Stress-responsive Genes Research Articles

Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus.

Enterococci are opportunistic pathogens notorious for causing a variety of infections. While both Enterococcus faecalis and Lactobacillus crispatus are commensal residents of the vaginal tract, the molecular mechanisms that enable E. faecalis to take advantage of a vaginal biome with lower counts of lactobacilli to colonize the vaginal tract and induce aerobic vaginitis remain unknown. Here, we show that L. crispatus eradicates E. faecalis in a contact-independent manner. Using transposon sequencing to identify E. faecalis OG1RF transposon (Tn) mutants that are either under-represented or over-represented when co-cultured with L. crispatus, we found that Tn mutants with disruption in the dltABCD operon, that encodes the proteins responsible for the D-alanylation of teichoic acids, and OG1RF_11697 encoding for an uncharacterized hypothetical protein are more susceptible to killing by L. crispatus. Inversely, Tn mutants with disruption in ldh1, which encodes for L-lactate dehydrogenase, are more resistant to L. crispatus killing. Using the Galleria mellonella infection model, we show that co-injection of L. crispatus with E. faecalis OG1RF enhances larvae survival while this L. crispatus-mediated protection was lost in larvae co-infected with either L. crispatus and E. faecalisΔldh1 or Δldh1Δldh2 strains. Last, using RNA sequencing to identify E. faecalis genes that are differently expressed in the presence of L. crispatus, we found major changes in the expression of genes associated with glycerophospholipid metabolism, central metabolism, and general stress responses. The findings in this study provide insights into how E. faecalis mitigate assaults by L. crispatus.IMPORTANCEEnterococcus faecalis is an opportunistic pathogen notorious for causing a multitude of infections. As vaginal commensals, E. faecalis must interact with Lactobacillus crispatus, but how E. faecalis overcomes or mitigate assaults by L. crispatus killing remains unknown. We show that L. crispatus eradicates E. faecalis temporally in a contact-independent manner. Using high-throughput molecular approaches, we identified genetic determinants that enable E. faecalis to compete with L. crispatus. This study represents an important first step for the identification of adaptive genetic traits required for enterococci to tolerate assaults by lactobacilli.

A Maize Calmodulin-like 3 Gene Positively Regulates Drought Tolerance in Maize and Arabidopsis

Drought stress is one of the important abiotic stresses that affects maize production. As an important Ca2+ sensor, calmodulin-like proteins (CMLs) play key roles in plant growth, development, and stress response, but there are a limited number of studies regarding CMLs in response to drought stress. In this study, a Calmodulin-like gene, namely ZmCML3, was isolated from maize (Zea mays L.). The coding sequence (CDS) of ZmCML3 was 474 bp and a protein of 158 aa which contains three EF-hand motifs. ZmCML3 was localized within the nucleus and plasma membrane. The expression of ZmCML3 was induced by polyethylene glycol (PEG) 6000, NaCl, methyl jasmonate (MeJA), and abscisic acid (ABA). Overexpression of ZmCML3 resulted in enhanced drought tolerance in maize through increasing proline (Pro) content and the activity of peroxide (POD) and superoxide dismutase (SOD). Meanwhile, ZmCML3 also positively regulated the expression of drought stress-responsive genes in maize under drought stress treatment. Taken together, ZmCML3 acts as a positive regulator in maize response to drought stress. These results will provide theoretical basis for breeding drought tolerance maize variety.

Transcriptomic and Phenotypic Responses of CucumberTrichome Density to Silver Nitrate and Sodium Thiosulfate Application

