Protter: interactive protein feature visualization and integration with experimental proteomic data

Comprehensive survey of disease-causing missense mutations of the cholesterol synthesis enzyme NSDHL: Low temperature and a chemical chaperone rescue low protein expression of select mutants

Cholesterol is essential to human life. Perturbations to any of the 22 cholesterol synthesis enzymes can lead to devastating developmental diseases. Each enzyme is exquisitely regulated both transcriptionally and post-translationally, playing a critical role in providing cholesterol to cells. We examined 13 missense mutations and one deletion mutation in the cholesterol synthesis enzyme NSDHL (NAD(P) Dependent Steroid Dehydrogenase-Like), known to cause the X-linked developmental disorders CHILD (congenital hemidysplasia with ichthyosiform erythroderma and limb defects) syndrome and CK syndrome. Little is known about the effect of these missense mutations on the stability and function of NSDHL. Here we show that protein expression levels were low for all mutants, but some could be rescued by a lower temperature (30°C vs. 37°C) and/or the chemical chaperone glycerol. Additionally, heat shock proteins 70 and 90 are needed for optimal NSDHL protein expression suggesting that disease mutations in NSDHL may interfere with this interaction, perhaps during translation resulting in lower protein synthesis. Our findings that these disease-causing mutations reduce NSDHL protein expression, but some respond to lower temperature and/or the chemical chaperone glycerol, can help inform future treatments for CHILD and CK syndrome.

Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function in Escherichia coli

Phenotypic outcomes can be heavily affected by environmental factors. In this study, we exploited the previously observed nutrient dependency of cell biological phenotypic features captured by a cross-condition image-based profiling assay of Escherichia coli deletion strains to examine this in more detail. We identified several general principles, including the existence of a spectrum of deviating phenotypes across nutrient conditions (i.e., from nutrient- or feature-specific to pleiotropic phenotypic deviations), limited conservation of phenotypic deviations across nutrient conditions (i.e., limited phenotypic robustness), and a subset of nutrient-independent phenotypic deviations (indicative of consistent genetic determinants of specific phenotypic features). In a subsequent step, we used this cross-condition data set to identify five genes of unknown function (yibN, yaaY, yfaQ, ybiJ, and yijD), of which the deletion displayed either nutrient-independent phenotypic deviations or phenotypic similarities to genes of known function. These genes showed different levels of phylogenetic conservation, ranging from conserved across the tree of life (yibN) to only present in some genera of the Enterobacterales (yaaY). Analysis of the structural properties of the proteins encoded by these y-genes, identification of structural similarities to other proteins, and the examination of their subcellular localization yielded new insights into their contribution to E. coli cell morphogenesis, cell cycle progression, and cell growth. Together, our approach showcases how bacterial image-based profiling assays and data sets can serve as a gateway to reveal the function of uncharacterized proteins.

IMPORTANCE

Despite unprecedented access to genomic information, predicting phenotypes based on genotypes remains notoriously difficult. One major confounding factor is the environment and its ability to modulate phenotypic outcomes. Another fact is that a large fraction of protein-coding genes in bacterial genomes remain uncharacterized and have no known function. In this work, we use a large-scale cross-condition image-based profiling dataset to characterize nutrient-dependent phenotypic variability of Escherichia coli deletion strains and exploit it to provide insight into the cellular role of genes of unknown function. Through our analysis, we identified five genes of unknown function that we subsequently further characterized by examining their phylogenetic conservation, predicted structural properties and similarities, and their intracellular localization. Combined, this approach highlights the potential of cross-condition image-based profiling, which extracts many cell biological phenotypic readouts across multiple conditions, to better understand nutrient-dependent phenotypic variability and uncover protein function.

Emerging roles of EGFL family members in neoplastic diseases: Molecular mechanisms and targeted therapies

Epidermal growth factor-like proteins (EGFLs) contain more than a single EGF/EGF-like domain within their protein structure. To date, ten EGFL family members (EGFL1-10) have been characterized across diverse tissues and developmental stages under different conditions. In this review, we conclude that EGFLs are instrumental in regulating biological activities and pathological processes. Under physiological conditions, EGFLs participate in angiogenesis, neurogenesis, osteogenesis, and other processes. Under pathological conditions, EGFLs are linked with different diseases, particularly cancers. Furthermore, we highlight recent advancements in the study of EGFLs in biological conditions and cancers. In addition, the regulatory role and key underlying mechanism of EGFLs in mediating tumorigenesis are discussed. This paper also examines potential antagonists that target EGFL family members in cancer therapeutics. In summary, this comprehensive review elucidates the critical role of EGFLs in neoplastic diseases and highlights their potential as therapeutic targets.

A FAM8A1 frameshift variant is associated with REM sleep behavior disorder, urinary retention, and mydriasis in Russian Blue cats

REM sleep behavior disorder (RBD) is a disease characterized by the loss of lower motor neuron inhibition responsible for skeletal muscle atonia during REM sleep. It has been reported in humans, dogs and cats, and can be idiopathic or secondary to a neurodegenerative disease. Five young adult Russian Blue cats from two related families were presented for progressively worsening RBD episodes frequently associated with urinary loss. Three of these cats also suffered urinary retention with overflow incontinence between RBD episodes. Neurological examination revealed a large bladder in three cats and a bilateral mydriasis with absent pupillary light reflexes in two cats; further examinations were unremarkable. Treatment attempts were unsatisfactory, with four cats being euthanized. Histopathology of the brain did not reveal any abnormalities. A disease-associated 23-bp deletion in exon 1 of FAM8A1 (NC_058372.1:g.11622168_11622190del), introducing a frameshift at codon 162 and a premature stop codon at codon 276 (XM_019831563.3:c.485_507del p.(Gln162Profs*115)), was identified by whole genome sequencing. The variant segregated in the affected families with a recessive mode of inheritance, showed an allele frequency of 1.5% in West-European Russian Blue cats (N = 68) and was not present in 276 cats belonging to 32 other breeds (including the closely related Nebelung breed). The variant FAM8A1 isoform is predicted to affect the assembly and activity of the endoplasmic reticulum-associated protein degradation pathway, which plays an important role in cell homeostasis. RBD and urinary retention syndrome is a hereditary encephalopathy affecting Russian Blue cats. A genetic test now allows diagnosis and prevention of this debilitating disease.

Genetic heterogeneity in patients with enlarged vestibular aqueduct and Pendred syndrome

BACKGROUND

Pathogenic variants in the SLC26A4 gene, encoding for Cl-/HCO3- and I- anion transporter pendrin, are associated with non-syndromic hearing loss with enlarged vestibular aqueduct (NSEVA) and Pendred syndrome (PDS). In the Caucasian population, up to 75% of patients fail to identify a genetic cause through biallelic mutations in the SLC26A4 gene. The CEVA haplotype could therefore play an important role in the diagnostics of NSEVA. The aim of the study was to determine the genetic etiology of hearing loss with EVA or with fully developed PDS in 37 probands and the functional characterization of novel variants identified in the SLC26A4 gene.

METHODS

To determine the genetic etiology, Sanger sequencing, WES and KASP genotyping assay were used. Functional characterization of SLC26A4 variants c.140G>A (p.R47Q), c.415G>A (p.G139R), c.441G>A (p.M147I), c.481T>A (p.F161I), c.1589A>C (p.Y530S) and c.2260del (p.D754Ifs*5) involved determination of iodide influx, total and plasma membrane pendrin expression level and subcellular localization of pendrin by confocal imaging. The nanopore sequencing of nasopharyngeal swab samples was performed to confirm the pathogenic effect of potential splice site variant c.415G>A.

RESULTS

Biallelic variants in the SLC26A4 gene (M2 genotype) were identified in ten probands and a complete CEVA haplotype was confirmed in three probands harbouring SLC26A4 monoallelic variants (M1 genotype). Fifteen variants in the SLC26A4 gene were identified in total, three of which are novel. The functional characterization of the novel variants and variants which were not yet functionally characterized confirmed the pathogenic potential of five out of six tested variants (p.G139R, p.M147I, p.Y530S, p.D754Ifs*5, and p.F161I). Analysis of nasopharyngeal swab samples confirmed exon 4 skipping due to novel variant SLC26A4:c.415G>A. Probands with biallelic SLC26A4 variants had significantly larger thyroid volume per m2 of body surface area than subjects with monoallelic SLC26A4 variants and the CEVA haplotype.

CONCLUSIONS

The genetic aetiology was determined in 13 out of 37 probands (35%), seven manifested with PDS and six with NSEVA. The present study highlights the importance of functional testing to confirm the pathogenicity of SLC26A4 variants and the phenotype-genotype correlation in SLC26A4-related disorders.

