Stress-responsive Transcription Factor Research Articles

Chromosome-scale genome assembly of Apocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin.

Apocynum pictum Schrenk is a semishrub of the Apocynaceae family with a wide distribution throughout the Tarim Basin that holds significant ecological, medicinal, and economic values. Here, we report the assembly of its chromosome-level reference genome using Nanopore long-read, Illumina HiSeq paired-end, and high-throughput chromosome conformation capture sequencing. The final assembly is 225.32 Mb in length with a scaffold N50 of 19.64 Mb. It contains 23,147 protein-coding genes across 11 chromosomes, 21,148 of which (91.36%) have protein functional annotations. Comparative genomics analysis revealed that A. pictum diverged from the closely related species Apocynum venetum approximately 2.2 million years ago and has not undergone additional polyploidizations after the core eudicot WGT-γ event. Karyotype evolution analysis was used to characterize interchromosomal rearrangements in representative Apocynaceae species and revealed that several A. pictum chromosomes were derived entirely from single chromosomes of the ancestral eudicot karyotype. Finally, we identified 50 members of the well-known stress-responsive WRKY transcription factor family and used transcriptomic data to document changes in their expression at 2 stages of drought stress, identifying a number of promising candidate genes. Overall, this study provides high-quality genomic resources for evolutionary and comparative genomics of the Apocynaceae, as well as initial molecular insights into the drought adaptation of this valuable desert plant.

Elevated proline and melatonin alter the methylation pattern in the promoter of their biosynthesis genes in rice

Salt stress upregulates osmoprotectants proline and melatonin in plants, and their exogenous application under salt stress can protect them from stress. While melatonin-induced plant epigenetic reprogramming is known in plants, such a mechanism is yet to be identified in the case of proline. The studies conducted so far used proline and melatonin along with one or more stress factors to look into their stress-alleviating effects. We investigated the impact of externally applied proline and melatonin on the methylation of promoter sequences of proline and melatonin biosynthesis genes in 14-day-old rice plants using a combination of biochemical, bioinformatics, and molecular techniques. Our findings demonstrate that exogenously applied proline and melatonin elevate endogenous levels of these compounds in rice, mimicking stress conditions in plants, as the biochemical assays corroborated the activation of antioxidant systems, particularly ascorbate peroxidase (APX) and catalase (CAT). Bioinformatics analysis unveiled multiple stress-responsive transcription factor binding sites on gene promoters associated with proline and melatonin biosynthesis pathways. Restriction analysis using the isoschizomer pair MspI/HpaII revealed distinct cytosine methylations at the restriction sites on the promoters analyzed in plants treated with proline and melatonin compared to the control. Differential methylation identified in the promoter sequences were matching with the biosynthesis of proline and melatonin and also the antioxidant enzyme levels. These observations are consistent with previous transcriptome data of proline and melatonin biosynthesis genes, providing insights into underlying regulatory mechanisms of proline and melatonin biosynthesis, their role in epigenome control during abiotic stress, and the evolution of various stress-tolerant varieties.

Transcription factor SlSTOP1 regulates Small Auxin-Up RNA Genes for tomato root elongation under aluminum stress.

Aluminum (Al) stress, a prevalent constraint in acidic soils, inhibits plant growth by inhibiting root elongation through restricted cell expansion. The molecular mechanisms of Al-induced root inhibition, however, are not fully understood. This study aimed to elucidate the role of Small Auxin-up RNAs (SlSAURs), which function downstream of the key Al stress-responsive transcription factor SENSITIVE TO PROTON RHIZOTOXICITY 1 (SlSTOP1) and its enhancer STOP1-INTERACTING ZINC-FINGER PROTEIN 1 (SlSZP1), in modulating root elongation under Al stress in tomato (Solanum lycopersicum). Our findings demonstrated that tomato lines with knocked out SlSAURs exhibited shorter root lengths when subjected to Al stress. Further investigation into the underlying mechanisms revealed that SlSAURs interact with Type 2C Protein Phosphatases (SlPP2Cs), specifically D-clade Type 2C Protein Phosphatases (SlPP2C.Ds). This interaction was pivotal as it suppresses the phosphatase activity, leading to the degradation of SlPP2C.D's inhibitory effect on plasma membrane H+-ATPase. Consequently, this promoted cell expansion and root elongation under Al stress. These findings increase our understanding of the molecular mechanisms by which Al ions modulate root elongation. The discovery of the SlSAUR-SlPP2C.D interaction and its impact on H+-ATPase activity also provides a perspective on the adaptive strategies employed by plants to cope with Al toxicity, which may lead to the development of tomato cultivars with enhanced Al stress tolerance, thereby improving crop productivity in acidic soils.