Cucumber (Cucumis sativus L.) is one of the most widely cultivated crops worldwide and is valued for its nutritional, economic, and ecological benefits. The regulation of defense mechanisms against herbivores, along with osmotic loss and environmental regulation, is greatly affected by trichomes in cucumbers. In this study, we attempted to characterize trichomes and examined fruit physiological and transcriptome profiles by RNA sequencing in cucumber breeding lines 6101-4 and 5634-1 at three stages of fruit development through foliar application with a combination of silver nitrate (AgNO3) and sodium thiosulfate (Na2S2O3) in comparison to non-treated controls. Notable increases in the number of trichomes and altered forms were observed for both inbred cultivars 6101-4 and 5634-1 against foliar application of chemical substances. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) involved in multiple pathways in cucumber trichome formation. The enrichment of differentially expressed transcripts showed that foliar application upregulated the expression of many stress-responsive and trichome-associated genes including plant hormone signal transduction, sesquiterpenoid and triterpenoid biosynthesis, and the mitogen-activated protein kinase (MAPK) signaling pathway. The dominant regulatory genes, such as allene oxide synthase (AOS) and MYB1R1 transcription factor, exhibited significant modulations in their expression in response to chemical application. The RNA-seq results were further confirmed by RT-PCR-based analysis, which revealed that after chemical application, the dominant regulatory genes, such as allene oxide synthase (AOS), PTB 19, MYB1R1, bHLH62-like, MADS-box transcription factor, and salicylic acid-binding protein 2-like, were differentially expressed, implying that these DEGs involved in multiple pathways are involved the positive regulation of the initiation and development of trichomes in C. sativus. A comparison of trichome biology and associated gene expression regulation in other plant species has shown that silver nitrate (AgNO3) and sodium thiosulfate (Na2S2O3) are also responsible for hormonal and signaling pathway regulation. This study improves our knowledge of the molecular mechanisms involved in C. sativus trichome development. It also emphasizes the possibility of utilizing chemical composition to modulate C. sativus trichome-related characteristics of C. sativus, leading to the improvement of plant defense mechanisms as well as environmental adaptation.

Dysregulated activation of Hippo-YAP1 signaling induces oxidative stress and aberrant development of intrahepatic biliary cells in biliary atresia

The canonical Hippo-YAP1 signaling pathway is crucial for liver development and regeneration but its role in repair and regeneration of intrahepatic bile duct in biliary atresia (BA) remains largely unknown. YAP1 expression in the liver tissues of patients with BA and rhesus rotavirus (RRV) induced experimental BA mouse model were examined using quantitative reverse transcriptase-PCR (qRT-PCR) and double immunofluorescence. Mouse EpCAM-expressing cells derived liver organoids were generated and treated with Hippo-YAP1 pathway activators (Xmu-mp-1 and TRULI) or an inhibitor (Peptide17). Morphological, immunofluorescence, RNA-seq, and bioinformatic analyses were performed. Oxidative stress in human intrahepatic biliary epithelial cells (HiBECs) transfected with a constitutively active YAP1 (YAPS127A) plasmid was assessed using qRT-PCR and fluorescence-activated cell sorting analysis. PRDX1 expression in BA and experimental BA mouse model livers was examined by double immunofluorescence. The mRNA expression and nuclear localization of YAP1 in EpCAM-expressing bile duct cells were increased in the livers of BA and experimental BA mouse model. Aberrant development of intrahepatic organoids, differential expression of oxidative stress response genes Sod3 and Prdx1, enrichment of oxidative stress, and mitochondrial reactive oxidative stress (mito-ROS)-associated gene sets were observed in organoids treated with Hippo-YAP1 activators, whereas organoid development was unaffected by the addition of the Hippo-YAP1 inhibitor. Transfection with constitutively active YAP1 led to the downregulation of PRDX1 and oxidative stress in HiBECs. Additionally, reduced PRDX1 expression was also observed in the bile duct of human BA and experimental BA mouse livers. In conclusion, dysregulated activation of Hippo-YAP1 signaling induces oxidative stress and impairs the development of intrahepatic biliary organoids, which indicates therapeutic strategies targeting Hippo-YAP1 signaling may offer potential to improve biliary repair and regeneration in patients with BA.

WRKY45 positively regulates salinity and osmotic stress responses in Arabidopsis.

Salt damage is a major issue that causes a decline in crop yield. WRKY transcription factors (TFs) extensively regulate plant biotic and abiotic stress responses, growth, and development. WRKY45 is crucial in regulating leaf senescence, low phosphorus responses, and cadmium stress response in Arabidopsis. However, the involvement of WRKY45 in salinity and osmotic stress responses is unclear. Here, we report that WRKY45 plays a vital role in responding to salinity and osmotic stress. NaCl and sorbitol treatments upregulate WRKY45 expression. Furthermore, the overexpression of WRKY45 (WRKY45-OXs) may enhance the tolerance of Arabidopsis to salinity and osmotic stress. Moreover, the root length, fresh weight, chlorophyll, and proline content were significantly higher in WRKY45-OXs than in the wide type (WT) Col-0 plants after salt or PEG treatment, whereas malondialdehyde and reactive oxygen species (ROS) levels were significantly lower than in the WT plants. Correspondingly, the overexpression of WRKY45 modulated the expression of stress-responsive genes. Dual luciferase assay and electrophoretic mobility shift assay further confirmed that WRKY45 can activate the promoter of RD29A by directly binding to specific W-box cis-acting elements. Overall, our experimental evidence suggesting that WRKY45 mainly acts as a key regulator coordinating the response to high salinity and osmotic stress through mechanisms dependent on ABA signaling along with enhanced antioxidant capacity.

