Age-related driving mechanisms of retinal diseases and neuroprotection by transcription factor EB-targeted therapy

Retinal aging has been recognized as a significant risk factor for various retinal disorders,including diabetic retinopathy,age-related macular degeneration,and glaucoma,following a growing understanding of the molecular underpinnings of their development.This comprehensive review explores the mechanisms of retinal aging and investigates potential neuroprotective approaches,focusing on the activation of transcription factor EB.Recent meta-analyses have demonstrated promising outcomes of transcription factor EB-targeted strategies,such as exercise,calorie restriction,rapamycin,and metformin,in patients and animal models of these common retinal diseases.The review critically assesses the role of transcription factor EB in retinal biology during aging,its neuroprotective effects,and its therapeutic potential for retinal disorders.The impact of transcription factor EB on retinal aging is cell-specific,influencing metabolic reprogramming and energy homeostasis in retinal neurons through the regulation of mitochondrial quality control and nutrient-sensing pathways.In vascular endothelial cells,transcription factor EB controls important processes,including endothelial cell proliferation,endothelial tube formation,and nitric oxide levels,thereby influencing the inner blood-retinal barrier,angiogenesis,and retinal microvasculature.Additionally,transcription factor EB affects vascular smooth muscle cells,inhibiting vascular calcification and atherogenesis.In retinal pigment epithelial cells,transcription factor EB modulates functions such as autophagy,lysosomal dynamics,and clearance of the aging pigment lipofuscin,thereby promoting photoreceptor survival and regulating vascular endothelial growth factor A expression involved in neovascularization.These cell-specific functions of transcription factor EB significantly impact retinal aging mechanisms encompassing proteostasis,neuronal synapse plasticity,energy metabolism,microvasculature,and inflammation,ultimately offering protection against retinal aging and diseases.The review emphasizes transcription factor EB as a potential therapeutic target for retinal diseases.Therefore,it is imperative to obtain well-controlled direct experimental evidence to confirm the efficacy of transcription factor EB modulation in retinal diseases while minimizing its risk of adverse effects.

Transcription factor OsSPL10 interacts with OsJAmyb to regulate blast resistance in rice

Transcription factors(TFs)play essential roles in transcriptional reprogramming during activation of plant immune responses to pathogens.OsSPL10(SQUAMOSA promoter binding protein-like10)is an important TF regulating trichome development and salt tolerance in rice.Here we report that knockout of OsSPL10 reduces whereas its overexpression enhances rice resistance to blast disease.OsSPL10 positively regulates chitin-induced immune responses including reactive oxygen species(ROS)burst and callose deposition.We show that OsSPL10 physically associates with OsJAmyb,an important TF involved in jasmonic acid(JA)signaling,and positively regulates its protein stability.We then prove that OsJAmyb positively regulates resistance to blast.Our results reveal a molecular module consisting of OsSPL10 and OsJAmyb that positively regulates blast resistance.

Wild soybean(Glycine soja)transcription factor GsWRKY40 plays positive roles in plant salt tolerance

Wild soybean(Glycine soja),a relative of cultivated soybean,shows high adaptability to adverse environmental conditions.We identified and characterized a wild soybean transcription factor gene,GsWRKY40,that promotes plant salt stress.GsWRKY40 was highly expressed in wild soybean roots and was up-regulated by salt treatment.GsWRKY40 was localized in nucleus and demonstrated DNA-binding activities but without transcriptional activation.Mutation and overexpression of GsWRKY40 altered salt tolerance of Arabidopsis plants.To understand the molecular mechanism of GsWRKY40 in regulating plant salt resistance,we screened a cDNA library and identified a GsWRKY40 interacting protein GsbHLH92 by using yeast two-hybrid approach.The physical interaction of GsWRKY40 and GsbHLH92 was confirmed by co-immunoprecipitation(co-IP),GST pull-down,and bimolecular fluorescence complementation(BiFC)techniques.Intriguingly,co-overexpression of GsWRKY40 and GsbHLH92 resulted in higher salt tolerance and lower ROS levels than overexpression of GsWRKY40 or GsbHLH92 in composite soybean plants,suggesting that GsWRKY40 and GsbHLH92 may synergistically regulate plant salt resistance through inhibiting ROS production.qRT-PCR data indicated that the expression level of GmSPOD1 gene encoding peroxidase was cooperatively regulated by GsWRKY40 and GsbHLH92,which was confirmed by using a dual luciferase report system and yeast one-hybrid experiment.Our study reveals a pathway that GsWRKY40 and GsbHLH92 collaboratively up-regulate plant salt resistance through impeding GmSPOD1 expression and reducing ROS levels,providing a novel perspective on the regulatory mechanisms underlying plant tolerance to abiotic stresses.