Development and validation of a carnitine cycle and transport disorders (CCD) panel: an ONT-compatible multi-gene diagnostic kit for newborn and selective screening

Carnitine transport and cycle disorders (CCD) are a group of metabolic disorders characterized by either carnitine depletion or dysfunction in the carnitine cycle, a critical process for the transport of fatty acids into the mitochondria and their subsequent β-oxidation. Clinically, CCD can manifest with a wide range of symptoms, including hypoketotic hypoglycemia, which may be accompanied by signs of liver dysfunction, hepatic steatosis, myopathy and cardiomyopathy. Biochemical diagnosis typically involves measuring carnitine and acylcarnitine levels in blood, alongside organic acid profiling in urine. However, due to phenotypic overlaps with other metabolic disorders, precise molecular diagnosis is essential for accurate disease classification and subtype determination. The present study aimed to develop and clinically validate a novel CCD panel, specifically designed for Oxford Nanopore Technologies (ONT) platform compatibility. The panel targeted four key CCD related genes (CPT-1, CPT-2, SLC22A5 and SLC25A20). An amplification-based library preparation method pooling 21 primers specific to the CCD-related genes into two tubes was optimized. The panel was then applied to screen 20 patients previously diagnosed with CCD via second-generation sequencing platform. Comparative analysis of results from both platforms revealed a 100% concordance in detecting pathogenic, likely pathogenic, and variants of unknown significance associated with CCD. In silico analysis was also performed to predict the pathogenic potential of the variants of unknown significance. Here we report the development and clinical validation of a multi-gene diagnostic panel for ONT platform. The results demonstrated the feasibility of ONT-based genetic testing for CCD and set the stage for the development of similar diagnostic panels for other genetic disorders, offering a streamlined and putatively cost-effective alternative to current sequencing methodologies.

Autosomal recessive (type 1B) pseudohypoaldosteronism: a novel mutation and its management

Pseudohypoaldosteronism (PHA) type 1B is a rare genetic disorder in which electrolyte imbalances are caused by resistance to the action of aldosterone. Clinical symptoms include episodes of salt wasting, metabolic acidosis and hyperkalaemia and may include intestinal salt wasting and a generalised rash. In this case report, the authors describe the presentation, initial and specific management, outcomes and molecular diagnostic confirmation of a neonate who presented with PHA type 1B. The patient was found to have a mutation in the gene encoding the beta subunit of sodium channel epithelial 1, which is a component of the epithelial sodium channel. The difficulty in managing the patient was not only due to a complex diagnostic work-up but also to recurrent electrolyte imbalances.

Modulating the Properties of GPCR-Based Sensors Via C-Terminus Isoforms

G-protein coupled receptors (GPCRs) play a key role in chemical biosensing, detecting chemicals from odorants and hormones to neurotransmitters and peptides. GPCR-based sensors in yeast can be rapidly engineered by coupling human GPCRs to the yeast mating pathway, resulting in cell fluorescence or luminescence upon chemical detection. Modulating the properties of GPCR-based sensors including their dynamic and linear ranges is nontrivial, often requiring the engineering of the yeast cell machinery. Here, we explore the use of GPCR C-terminal isoforms to modulate the properties of chemical biosensors. As a proof-of-concept, we leverage nine naturally occurring serotonin receptor 4 (5-HTR4) C-terminus isoforms to construct serotonin sensors with dynamic ranges spanning from 2- to 8.5-fold increases in signal after activation for a single integrated version, and from 3.4- to 62.7-fold for a double integrated version, and linear ranges reaching 5 orders of magnitude, from 10-8 to 10-3 M serotonin. Interestingly, the 5-HTR4 isoform-based sensors had different properties based on the chemical used to activate them, hinting at the potential differential activation of 5-HTR4 C-terminal isoforms in the body. Taken together, this work debuts the use of GPCR isoforms as a new strategy to rapidly modulate the dynamic and linear ranges of GPCR-based sensors in yeast.

The NSP6-L260F substitution in SARS-CoV-2 BQ.1.1 and XBB.1.16 lineages compensates for the reduced viral polymerase activity caused by mutations in NSP13 and NSP14

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants emerged at the end of 2021, and their subvariants are still circulating worldwide. While changes in the S protein of these variants have been extensively studied, the roles of amino acid substitutions in non-structural proteins have not been fully revealed. In this study, we found that SARS-CoV-2 bearing the NSP6-L260F substitution emerged repeatedly when we generated several SARS-CoV-2 variants by reverse genetics or when we passaged SARS-CoV-2 isolated from clinical samples and that it was selected under cell culture conditions. Although this substitution has been detected in BQ.1.1 and XBB.1.16 that circulated in nature, its effect on viral properties is unclear. Here, we generated SARS-CoV-2 with or without the NSP6-L260F by reverse genetics and found that NSP6-L260F promotes virus replication in vitro and in vivo by increasing viral polymerase activity and enhancing virus pathogenicity in hamsters. We also identified disadvantageous substitutions, NSP13-M233I and NSP14-D222Y, that reduced BQ.1.1 and XBB.1.16 replication, respectively. These adverse effects were compensated for by NSP6-L260F. Our findings suggest the importance of NSP6-L260F for virus replication and pathogenicity and reveal part of the evolutionary process of Omicron variants.IMPORTANCEAlthough the properties of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants continue to change through the acquisition of various amino acid substitutions, the roles of the amino acid substitutions in the non-structural proteins have not been fully explored. In this study, we found that the NSP6-L260F substitution enhances viral polymerase activity and is important for viral replication and pathogenicity. In addition, we found that the NSP13-M233I substitution in the BQ.1.1 lineage and the NSP14-D222Y substitution in the XBB.1.16 lineage reduce viral polymerase activity, and this adverse effect is compensated for by the NSP6-L260F substitution. Our results provide insight into the evolutionary process of SARS-CoV-2.

Phylogenetic and Structural Analyses of Vesicular Glutamate Transporters

Vesicular glutamate transporters are members of the solute carrier 17 (SLC17) family, and mammals express three closely related isoforms: vGluT1-3. While vGluT genes have been identified across various species in the Animalia kingdom, the evolutionary relationships and the natural history of vGluT members remain poorly understood. This study aimed to address these gaps by presenting a phylogenetic analysis of vGluTs across the animal kingdom. The study also included a detailed sequence analysis and structural modeling of vGluT isoforms among species. The phylogenetic tree revealed distinct clusters corresponding to the vGluts isoform 1, 2, and 3, with functional amino acid residues highly conserved among them. Invertebrate vGluTs emerged as the most divergent proteins, serving as the root of the tree. Sequence analysis confirmed the high conservation of vGluTs transmembrane core regions but identified high variations in the N and C-terminal ones. Structural analysis revealed that AlphaFold2-predicted models demonstrated high confidence quality in the transmembrane domains, but exhibited limited local similarity in the N-terminal, C-terminal, and loop regions. On the other hand, the expected topology of these helices was accurately captured and positioned in the Swiss-Model-generated structures, with the functionally relevant residues precisely positioned in three-dimensional space. In conclusion, we expect that our findings will contribute to a deeper understanding of vesicular glutamate transporter structure and function, as well as their roles across distinct species and biological contexts.

Rapid spread of Amitraz resistance linked to a unique T115N mutation in the octopamine receptor of Varroa mites in Korea

The Varroa mite, Varroa destructor, is an ectoparasitic pest of Western honey bees and poses a significant threat to apiculture. In Korea, widespread fluvalinate resistance has increased reliance on amitraz as an alternative acaricide. This study identified a novel mutation, T115N, in the β2-adrenergic-like octopamine receptor gene (Octβ2R) and confirmed its role in amitraz resistance. Genotyping of individual mites, based on time-dependent intoxication responses to a diagnostic dose of amitraz, revealed a strong correlation between genotype and resistance phenotype: mites with early intoxication responses were homozygous for the T115 allele, whereas those with delayed responses predominantly carried the homozygous N115 allele. Mites with homozygous N115 genotype exhibited a median lethal time approximately 2.8-fold longer than their T115 counterparts, confirming the resistance conferred by the T115N mutation. Quantitative sequencing was established to track the spread dynamics of T115N mutation in Korean Varroa mite populations over five years (2020-2024). While the mutation was rare from 2020 to 2022, its frequency increased sharply in 2023 and became widespread across Korea by 2024, coinciding with increased amitraz usage. These findings suggest region-specific selection for the T115N mutation driven by amitraz exposure.

Genome-Wide Identification of ATL Gene Family in Wheat and Their Expression Analysis in Response to Salt Stress

Wheat (Triticum aestivum) is one of the most important cereal crops globally, with significant economic value. The Arabidopsis Tóxicos en Levadura (ATL) gene family, which comprises members of ubiquitin ligase enzymes (E3s), functions in substrate protein tagging during ubiquitin-mediated protein modification. Recent studies have demonstrated its involvement in stress responses. However, the ATL gene family in wheat remains poorly characterized. This study aimed to identify the members of the ATL gene family in wheat and investigate their roles under salt stress. We identified 334 TaATL genes in the wheat genome, all of which contain either RING-H2, RING U-box, or RAD18 superfamily domains, exhibiting a remarkably low proportion of intron-containing genes. The Ka/Ks (non-synonymous to synonymous substitution rate) analysis and cis-acting element analysis of the TaATL gene family indicate that its sequences are highly conserved and functionally constrained, suggesting that it may participate in abiotic stress responses through the ABA, MeJA, and MYB signaling pathways. Both RNA-seq analysis and RT-qPCR data demonstrated that the expression levels of the TaATL gene family were significantly upregulated under stress conditions, indicating their crucial roles in stress responses. This study demonstrates that the targeted regulation of stress-responsive signaling pathways mediated by superior TaATL gene family members can effectively enhance wheat salt tolerance, thereby providing a viable strategy for the development of high-yielding cultivars adapted to saline agricultural ecosystems.