The transcriptional response of cortical neurons to concussion reveals divergent fates after injury.

Traumatic brain injury (TBI) is a risk factor for neurodegeneration, however little is known about how different neuron types respond to this kind of injury. In this study, we follow neuronal populations over several months after a single mild TBI (mTBI) to assess long ranging consequences of injury at the level of single, transcriptionally defined neuronal classes. We find that the stress responsive Activating Transcription Factor 3 (ATF3) defines a population of cortical neurons after mTBI. We show that neurons that activate ATF3 upregulate stress-related genes while repressing many genes, including commonly used markers for these cell types. Using an inducible reporter linked to ATF3, we genetically mark damaged cells to track them over time. Notably, we find that a population in layer V undergoes cell death acutely after injury, while another in layer II/III survives long term and retains the ability to fire action potentials. To investigate the mechanism controlling layer V neuron death, we genetically silenced candidate stress response pathways. We found that the axon injury responsive kinase MAP3K12, also known as dual leucine zipper kinase (DLK), is required for the layer V neuron death. This work provides a rationale for targeting the DLK signaling pathway as a therapeutic intervention for traumatic brain injury. Beyond this, our novel approach to track neurons after a mild, subclinical injury can inform our understanding of neuronal susceptibility to repeated impacts.

Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis.

Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.

Unraveling the Role of MYB Transcription Factors in Abiotic Stress Responses: An Integrative Approach in Eugenia uniflora L.

Unraveling the Role of MYB Transcription Factors in Abiotic Stress Responses: An Integrative Approach in Eugenia uniflora L.

Arabidopsis WRKY1 promotes monocarpic senescence by integrative regulation of flowering, leaf senescence, and nitrogen remobilization

Monocarpic senescence, characterized by whole-plant senescence following a single flowering phase, is widespread in seed plants, particularly in crops, determining seed harvest time and quality. However, how external and internal signals are systemically integrated into monocarpic senescence remains largely unknown. Here, we report that the Arabidopsis thaliana transcription factor WRKY1 plays essential roles in multiple key steps of monocarpic senescence. WRKY1 expression is induced by age, salicylic acid (SA), and nitrogen (N) deficiency. Flowering and leaf senescence are accelerated in the WRKY1 overexpression lines but are delayed in the wrky1 mutants. The combined DNA affinity purification sequencing and RNA sequencing analyses uncover the direct target genes of WRKY1. Further studies show that WRKY1 coordinately regulates three processes in monocarpic senescence: (1) suppressing FLOWERING LOCUS C gene expression to initiate flowering, (2) inducing SA biosynthesis genes to promote leaf senescence, and (3) activating the N assimilation and transport genes to trigger N remobilization. In summary, our study reveals how one stress-responsive transcription factor, WRKY1, integrates flowering, leaf senescence, and N remobilization processes into monocarpic senescence, providing important insights into plant lifetime regulation.

Co-exposure to microplastic and plastic additives causes development impairment in zebrafish embryos

