERRFI1 (the official gene symbol of MIG6) mutations exhibit impaired ability to suppress the enzymatic activation of EGFR at multiple levels. In summary, our data suggest that decreased or loss of MIG6 activity can lead to abnormal activation of EGFR, potentially contributing to cellular transformation. We propose that the mutation status of ERRFI1 and the expression levels of MIG6 can serve as additional biomarkers for guiding EGFR-targeted cancer therapies, including glioblastoma.

PMID:39129344 | DOI:10.1002/1878-0261.13717

J Exp Bot. 2024 Aug 12;75(15):4453-4458. doi: 10.1093/jxb/erae294.

NO ABSTRACT

PMID:39129311 | DOI:10.1093/jxb/erae294

Brain Behav Immun. 2024 Aug 9:S0889-1591(24)00538-5. doi: 10.1016/j.bbi.2024.08.016. Online ahead of print.

ABSTRACT

The olfactory bulb (OB), a major structure of the limbic system, has been understudied in human investigations of psychopathologies such as depression. To explore more directly the molecular features of the OB in depression, a global comparative proteome analysis was carried out with human post-mortem OB samples from 11 males having suffered from depression and 12 healthy controls. We identified 188 differentially abundant proteins (with adjusted p < 0.05) between depressed cases and controls. Gene ontology and gene enrichment analyses suggested that these proteins are involved in biological processes including the complement and coagulation cascades. Cell type enrichment analysis displayed a significant reduction in several canonical astrocytic proteins in OBs from depressed patients. Furthermore, using RNA-fluorescence in-situ hybridization, we observed a decrease in the percentage of ALDH1L1+ cells expressing canonical astrocytic markers including ALDOC, NFIA, GJA1 (connexin 43) and SLC1A3 (EAAT1). These results are consistent with previous reports of downregulated astrocytic marker expression in other brain regions in depressed patients. We also conducted a comparative phosphoproteomic analysis of OB samples and found a dysregulation of proteins involved in neuronal and astrocytic functions. To determine whether OB astrocytic abnormalities is specific to humans, we also performed proteomics on the OB of socially defeated male mice, a commonly used model of depression. Cell-type specific analysis revealed that in socially defeated animals, the most striking OB protein alterations were associated with oligodendrocyte-lineage cells rather than with astrocytes, highlighting an important species difference. Overall, this study further highlights cerebral astrocytic abnormalities as a consistent feature of depression in humans.

PMID:39128570 | DOI:10.1016/j.bbi.2024.08.016

New Phytol. 2024 Aug 11. doi: 10.1111/nph.20004. Online ahead of print.

ABSTRACT

Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non-model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity. We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ralstonia solanacearum, pathogens with completely different modes of action, and thereby has a different role than its orthologue in tomato. Remarkably, StPti5 is destabilised in healthy plants via the autophagy pathway and accumulates exclusively in the nucleus upon infection. We demonstrate that StEIN3 and StEIL1 directly bind the StPti5 promoter and activate its expression, while synergistic activity of the ethylene and salicylic acid pathways is required for regulated StPti expression. To gain further insight into the mode of StPti5 action in attenuating potato defence responses, we investigated transcriptional changes in salicylic acid deficient potato lines with silenced StPti5 expression. We show that StPti5 regulates the expression of other ERFs and downregulates the ubiquitin-proteasome pathway as well as several proteases involved in directed proteolysis. This study adds a novel element to the complex puzzle of immune regulation, by deciphering a two-level regulation of ERF transcription factor activity in response to pathogens.

PMID:39129060 | DOI:10.1111/nph.20004

Sci Rep. 2024 Aug 11;14(1):18635. doi: 10.1038/s41598-024-68965-9.

ABSTRACT

Evolution of unisexual flowers involves extreme changes in floral development. Spinach is one of the species to discern the formation and evolution of dioecy. MADS-box gene family is involved in regulation of floral organ identity and development and in many other plant developmental processes. However, there is no systematic analysis of MADS-box family genes in spinach. A comprehensive genome-wide analysis and transcriptome profiling of MADS-box genes were undertaken to understand their involvement in unisexual flower development at different stages in spinach. In total, 54 MADS-box genes found to be unevenly located across 6 chromosomes and can be divided into type I and type II genes. Twenty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups. While thirty-four type II SoMADSs consist of 3 MIKC*, and 31 MIKCC -type genes including sixteen floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in spinach. Gene structure, motif distribution, physiochemical properties, gene duplication and collinearity analyses for these genes are performed in detail. Promoters of both types of SoMADS genes contain mainly MeJA and ABA response elements. Expression profiling indicated that MIKCc genes exhibited more dynamic and intricate expression patterns compared to M-type genes and the majority of type-II genes AP1, SVP, and SOC1 sub-groups showed female flower-biased expression profiles, suggesting their role in carpel development, while PI showed male-biased expression throughout flower developmental stages, suggesting their role in stamen development. These results provide genomic resources and insights into spinach dioecious flower development and expedite spinach improvement.