Immunoinformatics based designing of a multi-epitope cancer vaccine targeting programmed cell death ligand 1

Tumor cells express programmed cell death ligand 1 (PD-L1), which recognizes the immune checkpoint molecule programmed cell death 1 (PD-1) on T cells, suppressing the antitumor immune response. Inhibiting the PD-1:PD-L1 interaction has the potential to reactivate the immune response against tumors. Recent advancements in cancer therapy have demonstrated remarkable promise of immunotherapy, which exploits immune checkpoint inhibition by small molecules or monoclonal antibodies. This strategy has shown impressive clinical success in treating a wide range of cancer subtypes, albeit with certain limitations. This study aims to design a novel multi-epitope vaccine against PD-L1 by using an immunoinformatics approach. For attaining enhanced efficacy and minimize side effects, the vaccine was constructed using antigenic, non-allergenic, and non-toxic epitopes (5 CTL, 3 HTL, and 2 B-cell epitopes) predicted from the IgV domain of PD-L1. The vaccine design includes a large ribosomal subunit protein bL12 adjuvant, a 6xHis tag for purification, and appropriate linkers to connect the epitopes. The modelled 3D structure of the vaccine construct was docked with TLR4 immune receptor, demonstrating strong antigenic properties and stable binding, as validated by molecular dynamics simulations. Immune simulation studies suggest that the vaccine construct could potentially elicit significant immune regulators such as B cells, T-cells, and memory cells. Thus, the findings indicate that the vaccine may effectively suppress the PD-1:PD-L1 axis by targeting PD-L1, restoring the anticancer immune response. However, its efficacy needs to be validated in both in vitro and in vivo settings.

Myxosortase: an intramembrane protease that sorts MYXO-CTERM proteins to the cell surface

Cell surface proteins determine how cells interact with their biotic and abiotic environments. In social myxobacteria, a C-terminal protein sorting tag called MYXO-CTERM is universally found within the Myxococcota phylum, where their genomes typically contain dozens of proteins with this motif. MYXO-CTERM harbors a tripartite architecture: a short signature motif containing an invariant cysteine, followed by a transmembrane helix and a short arginine-rich C-terminal region localized in the cytoplasm. In Myxococcus xanthus, MYXO-CTERM is predicted to be posttranslationally lipidated and cleaved for subsequent cell surface localization by the type II secretion system. Here, following our bioinformatic discovery, we experimentally show that myxosortase (MrtX, MXAN_2755) is responsible for the C-terminal cleavage and cell surface anchoring of TraA, a prototypic cell surface receptor. The cleavage by MrtX depends on conserved cysteines within the MYXO-CTERM motif of TraA. M. xanthus mutants lacking myxosortase are defective in TraA-mediated outer membrane exchange and exhibit cell envelope defects. In a heterologous Escherichia coli expression system, the MYXO-CTERM motif is cleaved when MrtX is co-expressed. Therefore, MrtX represents a new family of sorting enzyme that enables cell surface localization of MYXO-CTERM proteins.IMPORTANCEThe CPBP (CaaX protease and bacteriocin processing) protease family is widespread across the three domains of life. Despite considerable research on eukaryotic homologs, prokaryotic CPBP family members remain largely unexplored. In this study, we experimentally reveal the function of a novel CPBP protease called myxosortase. Our findings show that myxosortase is responsible for the C-terminal cleavage and cell surface anchoring of substrate proteins containing MYXO-CTERM motifs in Myxococcus xanthus. MYXO-CTERM cleavage also occurred in a heterologous Escherichia coli host when myxosortase is co-expressed. This is the first report that a CPBP protease is involved in protein sorting in prokaryotes. This work provides important insights into the biogenesis and anchoring of cell surface proteins in gram-negative bacteria.

SUN-domain proteins of the malaria parasite Plasmodium falciparum are essential for proper nuclear division and DNA repair

The protozoan parasite Plasmodium falciparum, which is responsible for the deadliest form of human malaria, accounts for over half a million deaths a year. These parasites proliferate in human red blood cells by consecutive rounds of closed mitoses called schizogony. Their virulence is attributed to their ability to modify the infected red cells to adhere to the vascular endothelium and to evade immunity through antigenic switches. Spatial dynamics at the nuclear periphery were associated with the regulation of processes that enable the parasites to establish long-term infection. However, our knowledge of components of the nuclear envelope (NE) in Plasmodium remains limited. One of the major protein complexes at the NE is the linker of nucleoskeleton and cytoskeleton (LINC) complex that forms a connecting bridge between the cytoplasm and the nucleus through the interaction of SUN and KASH domain proteins. Here, we have identified two SUN-domain proteins as possible components of the LINC complex of P. falciparum and show that their proper expression is essential for the parasite's proliferation in human red blood cells, and their depletion leads to the formation of membranous whorls and morphological changes of the NE. In addition, their differential expression highlights different functions at the nuclear periphery as PfSUN2 is specifically associated with heterochromatin, while PfSUN1 expression is essential for activation of the DNA damage response. Our data provide indications for the involvement of the LINC complex in crucial biological processes in the intraerythrocytic development cycle of malaria parasites.

IMPORTANCE

Plasmodium falciparum, the parasite causing the deadliest form of malaria, is able to thrive in its human host by tight regulation of cellular processes, orchestrating nuclear dynamics with cytoplasmic machineries that are separated by the nuclear envelope. One of the major protein complexes that connect nuclear and cytoplasmic processes in eukaryotes is the linker of nucleoskeleton and cytoskeleton (LINC) complex. However, while the nuclear periphery of P. falciparum was implicated in several important functions, the role of the LINC complex in Plasmodium biology is unknown. Here, we identify two components of P. falciparum LINC complex and demonstrate that they are essential for the parasites' proliferation in human blood, and their depletion leads to the formation of morphological changes in the cell. In addition, the two components have different functions in activating the DNA damage response and in their association with heterochromatin. Our data provide evidence for their essential roles in the parasites' cell cycle.

Bioinformatics Analysis of the Glutamate-Gated Chloride Channel Family in Bursaphelenchus xylophilus

Glutamate-gated chloride channels (GluCls), a class of ion channels found in the nerve and muscle cells of invertebrates, are involved in vital life processes. Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has induced major economic and ecological losses in invaded areas of Asia and Europe. We identified 33 GluCls family members by sequence alignment analysis. A subsequent bioinformatic analysis revealed the physicochemical properties, protein structure, and gene expression patterns in different developmental stages. The results showed that GluCls genes are distributed across all six chromosomes of B. xylophilus. These proteins indicated a relatively conserved structure by NCBI-conserved domains and InterPro analysis. A gene structure analysis revealed that GluCls genes consist of 5 to 14 exons. Expression pattern analysis revealed BxGluCls were extensively involved in the development of second instar larvae of B. xylophilus. Furthermore, BxGluCls15, BxGluCls25, and BxGluCls28 were mainly associated with the development of eggs of B. xylophilus. BxGluCls12, BxGluCls18, and BxGluCls32 were predominantly linked to nematode resistance and adaptation. Investigation the structure and expression patterns of BxGluCls is crucial to understand the developmental trends of B. xylophilus. It also helps identify molecular targets for the development of biopesticides or drugs designed to control this nematode.

GTP cyclohydrolase II (gch2) and axanthism in ball pythons: A new vertebrate model for pterin-based pigmentation

Pterin pigments are responsible for many of the bright colors observed across the animal kingdom. However, unlike melanin, the genetics of pterin-based pigmentation has received relatively little attention in animal coloration studies. Here, we investigate a lineage of axanthic ball pythons (Python regius) found in captivity as a model system to study pterin pigmentation in vertebrates. By crowdsourcing shed skin samples from commercial breeders and applying a case-control study design, we used whole-genome pool sequencing (pool-seq) and variant annotation. We identified a premature stop codon in the gene GTP cyclohydrolase II (gch2), which is associated with the axanthic phenotype. GCH2 catalyzes the first rate-limiting step in riboflavin biosynthesis. This study provides the first identification of an axanthism-associated gene in vertebrates and highlights the utility of ball pythons as a model to study pterin-based pigmentation.

The contribution of the Golgi and the endoplasmic reticulum to calcium and pH homeostasis in Toxoplasma gondii

The cytosolic Ca2+ concentration of all cells is highly regulated demanding the coordinated operation of Ca2+ pumps, channels, exchangers, and binding proteins. In the protozoan parasite Toxoplasma gondii, calcium homeostasis, essential for signaling, governs critical virulence traits. However, the identity of most molecular players involved in signaling and homeostasis in T. gondii is unknown or poorly characterized. In this work, we studied a putative calcium proton exchanger, TgGT1_319550 (TgCAXL1), which belongs to a family of Ca2+/proton exchangers that localize to the Golgi apparatus. We localized TgCAXL1 to the Golgi and the endoplasmic reticulum (ER) of T. gondii and validated its role as a Ca2+/proton exchanger by yeast complementation. Characterization of a knock-out mutant for TgCAXL1 (Δcaxl) underscored the role of TgCAXL1 in Ca2+ storage by the ER and acidic stores, most likely the Golgi. Most interestingly, TgCAXL1 function is linked to the Ca2+ pumping activity of the Sarcoendoplasmic Reticulum Ca2+-ATPase (TgSERCA). TgCAXL1 functions in cytosolic pH regulation and recovery from acidic stress. Our data showed for the first time the role of the Golgi in storing and modulating Ca2+ signaling in T. gondii and the potential link between pH regulation and TgSERCA activity, which is essential for filling intracellular stores with Ca2+.