Since the run off of microplastic and plastic additives into the aquatic environment through the disposal of plastic products, we investigated the adverse effects of co-exposure to microplastics and plastic additives on zebrafish embryonic development. To elucidate the combined effects between microplastic mixtures composed of microplastics and plastic additives in zebrafish embryonic development, polystyrene (PS), bisphenol S (BPS), and mono-(2-ethylhexyl) phthalate (MEHP) were chosen as a target contaminant. Based on non-toxic concentration of each contaminant in zebrafish embryos, microplastic mixtures which is consisted of binary and ternary mixed forms were prepared. A strong phenotypic toxicity to zebrafish embryos was observed in the mixtures composed with non-toxic concentration of each contaminant. In particular, the mixture combination with ≤ EC10 values for BPS and MEHP showed a with a strong synergistic effect. Based on phenotypic toxicity to zebrafish embryos, change of transcription levels for target genes related to cell damage and thyroid hormone synthesis were analyzed in the ternary mixtures with low concentrations that were observed non-toxicity. Compared with the control group, cell damage genes linked to the oxidative stress response and thyroid hormone transcription factors were remarkably down-regulated in the ternary mixture-exposed groups, whereas the transcriptional levels of cyp1a1 and p53 were significantly up-regulated in the ternary mixture-exposed groups (P < 0.05). These results demonstrate that even at low concentrations, exposure to microplastic mixtures can cause embryonic damage and developmental malformations in zebrafish, depending on the mixed concentration-combination. Consequently, our findings will provide data to examine the action mode of zebrafish developmental toxicity caused by microplastic mixtures exposure composed with microplastics and plastic additives.

ATF4 as a Prognostic Marker and Modulator of Glutamine Metabolism in Oestrogen Receptor-Positive Breast Cancer.

ATF4, a stress-responsive transcription factor that upregulates adaptive genes, is a potential prognostic marker and modulator of glutamine metabolism in breast cancer. However, its exact role remains to be elucidated. ATF4 expression was evaluated at genomic and transcriptomic levels using METABRIC (n = 1,980), GeneMiner (n = 4,712), and KM-Plotter datasets. Proteomic expression was assessed via immunohistochemistry (n = 2,225) in the Nottingham Primary Breast Cancer Series. ATF4 genomic copy number (CN) variation and mRNA/protein in association with clinicopathological parameters, amino acid transporters (AATs), and patient outcome were investigated. Genomic, transcriptomic, and proteomic overexpression of ATF4 was associated with more aggressive ER-negative tumours. ATF4 mRNA and protein expression were significantly associated with increased expression of glutamine related AATs including SLC1A5 (p &lt; 0.01) and SLC7A11 (p &lt; 0.02). High ATF4 and SLC1A5 protein expression was significantly associated with shorter breast cancer-specific survival (p &lt; 0.01), especially in ER+ tumours (p &lt; 0.01), while high ATF4 and SLC7A11 protein expression was associated with shorter survival (p &lt; 0.01). These findings suggest a complex interplay between ATF4 and AATs in breast cancer biology and underscore the potential role for ATF4 as a prognostic marker in ER+ breast cancer, offering a unique opportunity for risk stratification and personalized treatment strategies.

Regulation of stress-responsive transcription factors of rice by CPPU, a synthetic cytokinin, during water deficit stress at protein level

Regulation of stress-responsive transcription factors of rice by CPPU, a synthetic cytokinin, during water deficit stress at protein level

Unravelling the biostimulant activity of a protein hydrolysate in lettuce plants under optimal and low N availability: a multi-omics approach.

The application of protein hydrolysates (PH) biostimulants is considered a promising approach to promote crop growth and resilience against abiotic stresses. Nevertheless, PHs bioactivity depends on both the raw material used for their preparation and the molecular fraction applied. The present research aimed at investigating the molecular mechanisms triggered by applying a PH and its fractions on plants subjected to nitrogen limitations. To this objective, an integrated transcriptomic-metabolomic approach was used to assess lettuce plants grown under different nitrogen levels and treated with either the commercial PH Vegamin® or its molecular fractions PH1(>10 kDa), PH2 (1-10 kDa) and PH3 (<1 kDa). Regardless of nitrogen provision, biostimulant application enhanced lettuce biomass, likely through a hormone-like activity. This was confirmed by the modulation of genes involved in auxin and cytokinin synthesis, mirrored by an increase in the metabolic levels of these hormones. Consistently, PH and PH3 upregulated genes involved in cell wall growth and plasticity. Furthermore, the accumulation of specific metabolites suggested the activation of a multifaceted antioxidant machinery. Notwithstanding, the modulation of stress-response transcription factors and genes involved in detoxification processes was observed. The coordinated action of these molecular entities might underpin the increased resilience of lettuce plants against nitrogen-limiting conditions. In conclusion, integrating omics techniques allowed the elucidation of mechanistic aspects underlying PH bioactivity in crops. Most importantly, the comparison of PH with its fraction PH3 showed that, except for a few peculiarities, the effects induced were equivalent, suggesting that the highest bioactivity was ascribable to the lightest molecular fraction.