Decrypting proteomics, transcriptomics, genomics, and integrated omics for augmenting the abiotic, biotic, and climate change stress resilience in plants.

As our planet faces increasing environmental challenges, such as biotic pressures, abiotic stressors, and climate change, it is crucial to understand the complex mechanisms that underlie stress responses in crop plants. Over past few years, the integration of techniques of proteomics, transcriptomics, and genomics like LC-MS, IT-MS, MALDI-MS, DIGE, ESTs, SAGE, WGS, GWAS, GBS, 2D-PAGE, CRISPR-Cas, cDNA-AFLP, HLS, HRPF, MPSS, CAGE, MAS, IEF, MudPIT, SRM/MRM, SWATH-MS, ESI have significantly enhanced our ability to comprehend the molecular pathways and regulatory networks, involved in balancing the ecosystem/ecology stress adaptation. This review offers thorough synopsis of the current research on utilizing these multi-omics methods (including metabolomics, ionomics) for battling abiotic (salinity, temperature (chilling/freezing/cold/heat), flood (hypoxia), drought, heavy metals/loids), biotic (pathogens like fungi, bacteria, virus, pests, and insects (aphids, caterpillars, moths, mites, nematodes) and climate change stress (ozone, ultraviolet radiation, green house gases, carbon dioxide). These strategies can expedite crop improvement, and act as powerful tools with high throughput and instant database generation rates. They also provide a platform for interpreting intricate, systematic signalling pathways and knowing how different environmental stimuli cause phenotypic responses at cellular and molecular level by changing the expression of stress-responsive genes like RAB18, KIN1, RD29B, OsCIPK03, OsSTL, SIAGL, bZIP, SnRK, ABF. This review discusses various case studies that exemplify the successful implementation of these omics tools to enhance stress tolerance in plants. Finally, it highlights challenges and future prospects of utilizing these approaches in combating stress, emphasizing the need for interdisciplinary collaborations and bio-technological advancements for sustainable agriculture and food security.

Comprehensive transcriptomic analysis reveals turnip mosaic virus infection and its aphid vector Myzus persicae cause large changes in gene regulatory networks and co-transcription of alternative spliced mRNAs in Arabidopsis thaliana.

Virus infection and herbivory can alter the expression of stress-responsive genes in plants. This study employed high-throughput transcriptomic and alternative splicing analysis to understand the separate and combined impacts on host gene expression in Arabidopsis thaliana by Myzus persicae (green peach aphid), and turnip mosaic virus (TuMV). By investigating changes in transcript abundance, the data shows that aphids feeding on virus infected plants intensify the number of differentially expressed stress responsive genes compared to challenge by individual stressors. This study presents evidence that the combination of virus-vector-host interactions induces significant changes in hormone and secondary metabolite biosynthesis, as well as downstream factors involved in feedback loops within hormone signaling pathways. This study also shows that gene expressions are regulated through alternative pre-mRNA splicing and the use of alternative transcription start and termination sites. These combined data suggest that complex genetic changes occur as plants adapt to the combined challenges posed by aphids and the viruses they vector. This study also provides more advanced analyses that could be used in the future to dissect the genetic mechanisms mediating tripartite interactions and inform future breeding programs.

Alterations in Protein Phosphorylation and Arginine Biosynthesis Metabolism Confer β-Phenylethanol Tolerance in Saccharomyces cerevisiae.