SERTM2: a neuroactive player in the world of micropeptides

In this study, we analyze the long noncoding RNA, lncMN3, that is predominantly expressed in motor neurons and shows potential coding capabilities. Utilizing custom antibodies, we demonstrate the production of a lncMN3-derived type I transmembrane micropeptide, SERTM2. Patch-clamp experiments performed on both wild-type and SERTM2 knockout motor neurons, differentiated in vitro from mouse embryonic stem cells, show a difference in the resting membrane potential and overall decreased excitability upon SERTM2 depletion. In vivo studies indicate that the absence of the peptide impairs treadmill test performance. At the mechanistic level, we identify a two-pore domain potassium channel, TASK1, known to be a major determinant of the resting membrane potential in motor neurons, as a SERTM2 interactor. Our study characterizes one of the first lncRNA-derived micropeptides involved in neuronal physiology.

Conserved marseilleviruses harboring diverse antibiotic resistance genes isolated from the Yangtze river Delta and the Pearl river delta, China

Marseilleviruses are a group of double-stranded DNA viruses infecting Acanthamoeba within the phylum Nucleocytoviricota and are ubiquitous in water and soil globally. Here, we report six strains of marseilleviruses isolated from environmental samples in the Yangtze River Delta and the Pearl River Delta, China. Viral particles exhibited icosahedral shaped capsids measuring about 220 ~ 240 nm in diameter. Based on stability assays, viral particles were halotolerant and acid-tolerant, but sensitive to chloroform and high temperature. Genomics and phylogenetic analyses showed that these strains were highly conserved compared with other reported marseilleviruses. Diverse members of the small multidrug resistance (SMR) family of transporter, which is a type of antibiotics resistance gene (ARG) and contribute to the feature of antibiotic resistance in bacteria, to our best knowledge, are firstly described in Marseilleviridae. The alignments of primary structures and in-silico tertiary structures reveal structural and potential functional similarity between giant viral and bacterial SMR, suggesting a possible role in viruses' interaction with antibiotics. The biological properties of marseillevirus and the discovery of viral SMR provide insight in the external and intracellular environment fitness of these large amoeba-infecting viruses.

Regulatory and disruptive variants in the CLCN2 gene are associated with modified skin color pattern phenotypes in the corn snake

BACKGROUND

Snakes exhibit a broad variety of adaptive colors and color patterns, generated by the spatial arrangement of chromatophores, but little is known of the mechanisms responsible for these spectacular traits. Here, we investigate a mono-locus trait with two recessive alleles, motley and stripe, that both cause pattern aberrations in the corn snake.

RESULTS

We use mapping-by-sequencing to identify the genomic interval where the causal mutations reside. With our differential gene expression analyses, we find that CLCN2 (Chloride Voltage-Gated Channel 2), a gene within the genomic interval, is significantly downregulated in Motley embryonic skin. Furthermore, we identify the stripe allele as the insertion of an LTR-retrotransposon in CLCN2, resulting in a disruptive mutation of the protein. We confirm the involvement of CLCN2 in color pattern formation by producing knock-out snakes that present a phenotype similar to Stripe. In humans and mice, disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses in snakes reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain, but the behavior and fertility of Motley and Stripe corn snakes are not impacted.

CONCLUSIONS

Our genomic, transcriptomic, and functional analyses identify a plasma membrane anion channel to be involved in color pattern development in snakes and show that an active LTR-retrotransposon might be a key driver of trait diversification in corn snakes.

In vitro characterization of SLCO2B1 genetic variants

OATP2B1, encoded by SLCO2B1, is a drug transporter expressed widely throughout the body in tissues such as the intestine and liver. Genetic variation of this transporter may lead to altered disposition of OATP2B1 substrate drugs, but especially the effects of rare variants are poorly understood. The aim of this study was to characterize the effects of naturally occurring missense single nucleotide variants of SLCO2B1 (c.601G>A, c.935G>A, c.953C>T, c.1175C>, c.1457C>T, c.1559G>C, c.1596C>A, and the c.601G>A + c.935G>A haplotype) on the in vitro functionality of OATP2B1. To characterize transport activity, cellular uptake of dibromofluorescein, 5-carboxyfluorescein, estrone sulfate, and rosuvastatin was compared in OATP2B1 reference- and variant-expressing HEK293 cells. The abundance of OATP2B1 variants in HEK293 crude membrane preparations was quantified with LC-MS/MS-based quantitative targeted absolute proteomics analysis. Variant c.1559G>C impaired OATP2B1-mediated uptake of all tested substrates almost completely, but protein abundance was not reduced to the same extent. Other studied variants had comparable or only modestly reduced protein abundance and transport function compared to reference OATP2B1. These results can be utilized to understand findings from clinical pharmacogenetic studies. More importantly, the results can aid in predicting the consequences of rare variants, such as the loss-of-function variant c.1559G>C, which can be difficult to detect in clinical studies.

Amino acid substitutions in NSP6 and NSP13 of SARS-CoV-2 contribute to superior virus growth at low temperatures

In general, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates well at 37°C, which is the temperature of the human lower respiratory tract, but it poorly at 30°C‒32°C, which is the temperature of the human upper respiratory tract. The replication efficiency of SARS-CoV-2 in the upper respiratory tract may directly affect its transmissibility. In this study, an XBB.1.5 isolate showed superior replicative ability at 32°C and 30°C, whereas most other Omicron sub-variant isolates showed limited growth. Deep sequencing analysis demonstrated that the frequencies of viruses possessing the NSP6-S163P and NSP13-P238S substitutions increased to more than 97% during propagation of the XBB.1.5 isolate at 32°C but did not reach 55% at 37°C. Reverse genetics revealed that these substitutions contributed to superior virus growth in vitro at these low temperatures by improving virus genome replication. Mutant virus possessing both substitutions showed slightly higher virus titers in the upper respiratory tract of hamsters compared to the parental virus; however, transmissibility between hamsters was similar for the mutant and parental viruses. Taken together, our findings indicate that NSP6-S163P and NSP13-P238S contribute to superior virus growth at low temperatures in vitro and in the upper respiratory tract of hamsters.

IMPORTANCE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates efficiently at 37°C. However, the temperature of the human upper airway is 30°C-32°C. Therefore, the replicative ability of SARS-CoV-2 at low temperatures could influence virus replication in the upper airway and transmissibility. In this study, we assessed the growth of Omicron sub-variants at low temperatures and found that an XBB.1.5 isolate showed increased replicative ability. By deep sequencing analysis and reverse genetics, we found that amino acid changes in NSP6 and NSP13 contribute to the low-temperature growth; these changes improved RNA polymerase activity at low temperatures and enhanced virus replication in the upper airway of hamsters. Although these substitutions alone did not drastically affect virus transmissibility, in combination with other substitutions, they could affect virus replication in humans. Furthermore, since these substitutions enhance virus replication in cultured cells, they could be used to improve the production of inactivated or live attenuated vaccine virus.

The Coordination Chemistry of Two Peptidic Models of NFeoB and Core CFeoB Regions of FeoB Protein: Complexes of Fe(II), Mn(II), and Zn(II)

Often necessary for efficient Fe(II) trafficking into bacterial cell, the Feo system is a vital transporter for many pathogenic bacteria and indispensable for proper development and survival in the host organism during infection. In this work, we present the metal-binding characteristics of the peptidic models of two putative Fe(II)-binding sites of E. coliFeoB: L1 (Ac-477IMRGEATPFVMELPVYHVPH496-CONH2) being a fragment of the Core CFeoB region located between the transmembrane helices and L2 (Ac-38VERKEG43-CONH2), which represents the ExxE motif found within the NFeoB domain. With a variety of physicochemical methods, such as potentiometry, mass spectrometry, NMR, and EPR spectroscopy, we have determined the stability constants and metal-binding residues for the complexes of Fe(II), Mn(II), and Zn(II) with two ligands, L1 and L2, acting as models for the Core CFeoB and ExxE motif. We compare their affinities toward the studied metal ions with the previously studied C-terminal part of the protein and discuss a possible role in metal trafficking by the whole protein.

The role of TRAF2 in pan-cancer revealed by integrating informatics and experimental validation

Background

Tumor necrosis factor (TNF) receptor associated factor-2 (TRAF2) is an E3 ubiquitin ligase and scaffolding protein that contribute to the progression of various malignant tumors. However, the role of TRAF2 expression in epigenetic, cancer prognosis, and immune responses in tumor microenvironment is unclear.