From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance.

Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na+) by plant roots, causing disruptions in cellular balance, nutrient deficiencies, and hampered growth. Specific ion transporters and channels play crucial roles in maintaining a low Na+/K+ ratio in root cells which is pivotal for salt tolerance. The family of high-affinity potassium transporters, recently characterized in Avicennia officinalis, contributes to K+ homeostasis in transgenic Arabidopsis plants even under high-salt conditions. The salt overly sensitive pathway and genes related to vacuolar-type H+-ATPases hold promise for expelling cytosolic Na+ and sequestering Na+ in transgenic plants, respectively. Aquaporins contribute to mangroves' adaptation to saline environments by regulating water uptake, transpiration, and osmotic balance. Antioxidant enzymes mitigate oxidative damage, whereas genes regulating osmolytes, such as glycine betaine and proline, provide osmoprotection. Mangroves exhibit increased expression of stress-responsive transcription factors such as MYB, NAC, and CBFs under high salinity. Moreover, genes involved in various metabolic pathways, including jasmonate synthesis, triterpenoid production, and protein stability under salt stress, have been identified. This review highlights the potential of mangrove genes to enhance salt tolerance of crops. Further research is imperative to fully comprehend and apply these genes to crop breeding to improve salinity resilience.

An integrated approach to predict activators of NRF2 - the transcription factor for oxidative stress response

A variety of environmental and physiological conditions can cause oxidative stress that damage cellular components such as DNA, proteins and lipids. Oxidative stress is implicated in many human diseases including cancer, cardiovascular diseases, neurological diseases, inflammatory diseases, and aging. The nuclear factor erythroid 2–related factor 2 (NRF2) is a transcriptional factor that plays a key role in the cellular antioxidant defense system as it regulates transcription of antioxidant proteins and detoxifying enzymes. There is an urgent need to identify novel compounds that activate NRF2 and enhance antioxidant defense. We collected data from the high-throughput screening of NRF2 activators and identified molecular fragments (structural alerts) associated with the activation of NRF2. We also developed ten classification models using different types of molecular descriptors and machine learning techniques. Two approaches were used to establish the applicability domain of developed models: the structure-based approach and the distance to model approach. The best performing model that used message passing neural network (MPNN) technique showed accuracy of 87 % for the test set of chemicals within the distance to model of 0.3. The integrative approach using a combination of generated structural alerts and MPNN model was used to screen approved drugs collected in the DrugBank to identify potential NRF2 activators. Out of 2393 screened chemicals 138 compounds were predicted as NRF2 activators by both approaches. Analysis of these compounds showed that some drugs were already known activators of NRF2 while others are potentially novel activators.

ARV1 deficiency induces lipid bilayer stress and enhances rDNA stability by activating the unfolded protein response in Saccharomyces cerevisiae

The stability of ribosomal DNA (rDNA) is maintained through transcriptional silencing by the NAD+-dependent histone deacetylase Sir2 in Saccharomyces cerevisiae. Alongside proteostasis, rDNA stability is a crucial factor regulating the replicative lifespan (RLS) of S. cerevisiae. The unfolded protein response (UPR) is induced by misfolding of proteins or an imbalance of membrane lipid composition and is responsible for degrading misfolded proteins and restoring endoplasmic reticulum (ER) membrane homeostasis. Recent investigations have suggested that the UPR can extend the RLS of yeast by enhancing protein quality control mechanisms, but the relationship between the UPR and rDNA stability remains unknown. In this study, we found that the deletion of ARV1, which encodes an ER protein of unknown molecular function, activates the UPR by inducing lipid bilayer stress. In arv1Δ cells, the UPR and the cell wall integrity pathway are activated independently of each other, and the high osmolarity glycerol (HOG) pathway is activated in a manner dependent on Ire1, which mediates the UPR. Activated Hog1 translocates the stress response transcription factor Msn2 to the nucleus, where it promotes the expression of nicotinamidase Pnc1, a well-known Sir2 activator. Following Sir2 activation, rDNA silencing and rDNA stability are promoted. Furthermore, the loss of other ER proteins, such as Pmt1 or Bst1, and ER stress induced by tunicamycin or inositol depletion also enhance rDNA stability in a Hog1-dependent manner. Collectively, these findings suggest that the induction of the UPR enhances rDNA stability in S. cerevisiae by promoting the Msn2-Pnc1-Sir2 pathway in a Hog1-dependent manner.

