The ATPase ABCE1, a member of the ubiquitous ATP-Binding Cassette protein superfamily, is essential in eukaryotic and archaeal ribosome recycling. It comprises a pair of homologous nucleotide-binding domains (NBDs), each containing a consensus nucleotide-binding site (NBS), where ATP hydrolysis takes place. Each of these sites can be in either an open or closed conformation. Despite the near symmetry of the two NBDs, and quite unexpectedly, their hydrolysis kinetics are highly asymmetric. While substitution of the catalytic glutamate (E238Q) in NBSI reduced the overall turnover rate of the ATPase by a factor of 2, as one might expect, the corresponding substitution in NBSII (E485Q) shows a so far unexplained 10-fold increase. To address this issue, we used Markov models to study how such a drastic asymmetry can arise. Specifically, we asked whether this observation can be explained without previously proposed direct allosteric interactions, such as electrostatic interactions, between the two NBSs. Indeed, using a Bayesian approach, we found Markov models that quantitatively predict the experimentally observed kinetics, as well as additional steady-state ATP occupancy data, both without such direct allosteric interaction. In particular, our results show that the observed remarkable asymmetry is fully explained by the structure-induced property that opening and closing always involves both NBSs. These models can explain the unexpected fast kinetics of the mutant of NBSII in terms of a drastic population shift due to the mutation, which circumvents a kinetic trap state that slows wild-type kinetics. Our Bayesian Markov approach may help to quantitatively explain similar nonintuitive Braess-type kinetics also in other enzymes where chemical/conformation coupling is essential.

Transcription factor NlHsf regulates NlABCG7 overexpression in the sulfoxaflor resistance of Nilaparvata lugens.

Functional characterization of an MPEG1 homologue from Paralichthys olivaceus.

Intracellular organization is crucial for supporting cell function in an ever-changing environment. The eukaryotic microtubule cytoskeleton and its associated motor proteins are the vast molecular highways and motor vehicles that connect, position, and transport cellular cargoes, ranging from the cell nucleus to vesicles to mitotic spindles. The kinesin superfamily of motor proteins carries out a diverse array of functions and is thus a key player in these processes. While the mechanochemical cycle of kinesins has been extensively studied, mechanisms of kinesin activation and inhibition are not well understood. Over the past five years, several publications have significantly advanced our understanding of kinesin regulation, showing how inesin motors are turned off via autoinhibition and kinesin-binding protein. In this review, we will delve into these recent findings to introduce some 'rules of the road' in a model that captures the complexities of kinesin regulation.

Aquaporins (AQPs), key members of the major intrinsic protein (MIP) superfamily, have emerged as pivotal regulators of plant responses to diverse abiotic stresses. Beyond their natural role as water channels, AQPs function as integrators of transport, signaling, and acclimation. This review synthesizes current knowledge on their structural diversity, stress-specific isoform expression, and multilayered regulation by transcription factors, phytohormones, and signaling molecules. We highlight the modulation of AQP activity through post-translational mechanisms such as phosphorylation, gating, and trafficking, and emphasize the central role of plasma membrane intrinsic proteins (PIPs) in hydraulic adjustment under drought, salinity, and temperature stress. By linking AQPs with antioxidant systems, ion channels, and stress signaling pathways, we underscore their function as natural hubs of adaptation. We further evaluate their potential in crop improvement through genetic manipulation, including CRISPR-based strategies, while identifying key knowledge gaps in isoform-specific functions, subcellular dynamics, and interactions with soil microbiota. Taken together, AQPs represent promising targets for enhancing crop resilience in the face of climate change.

The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes and its sister project, the Vertebrate Gene Nomenclature Committee (VGNC), names genes across selected vertebrates (chimp, macaque, horse, cattle, pig, dog, cat) in line with their human orthologs. The A2M gene family, a subfamily of the thioester-containing protein (TEP) superfamily, is well conserved across vertebrates and several members of this family have already been characterized as non-specific peptidase inhibitors. Chicken ovostatin, originally termed "ovomacroglobulin", is an A2M family member that was first identified as being one of the most abundant proteins found in egg white. Two uncharacterized ovostatin homologs have also been reported in human. We wanted to assign standardized nomenclature to the multiple members of the A2M family across a wide range of vertebrate species, to capture the variation within this complex gene family. We constructed a maximum likelihood phylogenetic tree based on a multiple alignment of A2M protein sequences to help assign new nomenclature to previously unnamed A2M family genes, including the ovostatins, in human and across selected vertebrate species. This resulted in the naming of 4 human A2M family pseudogenes and 14 protein coding genes and 4 pseudogenes across VGNC species. An additional 48 genes were also named in model organisms (mouse, rat, xenopus, zebrafish, chicken) by their nomenclature committees based on this phylogenetic analysis.