Methods

We used The Human Protein Atlas (HPA) database, TIMER 2.0 database, and TCGA database to evaluate TRAF2 expression in human normal and tumor tissues. Correlation of TRAF2 expression with mutations and epigenetic in tumors was evaluated using the cBioPortal platform and the GSCA database. To assess the prognostic value of TRAF2, we performed Kaplan-Meier plots and Cox regression analysis. LinkedOmics database was used for PANTHER Pathways enrichment analysis. The relationship between TRAF2 expression and immune checkpoint genes, as well as immune cell infiltration, was examined using TIMER 2.0 and the R language. Single-cell sequencing data and multiple immunofluorescence staining were used to observe the co-expression of TRAF2 on hepatocellular carcinoma cells and immune cells. Furthermore, using siRNA-mediated knockdown, we explored the potential role of TRAF2 in liver cancer cell biology.

Results

Our findings indicate that TRAF2 is frequently mutated and significantly overexpressed in various types of cancers, and this overexpression is linked to a poor prognosis. The epigenetic alterations in TRAF2 was significant across various types of cancers. TRAF2 is associated with the levels of various immune checkpoint genes and multiple tumor-infiltrating immune cells, suggesting its potential involvement in tumor microenvironment. Of note, enrichment analysis revealed a significant correlation between TRAF2 and T cell activation, and single-cell sequencing indicated that TRAF2 was overexpressed in malignant cells and T cells. In vivo results demonstrated that TRAF2 was closely associated with T lymphocytes in hepatocellular carcinoma. The results of our in vitro experimental studies confirmed that the loss of TRAF2 function inhibits the malignant behavior of HepG2 cells in hepatocellular carcinoma.

Conclusion

TRAF2 represents a potential prognostic biomarker and therapeutic target for cancer immunotherapy, particularly in patients with hepatocellular carcinoma.

Characterization of Pseudomonas phage MME: a novel tool for combatting multidrug-resistant Pseudomonas aeruginosa and disinfection

AIM

Combatting Pseudomonas aeruginosa, known for its robust biofilm formation, presents significant challenges in healthcare, food, and industry. Phages offer promising alternatives against this resilient pathogen. We aim to demonstrate their viability as alternative therapeutic and decontamination options.

METHODS AND RESULTS

We introduce the lytic activity and decontamination efficacy of Pseudomonas phage MME, isolated from sewage, on solid surfaces, as well as on its biological and genomic characterization. The phage showed lytic activity against both antibiotic-resistant clinical strains and reference strains. About 90% of the phage adsorbed to its host within 20 min, with an average burst size of ∼53 PFU per infected cell. The bactericidal effect on the host at the 8th hour showed a 95% killing efficiency. Additionally, phage MME effectively reduced bacterial loads on glass, plastic, and metal surfaces, simulating hospital environments. Confocal laser scanning microscopy demonstrated the phage's bactericidal activity on glass surfaces at the 8th and 12th hours, preventing biofilm formation. Bioinformatic analysis confirmed that phage MME represents a new species within the Bruynoghevirus genus. Comparative genomic analysis revealed no virulence factors within the phage MME genome.

CONCLUSIONS

These findings highlight the potent lytic activity of phage MME against P. aeruginosa, underscoring its potential as a valuable tool in combatting this pathogen and its suitability for diverse applications, including as a decontaminating agent.

Not All Bark Beetles Smell the Same: Population-Level Functional Olfactory Polymorphisms in Ips typographus Pheromone Receptor ItypOR33

Eurasian spruce bark beetle Ips typographus, a natural part of forest ecosystems, is a major threat to Norway spruce forests during outbreaks. Olfaction plays a crucial role in the survival and range expansion of these beetles, amid forest disturbances and climate change. As the current management strategies are suboptimal for controlling outbreaks, the reverse chemical ecology approaches based on pheromone receptors offer promising alternatives. While the search for pheromone receptors is in progress, recently found chromosomal inversions indicates signs of adaptation in this species. Our attempts to characterise one of the highly expressed odorant receptors, ItypOR33, located in an inversion, led to the discovery of polymorphic variants distributed with similar frequency across 18 European populations. Deorphanizing ItypOR33 and its variant ItypOR33a using the Drosophila empty-neuron system (DeNS) revealed ItypOR33 tuned to amitinol, a heterospecific pheromone component in Ips spp., whereas its variant tuned to (S)-(-)-ipsenol, a conspecific pheromone component of I. typographus. The in silico approaches revealed the structural basis of variations by predicting putative ligand-binding sites, tunnels and ligand-receptor interactions. However, no sex-specific differences were found in the ItypOR33 expression, and its ligand amitinol elicited behavioural and electrophysiological responses. Reporting population-level functional olfactory polymorphisms for the first time in a non-model organism-bark beetles, provides key evidence for further exploring their survival and adaptation in forests. Additionally, these findings indicate potential long-term complexities of managing bark beetles in forests.

C1GALT1C1-Associated Mosaic Disorder of Glycosylation in a Female

Cosmc, encoded by the X-linked C1GALT1C1, is a molecular chaperone in the endoplasmic reticulum and a master regulator of O-glycosylation of mammalian glycoproteins. Recently, we described a germline mutation in C1GALT1C1 in two male patients, giving rise to a congenital disorder of glycosylation-COSMC-CDG. Here, we have identified a female patient with a de novo mosaic variant in C1GALT1C1 (c.202C>T, p.Arg68*), which results in a truncated and nonfunctional form of Cosmc (Cosmc-R68). The patient is mosaic, as ~27% of her buccal cells carry the mutation. The patient is now a 5-year old who presented with nonimmune hydrops fetalis. As Cosmc is essential for the generation of normal O-glycans through regulating T-synthase activity, thereby enabling the formation of the universal Core 1 O-glycan Galβ1-3GalNAcα1-Ser/Thr (T-antigen), the loss of Cosmc leads to the expression of the unusual precursor O-glycan termed Tn-antigen (CD175) (GalNAcα1-Ser/Thr). Owing to the mutational mosaicism, only a significant minority of cells would exhibit abnormal O-glycosylation. Analysis of red blood cells (RBCs), leukocytes, and serum from this patient indicated reduced expression of Cosmc and T-synthase proteins and lower T-synthase activity. Consistent with these findings, we observed reduced normal O-glycans in serum glycoproteins and RBCs from the patient, along with elevated expression of the Tn-antigen in serum glycoproteins compared to controls. This case represents the first description of a true mosaic loss-of-function variant in C1GALT1C1, that is, one that occurred postzygotically during embryogenesis, and raises interesting questions about the role of O-glycosylation during fetal development and its consequences on the clinical presentation.

PyPropel: a Python-based tool for efficiently processing and characterising protein data

BACKGROUND

The volume of protein sequence data has grown exponentially in recent years, driven by advancements in metagenomics. Despite this, a substantial proportion of these sequences remain poorly annotated, underscoring the need for robust bioinformatics tools to facilitate efficient characterisation and annotation for functional studies.

RESULTS

We present PyPropel, a Python-based computational tool developed to streamline the large-scale analysis of protein data, with a particular focus on applications in machine learning. PyPropel integrates sequence and structural data pre-processing, feature generation, and post-processing for model performance evaluation and visualisation, offering a comprehensive solution for handling complex protein datasets.

CONCLUSION

PyPropel provides added value over existing tools by offering a unified workflow that encompasses the full spectrum of protein research, from raw data pre-processing to functional annotation and model performance analysis, thereby supporting efficient protein function studies.

A "Dock-Work" Orange: A Dual-Receptor Biochemical Theory on the Deterrence Induced by Citrusy Aroma on Elephant Traffic Central to a Conservation Effort

Conservation of elephants requires physical, chemical, and biological approaches to ensure the protection of these gargantuan pachyderms. One such approach is using orange plants (as biofencing) for the repellence of elephants, which precludes catastrophic events related to the encroachment of elephants into human habitats. Elephants have sensitive olfactory discrimination of plant volatile compounds for foraging and other behavior using G-protein-coupled receptors (GPCRs). However, 2 such receptors are the A2A and A2B receptors mediating olfaction elicited by a host of ligands, including limonene, the main volatile compound in citrus plants, which is hypothesized to be the chief repelling agent. Bioinformatics at the protein and mRNA levels (BLAST/Multiple Sequence Alignments) were employed to explore the multiple expression products of A2B receptors, namely full-length and truncated proteins produced by isoform mRNAs translated from multiple methionines, while the comparison of the limonene-binding pockets of human and elephant A2B receptors and prediction servers [Netphos 3.1; Protter] was used to focus, respectively, on the contacts limonene binding entails and the post-translational modifications that are involved in cell signaling. Finally, the link between limonene and antifeedant activity was explored by considering limonene content on trees that are preferentially foraged or avoided as part of the feeding behavior by elephants. The African bush elephant (Loxodonta africana) possesses a full-length A2A receptor but unlike most mammals, expresses a highly truncated A2B receptor isoform possessing only transmembrane helices 5, 6, and 7. Truncation may lead to higher traffic and expression of the A2B receptor in olfactory interfaces/pathways and aid stronger activation. In addition, all residues in the putative limonene-binding cleft are perfectly conserved between the human and African bush elephant A2B receptors, both full length and truncated. Shallow activation sites require micromolar affinity and fewer side-chain interactions, which is speculated to be the case for the truncated A2B receptor. An N-terminal extremity N-glycosylation motif is indicative of membrane localization of the truncated A2B receptor following accurate folding. A combination of truncation, indels, substitutions, and transcript isoforms are the attributed roles in the evolution of the L. africana A2B receptor, out of which limonene receptivity may be the key. It is also inferred how limonene may act as a dietary repellent/antifeedant to a generalist herbivore, with the documented limonene content being absent in some dietary favorites including the iconic Sclerocarya birrea.