Abstract 610: ClpP-dependent and -independent activation of HRI kinase by small molecules

Abstract HRI was initially identified as a kinase essential for maintaining heme-globin balance within red blood cells as well as for controlling the ISR in response to oxidative stress. HRI also responds to a broad range of stresses such as osmotic stress, heat shock, proteasome inhibition. The recently discovered unexpected functions of HRI include innate immunity, translational control of immune evasion in cancer by upregulating PD-L1, proteostasis, mitochondrial stress, inhibition of histone H3 lysine 27 (H3K27) demethylase (KDM6A) and iron deficiency. Importantly, recent evaluation of patient data uncovered high expression of HRI mRNA in a subset of epithelial tumors versus normal tissues. Elevated expression of HRI protein in these tumor cells lead to cell death when BIRC6 ubiquitin complex is inhibited, which mediates degradation of HRI and is required for the survival of the tumors. These further broaden the importance of this member of the eIF2α kinase family as a cancer therapeutic strategy. Dordaviprone (ONC201), an imipridone small molecule, binds to and activates mitochondrial protease ClpP leading to integrated stress response (ISR) and ATF4 transcription factor activation. PG3, a prodigiosin analog, induces ATF4 and pro-apoptotic PUMA. Our data indicate that PG3 activates ATF4 through ISR via eIF2α kinase HRI. ALAS1 (5'-aminolevulinate synthase 1) catalyzes the first rate-limiting step in heme (Iron-protoporphyrin) biosynthesis. ONC201 treatment leads to potent downregulation and inhibition of ALAS1, indicating that ONC201 inhibits heme biosynthesis. It is well known that reduced heme results in activation of the HRI kinase. We show that an inhibitor of heme biosynthesis or knockdown of ALAS1 results in HRI activation, while silencing of HRI or knockout of HRI gene potently inhibit the eIF2α phosphorylation and upregulation of ATF4, CHOP and PUMA by PG3 and imipridones. Knockdown of ClpP rescues ONC201-induced downregulation of ALAS1 which blocks ONC201-induced upregulation of CHOP. Also, silencing of ClpP significantly reduced PARP cleavage in HCT116 p53−/- and MDA-MB-468 cancer cells. Our studies identify a novel link between ClpP activation induced by ONC201 treatment and ATF4 upregulation, via the ClpP/ALAS1/HRI/ATF4 pathway. However, PG3 treatment did not lead to degradation of ALAS1, indicating that PG3 does not activate ClpP. PG3 potently induced cell apoptosis through ISR via HRI/ATF4/PUMA pathway independent of ClpP. We are further investigating the targets of PG3 and the signaling pathway that leads to PG3-induced activation of HRI. Our results suggest that different small molecule inducers of the ISR such as ONC201 and PG3 can achieve an anti-tumor effect through different pathways converging on kinase HRI ultimately leading to ATF4 activation and tumor cell death. Citation Format: Xiaobing Tian, Praveen Srinivasan, Wafik S. El-Deiry. ClpP-dependent and -independent activation of HRI kinase by small molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 610.

Abstract 4295: Apoptotic DNase DFFB-induced DNA damage within cancer persister cells underlies acquired resistance to targeted therapies across multiple tumor types