The BEL1-like transcription factor GhBLH5-A05 participates in cotton response to drought stress

Drought stress impairs crop growth and development.BEL1-like family transcription factors may be involved in plant response to drought stress,but little is known of the molecular mechanism by which these proteins regulate plant response and defense to drought stress.Here we show that the BEL1-like transcription factor GhBLH5-A05 functions in cotton(Gossypium hirsutum)response and defense to drought stress.Expression of GhBLH5-A05 in cotton was induced by drought stress.Overexpression of GhBLH5-A05 in both Arabidopsis and cotton increased drought tolerance,whereas silencing GhBLH5-A05 in cotton resulted in elevated sensitivity to drought stress.GhBLH5-A05 binds to cis elements in the promoters of GhRD20-A09 and GhDREB2C-D05 to activate the expression of these genes.GhBLH5-A05 interacted with the KNOX transcription factor GhKNAT6-A03.Co-expression of GhBLH5-A05 and GhKNAT6-A03 increased the transcription of GhRD20-A09 and GhDREB2C-D05.We conclude that GhBLH5-A05 acts as a regulatory factor with GhKNAT6-A03 functioning in cotton response to drought stress by activating the expression of the drought-responsive genes GhRD20-A09 and GhDREB2C-D05.

Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen infection.However,the resistance mechanisms of WRKY genes in sugarcane remain unclear.In the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense response.We identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar ROC22.This gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)stress.Interestingly,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium scitamineum.Moreover,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani var.coeruleum and caused down-regulated expression of immune marker-related genes.Transcriptome analysis indicated suppressed expression of most JAZ genes in the signal transduction pathway.ScWRKY4 interacted with ScJAZ13 to repress its expression.We thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling pathway.The present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

Roles of NAC transcription factors in cotton

Climate deterioration,water shortages,and abiotic stress are the main threats worldwide that seriously affect cotton growth,yield,and fiber quality.Therefore,research on improving cotton yield and tolerance to biotic and abiotic stresses is of great importance.The NAC proteins are crucial and plant-specific transcription factors(TFs)that are involved in cotton growth,development,and stress responses.The comprehensive utilization of cotton NAC TFs in the improvement of cotton varieties through novel biotechnological methods is feasible.Based on cotton genomic data,genome-wide identification and analyses have revealed potential functions of cotton NAC genes.Here,we comprehensively summarize the recent progress in understanding cotton NAC TFs roles in regulating responses to drought,salt,and Verticillium wilt-related stresses,as well as leaf senescence and the development of fibers,xylem,and glands.The detailed regulatory network of NAC proteins in cotton is also elucidated.Cotton NAC TFs directly bind to the promoters of genes associated with ABA biosynthesis and secondary cell-wall formation,participate in several biological processes by interacting with related proteins,and regulate the expression of downstream genes.Studies have shown that the overexpression of NAC TF genes in cotton and other model plants improve their drought or salt tolerance.This review elucidates the latest findings on the functions and regulation of cotton NAC proteins,broadens our understanding of cotton NAC TFs,and lays a fundamental foundation for further molecular breeding research in cotton.

Cu Stress-Induced Transcriptome Alterations in Sorghum and Expression Analysis of the Transcription Factor-Encoding Gene SbWRKY24

Sorghum is not only an important bio-energy crop but also a vital raw material for brewing.Exogenous copper affects the growth and metabolism of crops in specific ways.This study identified 8475 differentially expressed genes(DEGs)by high-throughput transcriptome sequencing in the sorghum cultivar‘Jinnuoliang 2’after 24 h of treatment with 10 mM CuSO4.Using GO analysis,476 genes were functionally annotated,which were mainly related to catabolism and biosynthetic processes.Additionally,90 pathways were annotated by employing the KEGG analysis.Among them,glutathione metabolism and peroxisome were induced,while photosynthesis,photosynthesis-antenna protein,and carbon sequestration of photosynthetic organisms were inhibited.Of the DEGs,399 were identified to encode transcription factors belonging to 49 families.This study also identified a WRKY transcription factor-encoding gene SbWRKY24 from the transcriptome data.For studying its function,the relative expression levels of SbWRKY24 in roots and leaves post-treatment with different growth hormones and exposure to a variety of abiotic stresses were detected by RT-qPCR.SbWRKY24 showed treatment-and tis-sue-specific expression patterns,indicating its unique role in stress tolerance.This study lays a theoretical basis for the functional exploration of SbWRKY24,elucidating the mechanism of copper resistance,and elaborating on the stress responses in sorghum.It also guides the exploration of the molecular mechanism of copper ions inducing intracellular signal transduction pathways.