Receptor deorphanization in starfish reveals the evolution of relaxin signaling as a regulator of reproduction

BACKGROUND

Relaxins are a family of peptides that regulate reproductive physiology in vertebrates. Evidence that this is an evolutionarily ancient role of relaxins has been provided by the discovery of two relaxin-like gonad-stimulating peptides (RGP1 and RGP2) that trigger spawning in starfish. The main aim of this study was to identify the receptor(s) that mediate(s) the effects of RGP1 and RGP2 in starfish.

RESULTS

Here we show that RGP1 and RGP2 belong to a family of peptides that include vertebrate relaxins, Drosophila insulin-like peptide 8 (Dilp8), and other relaxin-like peptides in several protostome taxa. An ortholog of the human relaxin receptors RXFP1 and RXFP2 and the Drosophila receptor LGR3 was identified in starfish (RXFP/LGR3). In Drosophila, but not in humans and other vertebrates, there is a paralog of LGR3 known as LGR4, and here an LGR4-type receptor was also identified in starfish. In vitro pharmacological experiments revealed that both RGP1 and RGP2 act as ligands for RXFP/LGR3 in the starfish Acanthaster cf. solaris and Asterias rubens, but neither peptide acts as a ligand for LGR4 in these species.

CONCLUSIONS

Discovery of the RXFP/LGR3-type receptor for RGP1 and RGP2 in starfish provides a new insight into the evolution of relaxin-type signaling as a regulator of reproductive processes. Furthermore, our findings indicate that RXFP/LGR3-type receptors have been lost in several phyla, including urochordates, mollusks, bryozoans, platyhelminthes, and nematodes.

Synaptic vesicle glycoprotein 2 enables viable aneuploidy following centrosome amplification

Amplified centrosome number causes genomic instability, most severely through division into more than two aneuploid daughter cells (multipolar mitosis). Several mechanisms that suppress multipolar division have been uncovered, yet mechanisms that favor viable multipolar division are poorly understood. To uncover factors that promote viability in cells with frequent centrosome amplification and multipolar division, we conducted an unbiased Drosophila genetic screen. In 642 mutagenized lines, we exploited the ability of intestinal papillar cells to form and function despite multipolar divisions. Our top hit is an unnamed gene, CG3168 . We name this gene synaptic vesicle glycoprotein 2 , reflecting homology to human Synaptic Vesicle Glycoprotein 2 (SV2) proteins. GFP-tagged SV2 localizes to the plasma membrane. In cells with amplified centrosomes, SV2 positions membrane-adjacent centrosomes, which prevents severe errors in chromosome alignment and segregation. Our results uncover membrane-based multipolar division regulation and reveal a novel vulnerability in cells with common cancer properties.

Blood biomarker fingerprints in a cohort of patients with CHRNE-related congenital myasthenic syndrome

Mutations in CHRNE encoding the epsilon subunit of acetylcholine receptor result in impaired neuromuscular transmission and congenital myasthenic syndrome (CMS) with variying severity of symptoms. Although the pathophysiology is well-known, blood biomarker signatures enabling a patient-stratification are lacking. This retrospective two-center-study includes 19 recessive CHRNE-patients (AChR deficiency; mean age 14.8 years) from 13 families which were clinically characterized according to disease severity. 15 patients were classified as mildly and 4 patients as moderate to severely affected. Seven known pathogenic and one unreported variant (c.1032 + 2_1032 + 3delinsGT) were identified. Biomarker discovery was carried out on blood samples: proteomics was performed on white blood cells (WBC; n = 12) and on extracellular vesicles (EV) purified from serum samples (n = 7) in addition to amino acid profiling (n = 9) and miRNA screening (n = 18). For miRNA studies, 7 patients with other CMS-subtypes were moreover included. WBC-proteomics unveiled a significant increase of 7 and a decrease of 36 proteins. In silico studies of these proteins indicated affection of secretory granules and the extracellular space. Comparison across patients unveiled increase of two vesicular transport proteins (SCAMP2 and SNX2) in severely affected patients and indeed EV-proteomics revealed increase of 7 and decrease of 13 proteins. Three of these proteins (TARSH, ATRN & PLEC) are known to be important for synaptogenesis and synaptic function. Metabolomics showed decrease of seven amino acids/ amino acid metabolites (aspartic and glutamic acids, phosphoserine, amino adipate, citrulline, ornithine, and 1-methyhistidine). miRNA-profiling showed increase miR - 483 - 3p, miR-365a-3p, miR - 365b - 3p and miR-99a, and decrease of miR-4433b-3p, miR-6873-3p, miR-182-5p and let-7b-5p in CHRNE-patients whereas a comparison with other CMS subtypes showed increase of miR - 205 - 5p, miR - 10b - 5p, miR-125a-5p, miR-499-5p, miR-3120-5p and miR - 483 - 5p and decrease of miR - 1290. Our combined data introduce a molecular fingerprint on protein, metabolic and miRNA level with some of those playing different roles along the neuromuscular axis.

Bioluminescence and environmental light drive the visual evolution of deep-sea shrimp (Oplophoroidea)

Light functions as the universal language in the deep sea (>200 m). Both bioluminescent emissions and downwelling light sources dimly illuminate the water column and can drive sensory system evolution. In pelagic environments, vertically migrating animals can experience drastic changes to their lighting environment across depth, subjecting them to unique selective pressures, possibly to distinguish between changes in ambient light and bioluminescent sources. Here we show that visual opsin diversity across a group of variable vertical migrators -bioluminescent deep-sea shrimp belonging to the Superfamily Oplophoroidea- is higher among species who migrate to shallower waters with more variable light conditions. Further, we provide evidence for adaptive visual evolution among species who have evolved an additional mode of bioluminescence (photophores), including positive selection for a putative mid-wavelength sensitive opsin that may facilitate light source discrimination. Diversification of this opsin appears to play an important role in the visual ecologies of photophore-bearing shrimp with its diversification in Oplophoroidea likely playing a critical role in the fitness and evolutionary success of this group.

Packaging "vegetable oils": Insights into plant lipid droplet proteins

Plant neutral lipids, also known as "vegetable oils", are synthesized within the endoplasmic reticulum (ER) membrane and packaged into subcellular compartments called lipid droplets (LDs) for stable storage in the cytoplasm. The biogenesis, modulation, and degradation of cytoplasmic LDs in plant cells are orchestrated by a variety of proteins localized to the ER, LDs, and peroxisomes. Recent studies of these LD-related proteins have greatly advanced our understanding of LDs not only as steady oil depots in seeds but also as dynamic cell organelles involved in numerous physiological processes in different tissues and developmental stages of plants. In the past 2 decades, technology advances in proteomics, transcriptomics, genome sequencing, cellular imaging and protein structural modeling have markedly expanded the inventory of LD-related proteins, provided unprecedented structural and functional insights into the protein machinery modulating LDs in plant cells, and shed new light on the functions of LDs in nonseed plant tissues as well as in unicellular algae. Here, we review critical advances in revealing new LD proteins in various plant tissues, point out structural and mechanistic insights into key proteins in LD biogenesis and dynamic modulation, and discuss future perspectives on bridging our knowledge gaps in plant LD biology.

Proximal partners of the organellar N-terminal acetyltransferase NAA60: insights into Golgi structure and transmembrane protein topology

Biotin identification (BioID) is an interactomics approach that utilizes proximity labelling to map the local interactome or proxeome of proteins within a cell. This study applies BioID to investigate proteins proximal to NAA60 (N-alpha-acetyltransferase 60), an N-terminal acetyltransferase (NAT) of pathological significance in human disease, characterized by its unique Golgi localization. NAA60 is known to N-terminally acetylate transmembrane proteins that present their N-terminus on the cytosolic face of the membrane, and its involvement in maintaining Golgi structure has previously been established. Using a stable cell-line expressing an NAA60-BirA* fusion protein, we isolated biotinylated proteins through streptavidin affinity purification. Mass spectrometry analysis revealed over 100 proximal partners of NAA60, enriched in proteins localized on the trans-side of the Golgi apparatus. High-confidence proximity interactors included golgins and GRASP proteins, essential for Golgi integrity. Considering the transmembrane nature of NAA60, the identification of biotinylated peptides inferred the topology of transmembrane protein interactors within the secretory pathway. Subsequent suborganellar localization analysis revealed a more prominent medial/trans-Golgi localization of NAA60. Our findings underscore the role of NAA60 and its interactors in maintaining Golgi structural integrity and highlight the effectiveness of BioID in generating critical protein topology data, invaluable for enhancing the prediction of protein topology within cellular compartments.