Single-domain protein superfamilies mediate essential signaling functions in both prokaryotes and eukaryotes. Signal transduction mediated by single-residue phosphorylation involves subtle secondary structure, side chain rotamer, and hydrogen-bond fluctuations for transitions between active and inactive conformational states, rather than large fold variations. Its study requires molecular dynamics simulations for adequate sampling of the conformational landscape. Discrimination between functional states and subfamilies is achieved by subsequent network analysis designed to couple variations at the local residue or fragment levels to functional collective motions. We describe an integrated protocol for quantitative measurement of local fluctuations and their coupling to functional motions with phosphorylation of the CheY bacterial chemotaxis signal protein as a case study.

PCDH7 promotes EMT and chemoresistance by stabilizing ZEB1 via inhibition of TRIM26-mediated ubiquitination in lung adenocarcinoma.

To identify pyroptosis, apoptosis, and necroptosis (PANoptosis)-related genes (PRGs) in clear cell renal cell carcinoma (ccRCC) for patient stratification and prognosis prediction. We used differential expression analysis and weighted gene co-expression network analysis (WGCNA) to identify ccRCC-specific PRGs. A prognostic model, the PANoptosis-index (PANI), was constructed using least absolute shrinkage and selection operator (LASSO) and Cox regression. The PANI model, comprising PRGs, was validated through single-cell RNA-sequencing (scRNA-seq), immunohistochemistry, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Patient cohorts were categorized into high- and low-PANI groups, and the model's performance was appraised using various metrics. External validation was performed with the E-MTAB-1980 dataset. Functional and gene set enrichment analyses distinguished biological differences between groups. Mutational landscapes and tumor immune microenvironments were compared. Sensitivity to immunotherapy and antineoplastic drugs was also predicted using PANI. The effects of Z-DNA-binding protein 1 (ZBP1) on cell proliferation and migration were assessed by cell counting kit-8 (CCK-8) and Transwell assays. We identified five PRGs (ZBP1, tumor necrosis factor superfamily protein 14 (TNFSF14), cyclin-dependent kinase inhibitor 3 (CDKN3), parathyroid hormone-like hormone (PTHLH),and heme-oxygenase 1 (HMOX1)) constituting PANI, independently associated with ccRCC patient prognosis. The PANI-based nomogram, integrated with clinical factors, demonstrated high predictive accuracy for prognosis. High-PANI patients exhibited distinct co-mutation patterns in ccRCC driver genes and lower survival probabilities, with an enriched immune-related functional profile, indicating an activated immune environment. These patients also showed increased sensitivity to immunotherapy and antineoplastic drugs. The knockdown of ZBP1, a key PRG in the PANI, significantly reduced ccRCC cell proliferation and migration. PANI provides precise prognosis and immunotherapy response predictions for ccRCC patients, facilitating individualized treatment strategies.

The RNA thermometer motif ROSE-G regulates ABC transporter gene expression in bacteria.

Per- and Polyfluoroalkyl Substances (PFAS) are a diverse class of highly fluorinated persistent synthetic chemical pollutants. Major routes of human exposure include ingestion of contaminated drinking water and foods including dairy. Consumption of PFAS-contaminated milk and dairy is especially concerning for infants and children who are particularly sensitive and most highly exposed. Here we report findings of quantitative analysis of PFAS binding to β-lactoglobulin (β-Lg), the major whey protein in bovine milk, using differential scanning fluorimetry to determine binding affinities for 17 PFAS; except for uncharged fluorotelomer alcohols, β-Lg bound each PFAS congener tested, supporting a key role of charged functional groups in binding. The perfluoroalkyl carboxylic acid trifluoroacetic acid (TFA) bound with lowest affinity (Kd = 8.6 mM) and long chain congeners PFNA, PFDA, and PFUnDA bound with highest affinities. Evidence of significant cooperative binding was found for TFA, PFDA, PFUnDA, and PFOS. Molecular docking was used to define molecular mechanisms of PFAS binding by β-Lg and across the calycin super family of lipocalins and fatty acid binding proteins. All calycins were predicted to bind PFAS in the calyx domain with ΔG of binding ranging from -5.3 to -9.4 kcal/mol, revealing that the binding affinity for many PFAS are greater than those for binding albumin. In total, this study has identified the calycin protein superfamily as PFAS binding proteins, most of which have well-characterized functions related to key endocrine and toxicological pathways associated with the adverse consequences of PFAS exposure.