Prognostic significance of oligodendrocyte transcription factor 2 expression in glioma patients:A systematic review and metaanalys

BACKGROUND Gliomas are the most common primary central nervous system neoplasm.Despite recent advances in the diagnosis and treatment of gliomas,patient prognosis remains dismal.Therefore,it is imperative to identify novel diagnostic biomarkers and therapeutic targets of glioma to effectively improve treatment outcomes.AIM To investigate the association between oligodendrocyte transcription factor 2(Olig2)expression and the outcomes of glioma patients.METHODS The PubMed,Embase,Cochrane Library,and China National Knowledge Infrastructure databases were searched for studies(published up to October 2023)that investigated the relationship between Olig2 expression and prognosis of glioma patients.The quality of the studies was assessed using the Newcastle Ottawa Scale.Data analyses were performed using Stata Version 12.0 software.RESULTS A total of 1205 glioma patients from six studies were included in the metaanalysis.High Olig2 expression was associated with better outcomes in glioma patients[hazard ratio(HR):0.81;95%(confidence interval)CI:0.51-1.27;P=0.000].Furthermore,the results of subgroup meta-analysis showed that high expression of Olig2 was associated with poor overall survival in European patients(HR:1.34;95%CI:0.79-2.27)and better prognosis in Asian patients(HR:0.43;95%CI:0.22-0.84).The sensitivity analysis showed that no single study had a significant effect on pooled HR,and there was also no indication of publication bias according to the Egger’s and Begger’s P value test or funnel plot test.CONCLUSION High Olig2 expression may have a positive impact on the prognosis of glioma patients,and should be investigated further as a prognostic biomarker and therapeutic target for glioma.

High-throughput screening system of citrus bacterial cankerassociated transcription factors and its application to the regulation of citrus canker resistance

One of the main diseases that adversely impacts the global citrus industry is citrus bacterial canker(CBC),caused by the bacteria Xanthomonas citri subsp.citri(Xcc).Response to CBC is a complex process,with both proteinDNA as well as protein–protein interactions for the regulatory network.To detect such interactions in CBC resistant regulation,a citrus high-throughput screening system with 203 CBC-inducible transcription factors(TFs),were developed.Screening the upstream regulators of target by yeast-one hybrid(Y1H)methods was also performed.A regulatory module of CBC resistance was identified based on this system.One TF(CsDOF5.8)was explored due to its interactions with the 1-kb promoter fragment of CsPrx25,a resistant gene of CBC involved in reactive oxygen species(ROS)homeostasis regulation.Electrophoretic mobility shift assay(EMSA),dual-LUC assays,as well as transient overexpression of CsDOF5.8,further validated the interactions and transcriptional regulation.The CsDOF5.8–CsPrx25 promoter interaction revealed a complex pathway that governs the regulation of CBC resistance via H2O2homeostasis.The high-throughput Y1H/Y2H screening system could be an efficient tool for studying regulatory pathways or network of CBC resistance regulation.In addition,it could highlight the potential of these candidate genes as targets for efforts to breed CBC-resistant citrus varieties.

Isolation and Structural Analysis of DRE-Binding Transcription Factor from Maize (Zea mays L.)

Dehydration-responsive element-binding (DREB) proteins specifically binding with dehydration-responsive element (DRE) have been identified as a kind of important transcription activator of plants under drought, high salt and cold stress. The conserved amino, acid residues of Val (14th residue) and Glu (19th residue) in AP2/EREBP domain of DREB1A have been identified to be two key points in determining the binding ability of DREB gene with DRE element. Using the yeast one-hybrid system, we isolated one maize DREB gene named maDREB1 by screening cDNA library. Trans-activation experiment in yeast reporter strain demonstrated that maDREB1 protein could function as a DREB transcription factor activating target gene expression by specifically binding to the DRE cis-element. To assess the functional significance of these two residues in maDREB1, the V14 and E19 were substituted individually or doubly by Ala and Asp. Point mutation analysis showed that V14 substitution made significant loss of binding ability with DRE element, while point mutation of E19 had less effect. If the substitution happened simultaneously to these two residues, it would lead to great loss of the ability of binding with DRE element. It suggested that V14 and E19 were both important in protein-DNA interacting in maDREB1, though 14V was more essential. The copy number and expression pattern of maDREB1 was discussed.