The aromatic compound β-phenylethanol (2-PE) is inherently toxic and can inhibit cell activity in Saccharomyces cerevisiae, making it highly challenging to enhance strain tolerance through rational design due to the lack of reliable connections between tolerance phenotype and genetic loci. This study employed adaptive laboratory evolution strategy to investigate the tolerance characteristics of S. cerevisiae S288C under inhibitory concentrations of 2-PE. The tolerant mutant SEC4.0 was characterized through comprehensive analysis of whole genome sequence, transcriptome, and phosphoproteome. The findings revealed that the high resistance of SEC4.0 was not primarily due to large-scale transcriptional upregulation of stress response genes, but rather through alterations in the phosphorylation levels of lipid-related pathways. PKC1 mutations that affect stress signal transduction and SPT3 mutations that affect arginine biosynthesis have been shown to significantly enhance 2-PE resistance. This study also investigated the effects of exogenous amino acid addition and synergistic effects with two key mutanted genes on 2-PE resistance. This study provides a foundation for enhancing yeast tolerance to this aromatic compound through rational design strategies.

Current insights into molecular mechanisms of environmental stress tolerance in Cyanobacteria.

The photoautotrophic nature of cyanobacteria, coupled with their fast growth and relative ease of genetic manipulation, makes these microorganisms very promising factories for the sustainable production of bio-products from atmospheric carbon dioxide. However, both in nature and in cultivation, cyanobacteria go through different abiotic stresses such as high light (HL) stress, heavy metal stress, nutrient limitation, heat stress, salt stress, oxidative stress, and alcohol stress. In recent years, significant improvement has been made in identifying the stress-responsive genes and the linked pathways in cyanobacteria and developing genome editing tools for their manipulation. Metabolic pathways play an important role in stress tolerance; their modification is also a very promising approach to adapting to stress conditions. Several synthetic as well as systems biology approaches have been developed to identify and manipulate genes regulating cellular responses under different stresses. In this review, we summarize the impact of different stresses on metabolic processes, the small RNAs, genes and heat shock proteins (HSPs) involved, changes in the metabolome and their adaptive mechanisms. The developing knowledge of the adaptive behaviour of cyanobacteria may also be utilised to develop better stress-responsive strains for various applications.

The transcriptional and translational landscape of HCoV-OC43 infection.

The coronavirus HCoV-OC43 circulates continuously in the human population and is a frequent cause of the common cold. Here, we generated a high-resolution atlas of the transcriptional and translational landscape of OC43 during a time course following infection of human lung fibroblasts. Using ribosome profiling, we quantified the relative expression of the canonical open reading frames (ORFs) and identified previously unannotated ORFs. These included several potential short upstream ORFs and a putative ORF nested inside the M gene. In parallel, we analyzed the cellular response to infection. Endoplasmic reticulum (ER) stress response genes were transcriptionally and translationally induced beginning 12 and 18 hours post infection, respectively. By contrast, conventional antiviral genes mostly remained quiescent. At the same time points, we observed accumulation and increased translation of noncoding transcripts normally targeted by nonsense mediated decay (NMD), suggesting NMD is suppressed during the course of infection. This work provides resources for deeper understanding of OC43 gene expression and the cellular responses during infection.

Typical tetra-mediated signaling and plant architectural changes regulate salt-stress tolerance in indica rice genotypes.

Upon exposure to salt stress, calcium signaling in plants activates various stress-responsive genes and proteins along with enhancement in antioxidant defense to eventually regulate the cellular homeostasis for reducing cytosolic sodium levels. The coordination among the calcium signaling molecules and transporters plays a crucial role in salinity tolerance. In the present study, twenty-one diverse indigenous rice genotypes were evaluated for salt tolerance during the early seedling stage, and out of that nine genotypes were further selected for physio-biochemical study. Further analysis identified potential salt-tolerant and salt-sensitive genotypes with tolerant lines exhibiting lower Na+/K+ ratio. Plant phenotype clearly documented the root architectural changes among the most salt-tolerant and sensitive genotypes, while the histo-biochemical DAB and NBT staining and in-gel SOD activity clearly revealed the differential ROS accumulation between the contrasting genotypes and their antioxidant activity. Ultrastructural study depicted stronger UV autofluorescence in the hypodermal and vascular bundle regions, while phloroglucinol staining displayed intense coloration in the vascular bundle region of Bhutmuri, the salt-tolerant genotype, compared to Manipuri Black, the salt-sensitive one showing differential lignification among the contrasting genotype to combat salt stress. Based on expression study, our proposed model depicted immediate upregulation (short-term) of OsSOS3 and OsNHX1 along with gradual upregulation of OsHKT and downregulation of OsSOS1 throughout the stress period to protect the tolerant plant through signaling cascade, while the inadequate upregulation of OsSOS3, OsNHX1, and OsHKT under early stress, coupled with poor coordination between the expression of OsSOS1 and OsSOS3 genes, makes the plant salt sensitive.

