scholarly journals An ERF transcription factor from Brassica oleracea: a new member of the emerging pathogenicity hub in plant-Xanthomonas interactions

2020 ◽  
Author(s):  
Nikolay Zlobin ◽  
Marina Lebedeva ◽  
Yuliya Monakhova ◽  
Vera Ustinova ◽  
Vasiliy Taranov
Keyword(s):  
Transcription Factor ◽  
Brassica Oleracea ◽  
Xanthomonas Campestris ◽  
Target Genes ◽  
Computational Prediction ◽  
Amplicon Sequencing ◽  
List Type ◽  
Tal Effectors ◽  
Xanthomonas Species ◽  
Rot Disease

Summary- TAL effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of different Xanthomonas bacteria. However, investigation of TALEs from Xanthomonas campestris pv. campestris, which causes black rot disease of crucifers, is in its infancy.- In this study, we used PCR-based amplification in conjunction with SMRT amplicon sequencing to identify TALE genes in several Xanthomonas campestris pv. campestris strains and performed computational prediction in conjunction with RT-PCR-based analysis to identify their target genes in Brassica oleracea.- Transcription factor from the AP2/ERF family was predicted to be putative target gene for the conserved TALEs present in multiple Xanthomonas campestris pv. campestris strains. Its expression dramatically increased upon leaf inoculation with strains harbouring such TALEs.- Several members of the AP2/ERF factor family from different plant species were identified as targets of TALEs from various Xanthomonas species, which suggests that they constitute a new pathogenicity hub in plant-Xanthomonas interactions.

scholarly journals TET1 interacts directly with NANOG via independent regions containing hydrophobic and aromatic residues

2020 ◽  
Author(s):  
Raphaël Pantier ◽  
Nicholas Mullin ◽  
Elisa Hall-Ponsele ◽  
Ian Chambers
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Target Genes ◽  
Embryonic Stem ◽  
Physical Interaction ◽  
List Type ◽  
Aromatic Residues ◽  
Cpg Dinucleotides ◽  
Sites Of Action

AbstractThe DNA demethylase TET1 is highly expressed in embryonic stem cells. Knockout experiments indicate that TET1 is important for lineage commitment, and paradoxically, also for reprogramming to naïve pluripotency. TET1 binds to promoters through a CXXC domain which recognises unmethylated CpG dinucleotides. TET1 also binds to enhancers, presumably via interactions with partner proteins. The transcription factor NANOG interacts with TET1 and is predominantly localised at enhancers in ESCs. Therefore, NANOG may contribute to TET1 biological activity in pluripotent cells. However, the regions of TET1 involved in protein-protein interactions are mostly unknown. Here, we characterise the physical interaction between TET1 and NANOG using embryonic stem cells and bacterial expression systems. TET1 and NANOG interact through multiple binding sites that act independently. Critically, mutating conserved hydrophobic and aromatic residues within TET1 and NANOG abolishes the interaction. Comparative ChIP-seq analysis identifies genomic loci bound by both TET1 and NANOG, that correspond predominantly to pluripotency enhancers. Importantly, around half of NANOG transcriptional target genes are associated with TET1-NANOG co-bound sites. These results indicate a mechanism by which TET1 protein is targeted to specific sites of action at enhancers by direct interaction with a transcription factor.HighlightsNANOG and TET1 have regulatory roles in maintaining and reprogramming pluripotencyTET1 and NANOG interact via multiple independent binding regionsTET1 and NANOG interactions are mediated by aromatic and hydrophobic residuesTET1 residues that bind NANOG are highly conserved in mammalsCo-localisation of TET1 and NANOG on chromatin is enriched at NANOG target genes

scholarly journals Early Defense Mechanisms of Brassica oleracea in Response to Attack by Xanthomonas campestris pv. campestris

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2705
Author(s):  
Lu Lu ◽  
Sokrat G. Monakhos ◽  
Yong Pyo Lim ◽  
So Young Yi
Keyword(s):  
Brassica Oleracea ◽  
Defense Mechanisms ◽  
Xanthomonas Campestris ◽  
Radical Scavenging ◽  
Defense Responses ◽  
Black Rot ◽  
Enzymatic Antioxidants ◽  
Induced Expression ◽  
Rot Disease ◽  
Xanthomonas Campestris Pv Campestris