Important Roles of Transcription Factors in Regulating Seed Oil Biosynthesis to Increase Plant Storage Lipid Content

In this article, the biosynthetic pathways of storage oil accumulation in oilseed plants were briefly introduced, and the transcription factors, such as B3 do- main supeffamily genes, lecl gene, wril gene etc., and their important role in oil accumulation regulation was mainly elucidated. Overexpession of transcription factors as feasible ways of genetic manipulation to increase oJl content in oilseed crops are promising in a long-term perspective.

Sequence Analysis of Transcription Factor AtWRKY35 and Construction of Prokaryotic Expression Vector

As members of a super gene family, WRKY transcription factors are widely distributed in higher plants. ln this study, bioinformatic analysis of WRKY35, a member of the WRKY gene family, was carried out. Results indicated that tran-scription factor WRKY35 harbors a WRKYGQK core domain and a Cys2His2 or Cys2His/Cys zinc finger in the 5’ end without transmembrane domain. After PCR amplification and restriction digestion, WRKY35 gene fragment was ligated to prokaryotic expression vector PET28. This study provided basis for expression anal-ysis of WRKY35 protein and subsequent functional identification of WRKY35 gene.

Cloning of Atr MYB Transcription Factor Gene from Acer truncatum

[Objective] Cloning of the AtrMYB transcription factor gene from Acer truncatum was conducted to further explore the red leaf development mechanism and breed cultivars of colored-leaf maple. [Method] The Acer truncatum ‘Luhong No.1＇ cultivar was used as the material for cloning the MYB gene by mean of RTPCR and RACE-PCR. [Results] Sequence analysis showed that the fragment contained a full coding region of 831 bp encoding 276 amino acid residues with a molecular weight of 32.17 kD and a molecular formula C_（1430）H_（14052）N_（2247）O_（406）S_（14）. The gene was named as AtrMYB with a Gen Bank accession number of 1825712. This coded protein had apI of 9.44. The results showed that the AtrMYB exhibited typical features of the R2R3-MYB domain. The AtrMYB was highly homologous with the MYB of other species at nucleotide and amino acid levels. The AtrMYB had no signal peptide, but a nuclear localization signal. The phylogenetic tree showed that the AtrMYB was at the same clade as the MYB from Citrus sinensis. [Conclusion] The AtrMYB was cloned from Acer truncatum ‘Luhong No.1＇ cultivar. These results have provided a foundation for further purification and identification of target protein and function study of the AtrMYB.

羊驼transcription elongation factor B(S III)(Tceb2)cDNA的获取与序列分析

【研究目的】分离和鉴定羊驼transcription elongation factorB(S III)(Tceb2)基因,分析其序列特征,为今后研究其生物学功能奠定理论基础。【方法】用Southern Blotting法从羊驼皮肤cDNA文库中筛选Tceb2基因,通过BLAST等生物学相关软件对其进行结果分析。【结果】有6个阳性克隆,测序结果得知,序列片段大小大约为472bp,具有完整的开放阅读框,可编码119AA,分子量为13.2KDa。序列特征、结构和同源性分析表明:该序列预测为全长cDNA序列,该基因序列及其编码的氨基酸序列与大鼠和小鼠的troponinc2同源性可达100%。【结论】该基因是获得的羊驼全长Tceb2(GenBank DQ646397)(命名为AlpTceb2)。

Genome-wide analysis of the WRKY transcription factor gene family in Gossypium raimondii and the expression of orthologs in cultivated tetraploid cotton

WRKY proteins are members of a family of transcription factors in higher plants that function in plant responses to various physiological processes.We identified 120 candidate WRKY genes from Gossypium raimondii with corresponding expressed sequence tags in at least one of four cotton species,Gossypium hirsutum,Gossypium barbadense,Gossypium arboreum,and G.raimondii.These WRKY members were anchored on 13 chromosomes in G.raimondii with uneven distribution.Phylogenetic analysis showed that WRKY candidate genes can be classified into three groups,with 20 members in group I,88 in group II,and 12 in group III.The88 genes in group II were further classified into five subgroups,groups IIa–e,containing 7,16,37,15,and 13 members,respectively.We characterized diversity in amino acid residues in the WRKY domain and/or other zinc finger motif regions in the WRKY proteins.The expression patterns of WRKY genes revealed their important roles in diverse functions in cotton developmental stages of vegetative and reproductive growth and stress response.Structural and expression analyses show that WRKY proteins are a class of important regulators of growth and development and play key roles in response to stresses in cotton.

Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

The heat shock transcription factors （HSFs） are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins （HSPs）, which are critical in the protection against stress damage and many other important biological processes. Study of the HSF gene family is important for understanding the mechanism by which plants respond to stress. The completed genome sequences of rice （Oryza sativa） and Arabidopsis （Arabidopsis thaliana） constitute a valuable resource for comparative genomic analysis, as they are representatives of the two major evolutionary lineages within the angiosperms： the monocotyledons and the dicotyledons. The identification of phylogenefic relationships among HSF proteins in these species is a fundamental step to unravel the functionality of new and yet uncharacterized genes belonging to this family.In this study, the full complement of HSF genes in rice and Arabidopsis has probably been identified through the genome-wide scan. Phylogenetic analyses resulted in the identification of three major clusters of orthologous genes that contain members belonging to both species, which must have been represented in their common ancestor before the taxonomic splitting of the angiosperms. Fttrther analysis of the phylogenetic tree reveals a possible dicot specific gene group. We also identified nine pairs of paralogs, as evidence for studies on the evolution history of rice HSF family and rice genome evolution. Expression data analysis indicates that HSF proteins are widely expressed in plants. These results provide a solid base for future functional genomic studies of the HSF gene family in rice and Arabidopsis.

Epithelial-mesenchymal transition- activating transcription factors- multifunctional regulators in cancer

The process of epithelial to mesenchymal transition(EMT), first noted during embryogenesis, has also been reported in tumor formation and leads to the development of metastatic growth. It is a naturally occurring process that drives the transformation of adhesive,non-mobile epithelial like cells into mobile cells with a mesenchymal phenotype that have ability to migrate to distant anatomical sites. Activating complex network of embryonic signaling pathways, including Wnt, Notch,hedgehog and transforming growth factor-β pathways,lead to the upregulation of EMT activating transcription factors, crucial for normal tissue development and maintenance. However, deregulation of tightly regulated pathways affecting the process of EMT has been recently investigated in various human cancers. Given the critical role of EMT in metastatic tumor formation,better understanding of the mechanistic regulation provides new opportunities for the development of potential therapeutic targets of clinical importance.

Making a tooth:growth factors,transcription factors,and stem cells

Mammalian tooth development is largely dependent on sequential and reciprocal epithelial-mesenchymal interactions. These processes involve a series of inductive and permissive interactions that result in the determination, differentiation, and organization of odontogenic tissues. Multiple signaling molecules, including BMPs, FGFs, Shh, and Wnt proteins, have been implicated in mediating these tissue interactions. Transcription factors participate in epithelial-mesenchymal interactions via linking the signaling loops between tissue layers by responding to inductive signals and regulating the expression of other signaling molecules. Adult stem cells are highly plastic and multipotent. These cells including dental pulp stem cells and bone marrow stromal cells could be reprogrammed into odontogenic fate and participated in tooth formation. Recent progress in the studies of molecular basis of tooth development, adult stem cell biology, and regene- ration will provide fundamental knowledge for the realization of human tooth regeneration in the near future.

Molecular Characterization and Expression Analysis of TaZFP15, a C_2H_2-Type Zinc Finger Transcription Factor Gene in Wheat (Triticum aestivum L.)

Based on sequencing of part clones in a root subtractive cDNA library, an expressed sequence tag （EST） sharing high similarity to a rice C2H2 zinc finger transcription factor （ZFP15） was obtained in wheat. Through bioinformatics approach, the wheat C2H2-type ZFP gene referred to TaZFP15 has been identified and characterized. As a full-length cDNA of 670 bp, TaZFP15 has an open reading frame of 408 bp and encodes a 135-aa polypeptide. TaZFP15 contains two C2H2 zinc finger domains and each one has a conserved motif QALGGH. The typical L-box, generally identified in the C2H2 type transcription factors, has also been found in TaZFP15. Phylogenetic analysis suggested that TaZFP15 shares high similarities with rice ZFP15 （GenBank accession no. AY286473）, maize ZFP （GenBank accession no. NM_001159094） and a subset of other zinc-finger transcription factor genes in plant species. The expression of TaZFP15 was up-regulated by starved-Pi stress, showing a pattern to be gradually elevated along with the progression of the Pi-stress in a 23-h treatment regime. Similarly, the transcripts of TaZFP15 in roots were also induced by nitrogen deficiency, and abiotic stresses of drought and salinity. No responses of TaZFP15 were detected in roots to nutrition deficiencies of P, Zn, and Ca, and the external treatment of abscisic acid （ABA）. TaZFP15 could be specifically amplified in genome A, B, and D, and without variability in the sequences, suggesting that TaZFP15 has multi-copies in the homologous hexaploid species. Transgenic analysis in tobacco revealed that up-regulation of TaZFP15 could significantly improve plant dry mass accumulation via increasing the plant phosphorus acquisition capacity under Pi-deficiency condition. The results suggested that TaZFP15 is involved in mediation of signal transductions of diverse external stresses.