Abstract Cancer acquired drug resistance contributes to a large proportion of patient deaths. A major obstacle to the development of effective therapies which prevent resistance is our lack of understanding of the relevant fundamental molecular adaptive processes. Here we report the discovery that tumor cells rely upon sublethal engagement of apoptotic death machinery and apoptotic DNase DFFB to acquire resistance to targeted therapies in multiple tumor types in cell culture and in vivo. We found that while DFFB wild type tumor cells readily acquire resistance to targeted therapies by escaping from the quiescent “persister” state into proliferating resistant cells, persister cells lacking functional DFFB remain indefinitely in a quiescent state on treatment. Mechanistically, we found that DFFB, which is activated by apoptotic caspases in surviving cancer persister cells, induces persistent DNA damage which promotes resistance through acquired mutations and nongenetic resistance through suppression of growth-arresting interferon signaling. During drug treatment acute interferon induction arises from sublethal mitochondrial outer membrane permeabilization and cytoplasmic exposure of mitochondrial nucleic acids which activate pattern recognition receptors. However, during longer treatments we found that DFFB knockout persister cells exhibit strikingly elevated levels of STAT1 and STAT2 and interferon stimulated gene sets. This interferon signaling is growth arresting because treatment of DFFB knockout persister cells with a JAK1/2 inhibitor rescues their ability to regrow. Furthermore, in DFFB wild type persister cells we found that DFFB-dependent DNA damage activates stress response transcription factor ATF3 which blocks the transcriptional activation of interferon stimulated genes following initial interferon induction. This is consistent with prior data in other contexts demonstrating that ATF3 is induced by DNA damage and that ATF3 directly binds to promoters of multiple interferon genes repressing their expression. These findings reveal that DFFB activation in persister cells prevents chronic interferon signaling and enables escape into proliferating drug resistant tumor cells. Therefore, DFFB-mediated interferon suppression represents a novel mechanism that is fundamental to acquired drug resistance. In addition, high expression of DFFB and ATF3 correlates with worse overall survival in a pan-cancer analysis and DFFB knockout mice develop normally indicating DFFB is a nonessential gene in normal tissue. Therefore, we propose that DFFB is a promising therapeutic target to prevent acquired resistance to targeted therapy. Citation Format: August Finley Williams, David A. Gervasio, Claire E. Turkal, Anna E. Stuhlfire, Michael X. Wang, Brandon E. Mauch, Ariel H. Nguyen, Michelle H. Paw, Mehrshad Hairani, Cooper P. Lathrop, Sophie H. Harris, Jennifer L. Page, Matthew J. Hangauer. Apoptotic DNase DFFB-induced DNA damage within cancer persister cells underlies acquired resistance to targeted therapies across multiple tumor types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4295.

DNA-Binding with One Finger (Dof) Transcription Factor Gene Family Study Reveals Differential Stress-Responsive Transcription Factors in Contrasting Drought Tolerance Potato Species.

DNA-binding with one finger (Dof) proteins comprise a large family that play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Although the Dof TF has been identified in a variety of species, its systemic analysis in potato (Solanum tuberosum L.) is lacking and its potential role in abiotic stress responses remains unclear. A total of 36 potential Dof genes in potato were examined at the genomic and transcriptomic levels in this work. Five phylogenetic groups can be formed from these 36 Dof proteins. An analysis of cis-acting elements revealed the potential roles of Dofs in potato development, including under numerous abiotic stress conditions. The cycling Dof factors (CDFs) might be the initial step in the abiotic stress response signaling cascade. In potato, five CDFs (StCDF1/StDof19, StCDF2/StDof4, StCDF3/StDof11, StCDF4/StDof24, and StCDF5/StDof15) were identified, which are homologs of Arabidopsis CDFs. The results revealed that these genes were engaged in a variety of abiotic reactions. Moreover, an expression analysis of StDof genes in two potato cultivars ('Long10' (drought tolerant) and 'DXY' (drought susceptible)) of contrasting tolerances under drought stress was carried out. Further, a regulatory network mediated by lncRNA and its target Dofs was established. The present study provides fundamental knowledge for further investigation of the roles of Dofs in the adaptation of potato to drought stress, aiming to provide insights into a viable strategy for crop improvement and stress-resistance breeding.