Melatonin improves the lead tolerance in Plantago ovata by modulating ROS homeostasis, phytohormone status and expression of stress-responsive genes.

Melatonin increases Pb tolerance in P. ovata seedlings via the regulation of growth and stress-related phytohormones, ROS scavenging and genes responsible for melatonin synthesis, metal chelation, and stress defense. Lead (Pb) is a highly toxic heavy metal that accumulates in plants through soil and air contamination and impairs its plant growth and development. Because of its pharmaceutical importance, improvements in Plantago ovata yield against abiotic stresses are necessary. Melatonin (MEL) is a stress-alleviating biostimulator and our results showed a reduction in Pb induced phytotoxicity by enhancing plant growth attributes and balancing protective osmolytes. Pb-induced reactive oxygen species accumulation, including superoxide and peroxide free radicals and their mitigation through enzymatic antioxidants, was demonstrated in presence of MEL. Cell viability and Pb bioaccumulation were determined to understand the extent of cellular damage. Moreover, MEL increased secondary metabolite (flavonoids and anthocyanins) contents by 2-3-fold at the lowest Pb concentrations. Similar increases in the relative expression of genes (PoPAL and PoPPO), which are responsible for the production of non-enzymatic antioxidants, were observed. Notably, the upregulation of the PoCOMT gene up to 4-fold indicates increased melatonin production, as manifested in the phytomelatonin level. MEL supplementation also increased the auxin (IAA) level by 3-fold in the 100µM Pb treatment group, while the abscisic acid (ABA) level decreased (1.4-fold) and the expression of PoMYB (a stress-related transcription factor) increased (up to 2.66-fold). Additionally, we found extreme downregulation (up to 18-fold) in the relative expression of PoMT 2 (a metal binding thiol compound) with melatonin treatment, which is otherwise upregulated (by 6-fold) during Pb stress. In the current study, these effects collectively revealed that MEL contribute to enhanced plant growth and Pb stress tolerance.

Potential roles of mitochondrial carrier proteins in plant responses to abiotic stress.

The transport of metabolites across the inner mitochondrial membrane (IMM) is crucial for maintaining energy balance and efficient distribution of metabolic intermediates between cellular compartments. Under abiotic stress, mitochondrial function becomes particularly critical, activating complex signaling pathways essential for plant stress responses. These pathways modulate stress-responsive gene expression, influencing key physiological processes such as cell respiration and senescence, helping plants adapt to stress. Recent studies have emphasized the importance of finely tuned regulation of mitochondrial metabolite transport through the IMM, particularly under stress conditions, to optimize plant survival and resilience. This review summarizes the current knowledge on the possible roles of mitochondrial transport proteins and their contributions to plant adaptation under abiotic stress.

Calcium-binding protein CALU-1 is essential for proper collagen formation in Caenorhabditis elegans

Collagen, a major component of the extracellular matrix, is crucial for the structural integrity of the Caenorhabditis elegans cuticle. While several proteins involved in collagen biosynthesis have been identified, the complete regulatory network remains unclear. This study investigates the role of CALU-1, an ER-resident calcium-binding protein, in cuticle collagen formation and maintenance. We employed genetic analyses, including the generation of single and double mutants, scanning electron microscopy, and transcriptome profiling to characterize CALU-1 function. Our results demonstrate that CALU-1 is essential for proper cuticle structure, including annuli, furrows, and alae formation. Synthetic lethality was observed between calu-1 and dpy-18 (encoding a prolyl 4-hydroxylase subunit) mutations, while double mutants of calu-1 with peptidyl-prolyl cis–trans isomerase (PPIase) genes exhibited exacerbated phenotypes. CALU-1 deficiency led to altered collagen stability, increased cuticle permeability, and differential expression of stress response genes similar to collagen mutants. We conclude that CALU-1 plays a critical role in regulating collagen biosynthesis, possibly by modulating the ER environment to optimize the function of collagen-modifying enzymes. These findings provide new insights into the complex regulation of extracellular matrix formation in C. elegans, with potential implications for understanding related processes in other organisms.