Compromising the immunogenicity of diphtheria toxin-based immunotoxins through epitope engineering: An in silico approach

Immunotoxins are genetically engineered recombinant proteins consisting of a targeting moiety, such as an antibody, and a cytotoxic toxin moiety of microbial origin. Pseudomonas exotoxin A and diphtheria toxin (DT) have been abundantly used in immunotoxins, with the latter applied as the toxin moiety of the FDA-approved drug Denileukin diftitox (ONTAK®). However, the use of immunotoxins provokes an adverse immune response in the host body against the toxin moiety, limiting their efficacy. In silico approaches have received increasing attention in protein engineering. In this study, the epitopes responsible for immunogenicity were identified through multiple platforms. By subtracting conserved and ligand-binding residues, K33, T111, and E112 were identified as common epitopes across all platforms. Substitution analysis evaluated alternative residues regarding their impact on protein stability, considering 19 different amino acid substitutions. Among the mutants explored, the T111A-E112G mutant exhibited the most destabilizing substitution for DT, thereby reducing immunogenicity. Finally, a 3D model of the mutant was generated and verified. The model was then docked with its native ligand NADH, and the complex's molecular behavior was simulated using molecular dynamics.

Disulfide bonds are required for cell division, cell envelope biogenesis and antibiotic resistance proteins in mycobacteria

Mycobacteria, including Mycobacterium tuberculosis-the etiological agent of tuberculosis-have a unique cell envelope critical for their survival and resistance. The cell envelope's assembly and maintenance influence permeability, making it a key target against multidrug-resistant strains. Disulfide bond (DSB) formation is crucial for the folding of cell envelope proteins. The DSB pathway in mycobacteria includes two enzymes, DsbA and VKOR, required for survival. Using bioinformatics and cysteine profiling proteomics, we identified cell envelope proteins dependent on DSBs. We validated via in vivo alkylation that key proteins like LamA (MmpS3), PstP, LpqW, and EmbB rely on DSBs for stability. Furthermore, chemical inhibition of VKOR results in phenotypes similar to those of Δvkor. Thus, targeting DsbA-VKOR systems could compromise both cell division and mycomembrane integrity. These findings emphasize the potential of DSB inhibition as a novel strategy to combat mycobacterial infections.

Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes

Bacteria and archaea deploy diverse, sophisticated defence systems to counter virus infection, yet many immunity mechanisms remain poorly understood. Here, we characterise the Kiwa defence system as a membrane-associated supercomplex that senses changes in the membrane induced by phage infection and plasmid conjugation. This supercomplex, comprising KwaA tetramers bound to KwaB dimers, as its basic repeating unit, detects structural stress via KwaA, activating KwaB, which binds ejected phage DNA through its DUF4868 domain, stalling phage DNA replication forks and thus disrupting replication and late transcription. We show that phage-encoded DNA mimic protein Gam, which inhibits RecBCD, also targets Kiwa through KwaB recognition. However, Gam binding to one defence system precludes its inhibition of the other. These findings reveal a distinct mechanism of bacterial immune coordination, where sensing of membrane disruptions and inhibitor partitioning enhance protection against phages and plasmids.

Theoretical Study of Sphingomyelinases from Entamoeba histolytica and Trichomonas vaginalis Sheds Light on the Evolution of Enzymes Needed for Survival and Colonization

The path to survival for pathogenic organisms is not straightforward. Pathogens require a set of enzymes for tissue damage generation and to obtain nourishment, as well as a toolbox full of alternatives to bypass host defense mechanisms. Our group has shown that the parasitic protist Entamoeba histolytica encodes for 14 sphingomyelinases (SMases); one of them (acid sphingomyelinase 6, aSMase6) is involved in repairing membrane damage and exhibits hemolytic activity. The enzymatic characterization of aSMase6 has been shown to be activated by magnesium ions but not by zinc, as shown for the human aSMase, and is strongly inhibited by cobalt. However, no structural data are available for the aSMase6 enzyme. In this work, bioinformatic analyses showed that the protist aSMases are diverse enzymes, are evolutionarily related to hemolysins derived from bacteria, and showed a similar overall structure as parasitic, free-living protists and mammalian enzymes. AlphaFold3 models predicted the occupancy of cobalt ions in the active site of the aSMase6 enzyme. Cavity blind docking showed that the substrate is pushed outward of the active site when cobalt is bound instead of magnesium ions. Additionally, the structural models of the aSMase6 of E. histolytica showed a loop that is absent from the rest of the aSMases, suggesting that it may be involved in hemolytic activity, as demonstrated experimentally using the recombinant proteins of aSMase4 and aSMase6. Trichomonas vaginalis enzymes show a putative transmembrane domain and seem functionally different from E. histolytica. This work provides insight into the future biochemical analyses that can show mechanistic features of parasitic protists sphingomyelinases, ultimately rendering these enzymes potential therapeutic targets.

Curation of OCA2 Variants of Uncertain Significance From Chinese Oculocutaneous Albinism Patients Based on Multiplex Assays

Oculocutaneous albinism type 2 (OCA-2, OMIM: 203200) is associated with variants in the OCA2 gene. In this study, we aimed to re-classify variants of uncertain significance (VUS) in OCA2 by evaluating subcellular localization and channel activity through multiplex assays of variant effect (MAVEs). Following the ClinGen guidelines for PS3 evidence, we selected 13 OCA2 variants from ClinVar (6 benign/likely benign [B/LB] and 7 pathogenic/likely pathogenic [P/LP]) for OddsPath analysis. The P/LP variants exhibited abnormal functions, while the B/LB variants demonstrated normal functions, supporting the application of "PS3_moderate" evidence for VUS re-classification. In our functional evaluation of 30 VUS identified in 38 individuals with suspected OCA-2 by trio whole-exome sequencing, we observed 6 VUS with abnormal localization and 11 with abnormal channel activity. Based on PS3_moderate evidence, 8 VUS were re-classified as LP, while 22 remained VUS. Consequently, 7 out of 38 previously undiagnosed patients received a molecular diagnosis of OCA-2. These MAVEs offer a robust approach for curating OCA2 VUS, enhancing diagnostic accuracy, and informing genetic counseling. Additionally, this variant cohort is a valuable resource for public databases.

In Silico Analysis and Molecular Docking of Human Antimicrobial Peptides for Targeting Monkeypox Virus: Potential Therapeutic Implications of Histatin 5 Peptide

BACKGROUND

Monkeypox, a viral zoonotic disease akin to smallpox, has posed significant public health challenges, particularly in Africa. Recent outbreaks, including those in India, underscore the global threat it poses.

OBJECTIVE

In this study, we explore a novel approach to combat monkeypox virus (MPXV) infection by targeting its surface proteins, crucial for viral entry and fusion.

METHODS

Employing advanced computational techniques, we predict and refine the 3D structures of MPXV surface proteins and human antimicrobial peptides (hAMPs), specifically Histatin 1, 3, and their cleaved product, Histatin 5 (HIS 5). Further, molecular docking was carried out for MPXV surface proteins with hAMP HIS using HDOCK and Cluspro 2.0. Protein-peptide interactions were analyzed using PdbSum. Finally, the physicochemical properties of HIS peptides were determined using CamSol.

RESULTS

Our findings suggest HIS 5 as a potential therapeutic peptide against MPXV, warranting further investigation through in vitro and in vivo studies.

CONCLUSION

This study sheds light on the efficacy of the HIS family in targeting MPXV and advocates for continued exploration of HIS 5's antiviral effects.

A Ball Python Colour Morph Implicates MC1R in Melanophore-Xanthophore Distribution and Pattern Formation

Reptiles showcase an extensive array of skin colours and patterns, yet little is known about the genetics of reptile colouration. Here, we investigate the genetic basis of the Clown colour morph found in captive-bred ball pythons (Python regius) to study skin pigmentation and patterning in snakes. We obtained samples by crowdsourcing shed skin from commercial breeders and hobbyists. We applied a case-control design, whole-genome pool sequencing, variant annotation, histological analyses, and electron microscopy imaging. We identified a missense mutation in a transmembrane region of the melanocortin-1 receptor (MC1R) associated with the Clown phenotype. In classic avian and mammalian model species, MC1R is known for controlling the type and amount of melanin produced. In contrast, our results suggest that MC1R signalling might play a key role in pattern formation in ball pythons, affecting xanthophore-melanophore distribution. This work highlights the varied functions of MC1R across different vertebrate lineages and promotes a novel model system to study reptile colouration.

Cysteines in β-lactoglobulin affects its interfacial adsorption and protein film stabilization

HYPOTHESIS

Disulfide bonds in proteins are strong chemical bonds forming the secondary and tertiary structure like in the dairy protein β-lactoglobulin. We hypothesize that the partial or complete removal of disulfide bonds affects the structural rearrangement of proteins caused by intra- and intermolecular interactions that in turn define the interfacial activity of proteins at oil/water interfaces. The experimental and numerical investigations contribute to the mechanistic understanding of the structure-function relationship, especially for the interfacial adsorption behavior of proteins.

EXPERIMENTAL AND NUMERICAL

Systematically, the 5 cysteines of β-lactoglobulin were recombinantly exchanged by alanine. First, the protein structure of the variants in bulk was analyzed with Fourier-transform-infrared-spectroscopy and molecular dynamic simulations. Second, the structural changes after adsorption to the interface have been also analyzed by molecular dynamic simulations. The adsorption behavior was investigated by pendant drop analysis and the interfacial film properties by dilatational rheology.

FINDINGS

The structural flexibility of β-lactoglobulin with no cysteines encourages its unfolding at the interface, and accelerates the interfacial protein film formation that results in more visco-elastic films in comparison to the reference.