ASPTF: A computational tool to predict abiotic stress-responsive transcription factors in plants by employing machine learning algorithms

BackgroundAbiotic stresses pose serious threat to the growth and yield of crop plants. Several studies suggest that in plants, transcription factors (TFs) are important regulators of gene expression, especially when it comes to coping with abiotic stresses. Therefore, it is crucial to identify TFs associated with abiotic stress response for breeding of abiotic stress tolerant crop cultivars. MethodsBased on a machine learning framework, a computational model was envisaged to predict TFs associated with abiotic stress response in plants. To numerically encode TF sequences, four distinct sequence derived features were generated. The prediction was performed using ten shallow learning and four deep learning algorithms. For prediction using more pertinent and informative features, feature selection techniques were also employed. ResultsUsing the features chosen by the light-gradient boosting machine-variable importance measure (LGBM-VIM), the LGBM achieved the highest cross-validation performance metrics (accuracy: 86.81%, auROC: 92.98%, and auPRC: 94.03%). Further evaluation of the proposed model (LGBM prediction method + LGBM-VIM selected features) was also done using an independent test dataset, where the accuracy, auROC and auPRC were observed 81.98%, 90.65% and 91.30%, respectively. ConclusionsTo facilitate the adoption of the proposed strategy by users, the approach was implemented as a prediction server called ASPTF, accessible at https://iasri-sg.icar.gov.in/asptf/. The developed approach and the corresponding web application are anticipated to supplement experimental methods in the identification of transcription factors (TFs) responsive to abiotic stress in plants.

Convergent and divergent signaling pathways in C3 rice and C4 foxtail millet crops in response to salt stress

Salt stress is a global constraint on agricultural production. Therefore, the development of salt tolerant plants has become a current research hotspot. Salt tolerance evolves more frequently in C4 grass lineages. However, few studies have been carried out to explore the molecular bases underlying salt stress tolerance in C4 crop foxtail millet. In this study, we performed a multi-pronged approach spanning the omics analyses of transcriptomes and physiological analysis of C3 crop rice and C4 model crop foxtail millet in response to salt stress. Our results revealed specifically compared to C3 rice, C4 foxtail millet has upregulated ABA and notably reduced CK biosynthesis and signaling transduction under salt stress. Salt stress in C3 rice plants triggered rapid downregulation of photosynthesis related genes, which was coupled by severely decreased net photosynthetic rates. In the salt-threatened C3 rice and C4 foxtail millet, some stress responsive transcription factors (TFs), such as AP2/ERF, WRKY and MYB underwent strong and distinct transcriptional changes. Based on weighted gene co-expression network analysis (WGCNA), an AP2/ERF transcription factor Rice Starch Regulator1 SiRSR1 (Seita.3G044600) was identified as a key regulator of salt stress response. To confirmed its function, we generated OsRSR1-knockout lines with CRISPR/Cas9 genome editing in rice and its upstream repressor SiMIR172a-overexpressing (172a-OE) transgenic plants in foxtail millet, which increased salt tolerance. Overall, our study not only provided new insights into the convergent regulation of salt stress responses of foxtail millet and rice, but also shed light on the divergent signaling networks between them in response to salt stress.

Collective cell migration relies on PPP1R15-mediated regulation of the endoplasmic reticulum stress response

Collective cell migration is integral to many developmental and disease processes. Previously, we discovered that protein phosphatase 1 (Pp1) promotes border cell collective migration in the Drosophila ovary. We now report that the Pp1 phosphatase regulatory subunit dPPP1R15 is a critical regulator of border cell migration. dPPP1R15 is an ortholog of mammalian PPP1R15 proteins that attenuate the endoplasmic reticulum (ER) stress response. We show that, in collectively migrating border cells, dPPP1R15 phosphatase restrains an active physiological protein kinase R-like ER kinase- (PERK)-eIF2α-activating transcription factor 4 (ATF4) stress pathway. RNAi knockdown of dPPP1R15 blocks border cell delamination from the epithelium and subsequent migration, increases eIF2α phosphorylation, reduces translation, and drives expression of the stress response transcription factor ATF4. We observe similar defects upon overexpression of ATF4 or the eIF2α kinase PERK. Furthermore, we show that normal border cells express markers of the PERK-dependent ER stress response and require PERK and ATF4 for efficient migration. In many other cell types, unresolved ER stress induces initiation of apoptosis. In contrast, border cells with chronic RNAi knockdown of dPPP1R15 survive. Together, our results demonstrate that the PERK-eIF2α-ATF4 pathway, regulated by dPPP1R15 activity, counteracts the physiological ER stress that occurs during collective border cell migration. We propose that invivo collective cell migration is intrinsically "stressful," requiring tight homeostatic control of the ER stress response for collective cell cohesion, dynamics, and movement.