Gene expression and epigenetic changes in post-traumatic stress disorder, depression, and anxiety in first responders: A systematic review.

Police, firefighters, dispatchers, and emergency medical technicians-collectively known as first responders-are a unique population frequently exposed to chronic, traumatic incidents. This exposure results in a high prevalence of PTSD, depression, and anxiety, posing a substantial public health concern. Genetic predispositions and epigenetic modifications that regulate gene expression are significant contributors to trauma-related pathologies. This systematic review aims to summarize current data on epigenetic and gene expression changes in first responders related to three post-trauma pathologies: PTSD, depression, and anxiety. We also explore genetic pathways across these disorders to identify potential commonalities and therapeutic targets. Following PRISMA guidelines, databases were searched from July to October 2023, yielding 1103 studies, 12 of which met the inclusion criteria (total N=6943). Of the included studies, 11 examined PTSD, consistently implicating stress-response genes, such as those in the hypothalamic-pituitary-adrenal axis (e.g., FKBP5, NR3C1), and genes related to inflammation and immune responses. Three studies focused on depression-related genetic biomarkers but reported no significant genome-wide methylation differences between responders with current versus no major depressive disorder (MDD). No studies addressed epigenetic or gene expression changes linked to anxiety. This review identified novel genes and pathways related to trauma as potential targets for future research and pharmacological therapy. It also highlights a significant gap in the literature, emphasizing the need for broader research to investigate the genetic underpinnings of trauma exposure in first responders, aiming to identify relevant pathways and therapeutic targets.

A General Mechanism for Initiating the General Stress Response in Bacteria.

The General Stress Response promotes survival of bacteria in adverse conditions, but how sensor proteins transduce species-specific signals to initiate the response is not known. The serine/threonine phosphatase RsbU initiates the General Stress Response in B. subtilis upon binding a partner protein (RsbT) that is released from sequestration by environmental stresses. We report that RsbT activates RsbU by inducing otherwise flexible linkers of RsbU to form a short coiled-coil that dimerizes and activates the phosphatase domains. Importantly, we present evidence that related coiled-coil linkers and phosphatase dimers transduce signals from diverse sensor domains to control the General Stress Response and other signaling across bacterial phyla. This coiled-coil linker transduction mechanism additionally suggests a resolution to the mystery of how shared sensory domains control serine/threonine phosphatases, diguanylate cyclases and histidine kinases. We propose that this provides bacteria with a modularly exchangeable toolkit for the evolution of diverse signaling pathways.

De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability

Bumblebees are ubiquitous, cold-adapted, primitively eusocial bees and important pollinators for crops and vegetation. However, many species are declining worldwide due to multiple factors, including human-induced habitat loss, agricultural chemicals, global warming, and climate change. In particular, future climate scenarios predict a shift in the spatial distribution of bumblebees under global warming, with some species declining and others potentially expanding. Here, we report a de novo genome assembly and annotation for Bombus lapidarius and Bombus niveatus to decipher species-specific potential genomic capacity against such environmental stressors. With harboring more than 23,000 protein-coding genes, the assembled genomes of B. lapidarius and B. niveatus are 244.44 Mb (scaffold N50 of 9.45 Mb) and 259.84 Mb (scaffold N50 of 10.94 Mb), respectively, which exhibit similar trends in terms of genome size and composition with other bumblebees. Gene family analysis reveals differences in species-specific expanded gene families. B. lapidarius exhibits expanded genes related to pre/postsynaptic organization, while B. niveatus shows a distinct expansion in gene families regulating cellular growth, aging, and responses to abiotic and biotic stressors, such as those containing SCAN domains, WD-repeats, and Ras-related proteins. Our genome-wide screens revealed positive selection on environmental stress-responsive genes such as dip2, yme1l, and spg7 in B. lapidarius, whereas positive selection signatures were found in genes such as myd88, mybbp1A, and rhau, which are involved in environmental stress resistance for B. niveatus. These high-quality genome assemblies and comparative genome analysis unveil potential drivers that underlie genome evolution in bumblebees, offering valuable insights into environmental adaptation and conservation efforts.