Black rot disease, caused by Xanthomonas campestris pv. campestris (Xcc), results in significant yield losses in Brassica oleracea crops worldwide. To find black rot disease-resistant cabbage lines, we carried out pathogenicity assays using the scissor-clipping method in 94 different B. oleracea lines. By comparing the lesion areas, we selected a relatively resistant line, Black rot Resistance 155 (BR155), and a highly susceptible line, SC31. We compared the two cabbage lines for the Xcc-induced expression pattern of 13 defense-related genes. Among them, the Xcc-induced expression level of PR1 and antioxidant-related genes (SOD, POD, APX, Trx H, and CHI) were more than two times higher in BR155 than SC31. Nitroblue tetrazolium (NBT) and diaminobenzidine tetrahydrochloride (DAB) staining analysis showed that BR155 accumulated less Xcc-induced reactive oxygen species (ROS) than did SC31. In addition, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assays showed that BR155 had higher antioxidant activity than SC31. This study, focused on the defense responses of cabbage during the early biotrophic stage of infection, indicated that Xcc-induced ROS might play a role in black rot disease development. We suggest that non-enzymatic antioxidants are important, particularly in the early defense mechanisms of cabbage against Xcc.

scholarly journals LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat

2019 ◽  
Author(s):  
Beata Orman-Ligeza ◽  
Philippa Borrill ◽  
Tansy Chia ◽  
Marcella Chirico ◽  
Jaroslav Doležel ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
List Type ◽  
Biological Processes ◽  
Organ Development ◽  
Starch Metabolism ◽  
Embryo Size ◽  
Binding Factor ◽  
Wide Range ◽  
Endosperm Starch

ABSTRACTMutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks.HIGHLIGHTSLYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only.Wheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth.The down-stream target genes of PBF in wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism.

scholarly journals Arabidopsis bZIP11 is a susceptibility factor during Pseudomonas syringae infection

2021 ◽  
Author(s):  
Matthew James Prior ◽  
Jebasingh Selvanayagam ◽  
Jung-Gun Kim ◽  
Monika Tomar ◽  
Martin Jonikas ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Pseudomonas Syringae ◽  
Leucine Zipper ◽  
Host Cells ◽  
Amino Acid Transporters ◽  
Secretion Systems ◽  
Transcription Activator ◽  
Tal Effectors ◽  
Basic Leucine Zipper ◽  
Xanthomonas Species

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens, e.g. Xanthomonas species, use TAL (transcription activator-like) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pathovar (pv.) tomato strain DC3000 lacks TAL effectors, yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Since bacteria require other nutrients besides sugars for efficient reproduction, we hypothesized that Pseudomonas may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11 regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells.

scholarly journals Black Rot Disease Decreases Young Brassica oleracea Plants’ Biomass but Has No Effect in Adult Plants

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 569
Author(s):  
Carmen Vega-Álvarez ◽  
Marta Francisco ◽  
Pilar Soengas
Keyword(s):  
Brassica Oleracea ◽  
Xanthomonas Campestris ◽  
Developmental Stages ◽  
Black Rot ◽  
Dependent Manner ◽  
Yield Losses ◽  
Aerial Parts ◽  
Rot Disease ◽  
The Impact ◽  
Adult Plants

Black rot disease, caused by the bacterium Xanthomonas campestris pv. campestris (Pammel) Dowson (Xcc), causes important yield losses in Brassica oleracea L. crops worldwide. In temperate areas, yield losses are mostly due to the discarding of those plants showing chlorotic and necrotic lesions, since they may be unmarketable. However, the biomass loss caused by the diversion of resources from the primary to the secondary defense metabolism could also affect the final crop yield. In this work, we have focused on studying the impact of Xcc race 1 invasion on the biomass production of young and adult B. oleracea plants. The results have shown that Xcc infection reduces biomass and photosynthesis in the aerial parts of seedlings and modifies their water percentage in a time-dependent manner. When adult plants were inoculated in the field, no effect was detected on the leaves or the biomass of marketable products. This was probably due to a better immune response when compared to seedlings. Since the first developmental stages of B. oleracea crops are especially vulnerable to Xcc, plant disease control should be increased in order to avoid yield losses of marketable products at the adult stage.