A novel de novo GABRA2 gene missense variant causing developmental epileptic encephalopathy in a Chinese patient

BACKGROUND

Variants in the GABRA2 gene, which encodes the α2 subunit of the γ-aminobutyric acid A receptor, have been linked to a rare form of developmental and epileptic encephalopathy (DEE) referred to as DEE78. Only eight patients have been reported globally. This study presents the clinical presentation and genetic analysis of a Chinese family with a child diagnosed with DEE78, due to a novel GABRA2 variant.

METHODS

Genetic diagnosis was performed using trio-whole exome sequencing, followed by bioinformatics predictions of pathogenicity. Structural modeling assessed the potential impact of the variant. A mutant plasmid was constructed and transfected into 293 T cells. Western blotting (WB) was used to evaluate mutant protein expression, while co-immunoprecipitation (Co-IP) analyzed interactions with GABRB3 and GABRG2 proteins. Immunofluorescence (IF) assessed the subcellular localization of the mutant protein.

RESULTS

The 6-year-old male proband presented with seizures starting at age two, along with global developmental delay and hypotonia. Genetic testing revealed a heterozygous de novo variant in GABRA2 gene (NM_000807: c.923C>T, p.Ala308Val). Structural modeling suggested that this variant is located within the extracellular domain, which may disrupt hydrogen bonding interactions with GABRB3 and GABRG2. WB and Co-IP showed reduced protein expression and impaired interactions, potentially destabilizing the pentamer receptor complex. If analysis revealed that the variant did not affect subcellular localization.

CONCLUSION

This study identified a novel likely pathogenic GABRA2 extracellular domain variant in a Chinese family causing the DEE phenotype. The results expand the genotypic and phenotypic spectrum of GABRA2-related DEE.

Evolution of a bipolar sexual compatibility system in Marasmius

Sexual compatibility in the Basidiomycota is governed by genetic identity at one or two loci, resulting in compatibility systems called bipolar and tetrapolar. The loci are known as HD and P/R, encoding homeodomain transcription factors and pheromone precursors and receptors, respectively. Bipolarity is known to evolve either by linkage of the two loci or by loss of mating-type determination of either the HD or the P/R locus. The ancestor to basidiomycete fungi is thought to have been tetrapolar, and many transitions to bipolarity have been described in different lineages. In the diverse genus Marasmius (Agaricales), both compatibility systems are found, and the system has been shown to follow the infrageneric sections of the genus, suggesting a single origin of bipolarity. Here, we tested this hypothesis using a comprehensive phylogenetic framework and investigated the mode by which bipolarity has evolved in this group. We utilized available genomic data and marker sequences to investigate evolution of sexual compatibility in Marasmius and allied genera. By generating a concatenated multilocus phylogeny, we found support for a single transition to known bipolarity within Marasmius. Furthermore, utilizing genomic data of the bipolar species Marasmius oreades, we found that the HD and P/R loci likely have remained unlinked through this transition. By comparing nucleotide diversity at the HD and P/R loci in Ma. oreades, we show that the HD locus has retained high diversity, and thus likely the function of determining sexual identity, as similarly in other bipolar mushroom-forming fungi. Finally, we describe the genomic architecture of the MAT loci of species of both sexual compatibility systems in Marasmiaceae and related families.

Genome assembly of a nocturnal butterfly (Macrosoma leucophasiata) reveals convergent adaptation of visual genes

Nearly all animals exhibit a preferred period of daily activity (diel-niche), strongly influenced by the light environment. Vision is a sensory system that is strongly adapted to light, and evolutionary transitions to novel light environments can impose strong constraints on eye evolution, color, and motion vision. While the genetic and neural basis of visual adaptation are well-studied in a few model systems, our understanding across the tree of life remains incomplete. Butterflies and moths are an ideal system to investigate the association between gene evolution and diel-niche transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, representing an important evolutionary shift from diurnality to nocturnality. We sequenced the first Hedylidae genome and annotated it to understand genomic changes associated with diel niche shifts. Comparing Hedylidae visual genes to those of other diurnal and nocturnal Lepidoptera revealed that visual genes are highly conserved, with no major losses. However, hedylid opsins were more similar to nocturnal moths than their diurnal congeners, suggesting that these opsins convergently evovled to adapt to the nocturnal environment. Evolutionary rate tests (dN/dS) confirmed strong selection on color vision opsins, with some sites being mapped to the functional domain of the blue opsin. Our study provides new insight into the molecular evolutionary adaptations associated with species' changes to new light environments.

The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance

BACKGROUND

Pineapple (Ananas comosus L.) is a major tropical fruit crop with considerable economic importance, and its growth and development are significantly impacted by low temperatures. The plant-specific GRAS gene family plays crucial roles in diverse processes, including flower and fruit development, as well as in stress responses. However, the role of the GRAS family in pineapple has not yet been systematically analyzed.

RESULTS

In this study, 43 AcGRAS genes were identified in the pineapple genome; these genes were distributed unevenly across 19 chromosomes and 6 scaffolds and were designated as AcGRAS01 to AcGRAS43 based on their chromosomal locations. Phylogenetic analysis classified these genes into 14 subfamilies: OS19, HAM-1, HAM-2, SCL4/7, LISCL, SHR, PAT1, DLT, LAS, SCR, SCL3, OS43, OS4, and DELLA. Gene structure analysis revealed that 60.5% of the AcGRAS genes lacked introns. Expression profiling demonstrated tissue-specific expression, with most AcGRAS genes predominantly expressed in specific floral organs, fruit tissues, or during particular developmental stages, suggesting functional diversity in pineapple development. Furthermore, the majority of AcGRAS genes were induced by cold stress, but different members seemed to play distinct roles in short-term or long-term cold adaptation in pineapple. Notably, most members of the PAT1 subfamily were preferentially expressed during late petal development and were upregulated under cold stress, suggesting their special roles in petal development and the cold response. In contrast, no consistent expression patterns were observed among genes in other subfamilies, suggesting that various regulatory factors, such as miRNAs, transcription factors, and cis-regulatory elements, may contribute to the diverse functions of AcGRAS members, even within the same subfamily.

CONCLUSIONS

This study provides the first comprehensive analysis of GRAS genes in pineapple, offers valuable insights for further functional investigations of AcGRASs and provides clues for improving pineapple cold resistance breeding.

Structural Analysis of Variants of the Ferritin Light Chain Protein and Its Relationship with Neuroferritinopathy

Ferritin is a highly conserved spherical protein that stores iron and possesses triple and quadruple symmetry input ports. Additionally, it is composed of light chains that can be affected by post-translational mutations, reducing the iron storage capacity in the brain and leading to neuroferritinopathy, which is a rare disease with limited bioinformatics data. In this study, we analyzed the biochemical mechanism of different ferritin mutations reported in the literature, through the characterization and determination of the in silico structural model by searching databases, implementing bioinformatics programs such as Jalview, NetNGlyc 1.0, NetOGlyc 3.1, and three-dimensional structure predictors with machine learning such as Alphafold, demonstrating the generation of hairpin and steric hindrances that hinder the aggregation of subunits and changes in the size and arrangement of quadruple and triple entry holes of the A96T mutation compared to the wild-type protein, since in the quadruple entry hole, a decrease in area is observed compared to the wild-type protein and the triple entry hole has a decrease in distance measurements of 6.504 Å. This possibly affects the functionality of the protein, thus releasing high concentrations of iron in the brain and causing neurodegeneration.

Broccoli (Brassica oleracea var. italica) leaves exhibit significant antidiabetic potential in alloxan-induced diabetic rats: the putative role of ABC vacuolar transporter for accumulation of Quercetin and Kaempferol

Background

The global prevalence of diabetes among adults over 18 years of age is expected to increase from 10.5% to 12.2% (between 2021 and 2045). Plants can be a cost-effective source of flavonoids like quercetin and kaempferol with anti-diabetic properties.

Methodology

We aimed to assess the antidiabetic potential of leaves of Brassica oleracea cvs. Green Sprout and Marathon. Further, flavonoid contents were measured in broccoli leaves grown under light and dark conditions. The methanolic extracts of Green Sprout (GSL-M) and Marathon (ML-M) were first evaluated in vitro for their α-amylase and α-glucosidase inhibitory potential and then for antidiabetic activity in vivo in alloxan-induced diabetic rat models.

Results

Treatment with plant extracts promoted the reduced glutathione (GSH) content and CAT, POD, and SOD activities in the pancreas, liver, kidney, heart, and brain of diabetic rats, whereas lowered lipid peroxidation, H2O2, and nitrite concentrations. The histopathological studies revealed the protective effect of plant extracts at high dose (300 mg/kg), which could be due to broccoli's rich content of chlorogenic acid, quercetin, and kaempferol. Strikingly, etiolated leaves of broccoli manifested higher levels of quercetin and kaempferol than green ones. The putative role of an ABC transporter in the accumulation of quercetin and kaempferol in etiolated leaves was observed as evaluated by qRT-PCR and in silico analyses.

Conclusion

In conclusion, the present study shows a strong link between the antidiabetic potential of broccoli due to the presence of chlorogenic acid, quercetin, and kaempferol and the role of an ABC transporter in their accumulation within the vacuole.