Genome-Wide Analysis of bZIP Transcription Factors and Expression Patterns in Response to Salt and Drought Stress in Vaccinium corymbosum.

The basic leucine zipper (bZIP) transcription factors play essential roles in multiple stress responses and have been identified and functionally characterized in many plant species. However, the bZIP family members in blueberry are unclear. In this study, we identified 102 VcbZIP genes in Vaccinium corymbosum. VcbZIPs were divided into 10 groups based on phylogenetic analysis, and each group shared similar motifs, domains, and gene structures. Predictions of cis-regulatory elements in the upstream sequences of VcbZIP genes indicated that VcbZIP proteins are likely involved in phytohormone signaling pathways and abiotic stress responses. Analyses of RNA deep sequencing data showed that 18, 13, and 7 VcbZIP genes were differentially expressed in response to salt, drought, and ABA stress, respectively, for the blueberry cultivar Northland. Ten VcbZIP genes responded to both salt and drought stress, indicating that salt and drought have unique and overlapping signals. Of these genes, VcbZIP1-3 are responsive to salt, drought, and abscisic acid treatments, and their encoded proteins may integrate salt, drought, and ABA signaling. Furthermore, VcbZIP1-3 from group A and VcbZIP83-84 and VcbZIP75 from group S exhibited high or low expression under salt or drought stress and might be important regulators for improving drought or salt tolerance. Pearson correlation analyses revealed that VcbZIP transcription factors may regulate stress-responsive genes to improve drought or salt tolerance in a functionally redundant manner. Our study provides a useful reference for functional analyses of VcbZIP genes and for improving salt and drought stress tolerance in blueberry.

Adaptive evolution of stress response genes in parasites aligns with host niche diversity

BackgroundStress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness. We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses.ResultsWe assembled the sequences of 48 stress-related genes and report the first foraging (For) gene orthologs in flatworms. We found duplications of heat shock (Hsp) and oxidative stress genes in Cichlidogyrus compared to Kapentagyrus. We also observed positive selection patterns in genes related to mitochondrial protein import (Hsp) and behaviour (For) in species of Cichlidogyrus infecting East African cichlids—a host lineage under adaptive radiation. These patterns are consistent with a potential adaptation linked to a co-radiation of these parasites and their hosts. Additionally, the absence of cytochrome P450 and kappa and sigma-class glutathione S-transferases in monogenean flatworms is reported, genes considered essential for metazoan life.ConclusionsThis study potentially identifies the first molecular function linked to a flatworm radiation. Furthermore, the observed gene duplications and positive selection indicate the potentially important role of stress responses for the ecological adaptation of parasite species.

Enhancing Soybean Salt Tolerance with GSNO and Silicon: A Comprehensive Physiological, Biochemical, and Genetic Study.

Soil salinity is a major global challenge affecting agricultural productivity and food security. This study explores innovative strategies to improve salt tolerance in soybean (Glycine max), a crucial crop in the global food supply. This study investigates the synergistic effects of S-nitroso glutathione (GSNO) and silicon on enhancing salt tolerance in soybean (Glycine max). Two soybean cultivars, Seonpung (salt-tolerant) and Cheongja (salt-sensitive), were analyzed for various physiological, biochemical, and genetic traits under salt stress. The results showed that the combined GSNO and Si treatment significantly improved several key traits, including plant height, relative water content, root development, nodule numbers, chlorophyll content, and stomatal aperture, under both control and salt stress conditions. Additionally, this treatment optimized ion homeostasis by enhancing the Na/K ratio and Ca content, while reducing damage markers such as electrolyte leakage, malondialdehyde, and hydrogen peroxide. The stress-responsive compounds, including proline, ascorbate peroxidase, and water-soluble proteins, were elevated under stress conditions, indicating improved tolerance. Gene expression analysis revealed significant upregulation of genes such as GmNHX1, GmSOS2, and GmAKT1, associated with salt stress response, while GmNIP2.1, GmNIP2.2, and GmLBR were downregulated in both varieties. Notably, the salt-sensitive variety Cheongja exhibited higher electrolyte leakage and oxidative damage compared to the salt-tolerant Seonpung. These findings suggest that the combination of GSNO and silicon enhances salt tolerance in soybean by improving physiological resilience, ion homeostasis, and stress-responsive gene expression.