OX40 and OX40L belong to the tumor necrosis factor receptor superfamily (TNFRSF) and tumor necrosis factor superfamily (TNFSF), respectively. Protein–protein interactions between OX40 and OX40L facilitate T cell responses, triggering various immunological and pathophysiological events. Excessive activation frequently contributes to the onset of autoimmune and allergic diseases. Therefore, the OX40/OX40L system is considered a promising target for drug discovery. Given that the structure of the OX40–OX40L complex exhibits some unique features compared to other members of these protein super families, it is reasonable to assume that this tandem possesses distinct interaction mechanisms. However, detailed interaction analysis using quantitative parameters such as binding kinetics or thermodynamics, with remains to be performed for OX40/OX40L. In this study, we identified several hot spot residues from the OX40 cysteine‐rich domains (CRDs) 1 to 3 by alanine scanning. Kinetic and thermodynamic analysis combined with molecular dynamics simulations highlighted the characteristics of a hot spot from CRD3 due to its indirect influence on those from CRD1 and CRD2, providing insights into the interaction mechanism and a strategy for drug discovery targeting this interaction.

Viroporins are small multifunctional proteins that modify cellular membranes facilitating processes such as viral nucleic acid entry and the release of virions from infected cells. We are interested in studying the evolutionary relationships among these proteins, in particular their organization into families and superfamilies. Comparative genomics analysis of 120 viral genomes, using the Phylogenetic Profiles method, allowed the identification of 12 families, organized into four functionally related groups. Additionally, we compiled a list of 40 families from the Transporter Classification Database (TCDB) with viroporin-like attributes (i.e., length  300 aas, similar topologies and/or documented viroporin activities). We then used TCDB as a reference to search for evidence of homology among families. Our well-established bioinformatic pipeline for inference of homology included (1) sequence similarity, (2) compatibility of topology and hydropathy profiles, (3) similarity of family based HMM-profiles, (4) shared motifs, and (5) conserved domains. We were able to infer homology among 15 families, four of which (Vpu-C, p10 Viroporin/GDU1, FAST and R-FAST) expanded the established Influenza A/B Virus M2 Protein (M2) Superfamily. The other families constituted three novel superfamilies: Viroporin-1, consisting of three families (RVP10, NS3 and NSP4); Viroporin-2, composed of two functionally-linked families (SARS-VP and M-Protein); and Viroporin-3 composed of 3 functionally-related families (Viroporin E, IBV-E, and PRRSV).

Hepatocellular carcinoma (HCC) is one of the most frequent diagnosed malignancies globally with dismalprognosis and high mortality. Transformer 2 beta homolog (TRA2B), known as serine/arginine-rich splicing factor 10 (SRSF10), is a member of the serine/arginine (SR) protein superfamily that modulates gene expression by regulating mRNA splicing. The significance of TRA2B in cancer has received considerable attention in recent years, however, its specific role and molecular mechanisms in HCC remain unknown. This study aimed to analyze the expression of TRA2B in LIHC with the support of integrative bioinformatic analysis. The study conducted Kaplan-Meier and cox regression analyses and showed that the upregulated TRA2B was notably correlated with the dismal prognosis in HCC. TRA2B was identified as a potential proto-oncogene in HCC associated with poor prognosis. TRA2B expression in tumor tissues was found to be elevated using bioinformatics analysis. Following that, non-coding RNAs (ncRNA) related to TRA2B were extracted using series analysis. The CRNDE/LINC00511-miR-29c-3p axis was characterized as a potential upstream ncRNA-correlated signaling of TRA2B in HCC. Subsequently, the role of TRA2B in the tumor immune microenvironment (TIME) was investigated. In summary, this research provides novel insight into the potential role of TRA2B across various cancers and indicated that ncRNA-mediated overexpression of TRA2B is associated with the dismal prognosis in HCC.

Apicomplexan parasites, including Plasmodium falciparum and Toxoplasma gondii, contain specialized secretory organelles such as micronemes, rhoptries, and dense granules, which are essential for parasite motility, host cell invasion, development, and egress. DedA superfamily proteins are implicated in lipid mobilization, which is a key requirement for organelle biogenesis. Herein, we identify and investigate the vacuole membrane protein 1 (VMP1), a DedA superfamily member, of P. falciparum (PfVMP1) and T. gondii (TgVMP1). PfVMP1 and TgVMP1 are ER-localized lipid scramblases. TgVMP1 depletion adversely affects parasite development, motility, host cell invasion, and egress. These phenotypes are consistent with impaired rhoptry and dense granule biogenesis, and decreased secretion of micronemes and rhoptries in TgVMP1-depleted parasites, indicating a crucial role for TgVMP1 in the biogenesis and function of these organelles. TgVMP1 depletion impairs lipid droplet homeostasis and ER organization, and causes loss of intravacuolar network in the parasitophorous vacuole, which are key for parasite development. Restoration of the ER-localized lipid scramblase by complementing TgVMP1-depleted parasites with PfVMP1 or a homolog as distant as human VMP1 rescues the depleted parasites, indicating their functional conservation and a crucial role for ER-resident lipid scramblase activity in the biogenesis and function of secretory organelles.