PMID:39128921 | DOI:10.1038/s41598-024-68965-9

NPJ Syst Biol Appl. 2024 Aug 11;10(1):86. doi: 10.1038/s41540-024-00413-w.

ABSTRACT

Ligand-receptor systems, covalent modification cycles, and transcriptional networks are the fundamental components of cell signaling and gene expression systems. While their behavior in reaching a steady-state regime under step-like stimulation is well understood, their response under repetitive stimulation, particularly at early time stages is poorly characterized. Yet, early-stage responses to external inputs are arguably as informative as late-stage ones. In simple systems, a periodic stimulation elicits an initial transient response, followed by periodic behavior. Transient responses are relevant when the stimulation has a limited time span, or when the stimulated component's timescale is slow as compared to the timescales of the downstream processes, in which case the latter processes may be capturing only those transients. In this study, we analyze the frequency response of simple motifs at different time stages. We use dose-conserved pulsatile input signals and consider different metrics versus frequency curves. We show that in ligand-receptor systems, there is a frequency preference response in some specific metrics during the transient stages, which is not present in the periodic regime. We suggest this is a general system-level mechanism that cells may use to filter input signals that have consequences for higher order circuits. In addition, we evaluate how the described behavior in isolated motifs is reflected in similar types of responses in cascades and pathways of which they are a part. Our studies suggest that transient frequency preferences are important dynamic features of cell signaling and gene expression systems, which have been overlooked.

PMID:39128915 | DOI:10.1038/s41540-024-00413-w

Planta. 2024 Aug 10;260(3):69. doi: 10.1007/s00425-024-04500-4.

ABSTRACT

Supplying monochromatic blue LED light during the day, but not at night, promotes early coloration and improves anthocyanin accumulation in the skin of grape berries. Specific light spectra, such as blue light, are known to promote the biosynthesis and accumulation of anthocyanins in fruit skins. However, research is scarce on whether supplement of blue light during different periods of one day can differ in their effect. Here, we compared the consequences of supplying blue light during the day and night on the accumulation of anthocyanins in pigmented grapevine (Vitis vinifera) berries. Two treatments of supplemented monochromatic blue light were tested, with light emitting diodes (LED) disposed close to the fruit zone, irradiating between 8:00 and 18:00 (Dayblue) or between 20:00 and 6:00 (Nightblue). Under the Dayblue treatment, berry coloration was accelerated and total anthocyanins in berry skins increased faster than the control (CK) and also when compared to the Nightblue condition. In fact, total anthocyanin content was similar between CK and Nightblue. qRT-PCR analysis indicated that Dayblue slightly improved the relative expression of the anthocyanin-structural gene UFGT and its regulator MYBA1. Instead, the expression of the light-reception and -signaling related genes CRY, HY5, HYH, and COP1 rapidly increased under Dayblue. This study provides insights into the effect of supplementing monochromatic LED blue light during the different periods of one day, on anthocyanins accumulation in the berry skin.

PMID:39127837 | DOI:10.1007/s00425-024-04500-4

Nat Commun. 2024 Aug 11;15(1):6873. doi: 10.1038/s41467-024-51284-y.

ABSTRACT

Ribosomes are regulated by evolutionarily conserved ubiquitination/deubiquitination events. We uncover the role of the deubiquitinase OTUD6 in regulating global protein translation through deubiquitination of the RPS7/eS7 subunit on the free 40 S ribosome in vivo in Drosophila. Coimmunoprecipitation and enrichment of monoubiquitinated proteins from catalytically inactive OTUD6 flies reveal RPS7 as the ribosomal substrate. The 40 S protein RACK1 and E3 ligases CNOT4 and RNF10 function upstream of OTUD6 to regulate alkylation stress. OTUD6 interacts with RPS7 specifically on the free 40 S, and not on 43 S/48 S initiation complexes or the translating ribosome. Global protein translation levels are bidirectionally regulated by OTUD6 protein abundance. OTUD6 protein abundance is physiologically regulated in aging and in response to translational and alkylation stress. Thus, OTUD6 may promote translation initiation, the rate limiting step in protein translation, by titering the amount of 40 S ribosome that recycles.

PMID:39127721 | DOI:10.1038/s41467-024-51284-y