The SNPs within 3'UTR of miRNA Target Genes Related to Multiple Sclerosis: A Computational Prediction

2020 ◽  
Vol 17 (2) ◽  
pp. 133-147
Author(s):  
Mina Zafarpiran ◽  
Roya Sharifi ◽  
Zeinab Shirvani-Farsani
Keyword(s):  
Multiple Sclerosis ◽  
Gene Regulation ◽  
Binding Sites ◽  
Target Genes ◽  
Demyelinating Disease ◽  
Target Prediction ◽  
Computational Prediction ◽  
Functional Verification ◽  
Candidate Snps ◽  
Inflammatory Genes

Background: Multiple Sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system, and genetic factors play an important role in its susceptibility. The expressions of many inflammatory genes implicated in MS are regulated by microRNA (miRNAs), whose function is to suppress the translation by pairing with miRNA Recognition Elements (MREs) present in the 3' untranslated region (3'UTR) of target mRNA. Recently, it has been shown that the Single Nucleotide Polymorphism (SNPs) present within the 3'UTR of mRNAs can affect the miRNA-mediated gene regulation and susceptibility to a variety of human diseases. Objective: The aim of this study was to analyze the SNPs within the 3'UTR of miRNA inflammatory target genes related to multiple sclerosis. Methods: By DisGeNET, dbGaP, Ovid, DAVID, Web of knowledge, and SNPs databases, 3'UTR genetic variants were identified in all inflammatory genes associated with MS. Also, miRNA's target prediction databases were used for predicting the miRNA binding sites. Results: We identified 125 SNPs with MAF>0.05 located in the binding site of the miRNA of 35 genes among 59 inflammatory genes related to MS. Bioinformatics analysis predicted 62 MRE-modulating SNPs and 59 MRE-creating SNPs in the 3'UTR of MSimplicated inflammatory genes. These candidate SNPs within miRNA binding sites of inflammatory genes can alter the miRNAs binding, and consequently lead to the mRNA gene regulation. Conclusion: Therefore, these miRNA and MRE-SNPs may play important roles in personalized medicine of MS, and hence, they would be valuable for further functional verification investigations.

scholarly journals Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Mirna Target ◽  
Target Genes ◽  
Functional Characterization ◽  
Human Endothelial Cells ◽  
Mrna Targets ◽  
Canonical Pathways

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.

scholarly journals Linking metabolic dysfunction with cardiovascular diseases: Brn-3b/POU4F2 transcription factor in cardiometabolic tissues in health and disease

2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Vishwanie S. Budhram-Mahadeo ◽  
Matthew R. Solomons ◽  
Eeshan A. O. Mahadeo-Heads
Keyword(s):  
Transcription Factor ◽  
Cardiovascular Diseases ◽  
Cell Fate ◽  
Target Genes ◽  
Cardiovascular Responses ◽  
Normal Function ◽  
Valuable Insight ◽  
Metabolic Dysfunction ◽  
Pathological Changes ◽  
Cardiac Responses

AbstractMetabolic and cardiovascular diseases are highly prevalent and chronic conditions that are closely linked by complex molecular and pathological changes. Such adverse effects often arise from changes in the expression of genes that control essential cellular functions, but the factors that drive such effects are not fully understood. Since tissue-specific transcription factors control the expression of multiple genes, which affect cell fate under different conditions, then identifying such regulators can provide valuable insight into the molecular basis of such diseases. This review explores emerging evidence that supports novel and important roles for the POU4F2/Brn-3b transcription factor (TF) in controlling cellular genes that regulate cardiometabolic function. Brn-3b is expressed in insulin-responsive metabolic tissues (e.g. skeletal muscle and adipose tissue) and is important for normal function because constitutive Brn-3b-knockout (KO) mice develop profound metabolic dysfunction (hyperglycaemia; insulin resistance). Brn-3b is highly expressed in the developing hearts, with lower levels in adult hearts. However, Brn-3b is re-expressed in adult cardiomyocytes following haemodynamic stress or injury and is necessary for adaptive cardiac responses, particularly in male hearts, because male Brn-3b KO mice develop adverse remodelling and reduced cardiac function. As a TF, Brn-3b regulates the expression of multiple target genes, including GLUT4, GSK3β, sonic hedgehog (SHH), cyclin D1 and CDK4, which have known functions in controlling metabolic processes but also participate in cardiac responses to stress or injury. Therefore, loss of Brn-3b and the resultant alterations in the expression of such genes could potentially provide the link between metabolic dysfunctions with adverse cardiovascular responses, which is seen in Brn-3b KO mutants. Since the loss of Brn-3b is associated with obesity, type II diabetes (T2DM) and altered cardiac responses to stress, this regulator may provide a new and important link for understanding how pathological changes arise in such endemic diseases.

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