AimATP-binding cassette (ABC) transporters are among the most functionally diverse protein superfamilies, essential for transmembrane substrate transport and implicated in various diseases, including cancer and cystic fibrosis [1]. While previous studies have focused on conserved nucleotide-binding domains (NBDs) and transmembrane domains (TMDs) [2], the functional and evolutionary significance of non-canonical regions, particularly intrinsically disordered linkers, remains poorly understood.MethodsA comprehensive computational pipeline were applied to analyze the domain organization, structural disorder, selection pressure, and post-translational modification (PTM) patterns across ABC transporter subfamilies. Phylogenetic trees were constructed from aligned protein sequences. Codon-based evolutionary tests were conducted using the HyPhy package (FEL and MEME). Structural disorder and secondary structure were predicted using AIUPred and NetSurfP, respectively. Structural transitions were inferred using GLOOME and PTM sites were predicted with MusiteDeep.ResultsLinker regions in full transporters were highly disordered, enriched in predicted PTMs, and subject to episodic positive selection. While conserved domains exhibited subfamily-specific divergence and structural rigidity. These findings suggest that linker regions may function as flexible modules with adaptive and regulatory potential.ConclusionOur findings indicate that, within the ABC transporter structure, besides conserved domains, linker regions also play crucial roles by combining structural dynamics with regulatory control, offering new insight into how modular evolution drives their functional diversification and structural complexity.

Kinesins, which are motor proteins that primarily move along microtubules by hydrolyzing adenosine triphosphate (ATP), constitute a superfamily of proteins known as kinesin superfamily proteins (KIFs). These molecules play crucial roles not only in intracellular transport but also in cell division, cell survival, morphogenesis, and higher brain functions such as memory, learning, and neural network formation. We previously reported that KIF26A plays a key role in the development of the enteric nervous system of the colon. Here, we demonstrate that KIF26A plays a role in olfaction. Analysis of Kif26a−/− mice reveals that Kif26a is critical for the development of the neuronal layer in the main olfactory epithelium (MOE). At postnatal day 7, Kif26a−/− mice exhibit decreased thickness and disorganization of the MOE with disproportionate numbers of mature and immature olfactory sensory neurons (OSNs). Loss of KIF26A leads to increased apoptosis and accelerated precursor cell proliferation of OSNs. Additionally, in vitro experiments using primary cultures of neurons reveal that KIF26A deficiency impaired neurite outgrowth and disrupted nerve bundle formation in OSNs. Furthermore, Kif26a haploinsufficiency results in impaired olfactory responses. These findings suggest that KIF26A plays important roles in both olfactory epithelium development and olfactory function.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-30412-8.

Salinity is a major constraint on tomato production, increasingly intensified by climate change. This study aimed to develop superior salt-tolerant tomato cultivars by evaluating genetic variation in salt tolerance, identifying associated single-nucleotide polymorphism (SNP) markers through genome-wide association studies (GWAS), and applying genomic prediction (GP). A total of 265 tomato accessions from the USDA germplasm collection were evaluated at the seedling stage under controlled greenhouse conditions with saline stress (200 mM NaCl). Nineteen accessions were identified as salt-tolerant, exhibiting a leaf injury score (LIS) ≤ 3.0 (on a 1–7 scale) and less than 40% chlorophyll reduction compared to non-stressed controls. GWAS was conducted using 27,046 SNPs generated via genotyping-by-sequencing (GBS), utilizing five models in GAPIT3 (GLM, MLM, MLMM, FarmCPU, and BLINK), three models in TASSEL 5 (SMR, GLM, and MLM), and three models in rMVP (GLM, MLM, and FarmCPU). Eight SNPs with LOD scores > 5.73 were significantly associated with salt tolerance (RST_C), located on chromosomes 1, 3, 4, 5, 6, and 7. One SNP (SL4.0CH05_60973295) was also associated with LIS. Candidate genes near these loci included Solyc05g051265 (encoding an alpha/beta-hydrolase superfamily protein and calmodulin-binding heat shock protein) on Chr 5, Solyc06g005680 (a homeodomain-like superfamily protein) on Chr 6, and Solyc06g005690 (a tetratricopeptide repeat [TPR]-like superfamily protein) on Chr 6. Genomic prediction models using GWAS-derived SNPs achieved prediction accuracies (r-values) up to 0.38 for salt tolerance in cross-population analyses. These findings provide insights into the genetic architecture of salt tolerance and valuable tools for molecular breeding of salt-tolerant tomato cultivars.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-30759-y.

Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut.

Identification and recombinant expression of a novel defluorinase from Rhodococcus jostii RHA1, for defluorination and biotransformation of the PFAS compound 6:2 fluorotelomer carboxylic acid.