RsmA Regulates Biofilm Formation in Xanthomonas campestris through a Regulatory Network Involving Cyclic di-GMP and the Clp Transcription Factor

Bacterial spot (BS), caused by Xanthomonas campestris pv. Vesicatoria (Xcv), severely affects the quality and yield of pepper. Thus, breeding new pepper cultivars with enhanced resistance to BS can improve economic benefits for pepper production. Identification of BS resistance genes is an essential step to achieve this goal. However, very few BS resistance genes have been well characterized in pepper so far. In this study, we reanalyzed public multiple time points related to RNA-seq data sets from two pepper cultivars, the Xcv-susceptible cultivar ECW and the Xcv-resistant cultivar VI037601, post Xcv infection. We identified a total of 3568 differentially expressed genes (DEGs) between two cultivars post Xcv infection, which were mainly involved in some biological processes, such as Gene Ontology (GO) terms related to defense response to bacterium, immune system process, and regulation of defense response, etc. Through weighted gene co-expression network analysis (WGCNA), we identified 15 hub (Hub) transcription factor (TF) candidates in response to Xcv infection. We further selected 20 TFs from the gene regulatory network (GRN) potentially involved in Xcv resistance response. Finally, we predicted 4 TFs, C3H (p-coumarate 3-hydroxylase), ERF (ethylene-responsive element binding factor), TALE (three-amino-acid-loop-extension), and HSF (heat shock transcription factor), as key factors responsible for BS disease resistance in pepper. In conclusion, our study provides valuable resources for dissecting the underlying molecular mechanism responsible for Xcv resistance in pepper. Additionally, it also provides valuable references for mining transcriptomic data to identify key candidates for disease resistance in horticulture crops.

Download Full-text

Construction of transcription factor mutual regulatory network based on a new database

Medical Engineering and Bioinformatics ◽

10.2495/meb140541 ◽

2014 ◽

Author(s):

Zhenping Yang ◽

Wei Wang ◽

Yang Yang ◽

Hongfei Chen ◽

Jinke Wang

Keyword(s):

Transcription Factor ◽

Regulatory Network

Download Full-text

Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis

npj Systems Biology and Applications ◽

10.1038/s41540-020-00164-4 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Albert T. Young ◽

Xavier Carette ◽

Michaela Helmel ◽

Hanno Steen ◽

Robert N. Husson ◽

...

Keyword(s):

Transcription Factor ◽

Mycobacterium Tuberculosis ◽

Regulatory Network ◽

Regulatory Networks ◽

Protein Interaction Data ◽

Kinase Inhibition ◽

Protein Protein Interaction ◽

Downstream Effects ◽

Regulate Cell Growth ◽

Regulatory Effects

AbstractThe ability of Mycobacterium tuberculosis (Mtb) to adapt to diverse stresses in its host environment is crucial for pathogenesis. Two essential Mtb serine/threonine protein kinases, PknA and PknB, regulate cell growth in response to environmental stimuli, but little is known about their downstream effects. By combining RNA-Seq data, following treatment with either an inhibitor of both PknA and PknB or an inactive control, with publicly available ChIP-Seq and protein–protein interaction data for transcription factors, we show that the Mtb transcription factor (TF) regulatory network propagates the effects of kinase inhibition and leads to widespread changes in regulatory programs involved in cell wall integrity, stress response, and energy production, among others. We also observe that changes in TF regulatory activity correlate with kinase-specific phosphorylation of those TFs. In addition to characterizing the downstream regulatory effects of PknA/PknB inhibition, this demonstrates the need for regulatory network approaches that can incorporate signal-driven transcription factor modifications.

Download Full-text

Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

International Journal of Molecular Sciences ◽

10.3390/ijms22158193 ◽

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.

Download Full-text

Investigating microRNA-transcription factor mediated regulatory network in glioblastoma

2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) ◽

10.1109/bibmw.2010.5703809 ◽

2010 ◽

Cited By ~ 1

Author(s):

Xue Gong ◽

Peilin Jia ◽

Zhongming Zhao

Keyword(s):

Transcription Factor ◽

Regulatory Network

Download Full-text

Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation

Zebrafish ◽

10.1089/zeb.2017.1486 ◽

2018 ◽

Vol 15 (2) ◽

pp. 202-205 ◽

Cited By ~ 4

Author(s):

Justin King ◽

Justin Foster ◽

James M. Davison ◽

John F. Rawls ◽

Ghislain Breton

Keyword(s):

Transcription Factor ◽

Regulatory Network ◽

Gene Discovery

Download Full-text

Deciphering the transcription factor-microRNA-target gene regulatory network associated with graphene oxide cytotoxicity

Nanotoxicology ◽

10.1080/17435390.2018.1513090 ◽

2018 ◽

Vol 12 (9) ◽

pp. 1014-1026 ◽

Cited By ~ 3

Author(s):

Masoumeh Farahani ◽

Mostafa Rezaei–Tavirani ◽

Hakimeh Zali ◽

Afsaneh Arefi Oskouie ◽

Meisam Omidi ◽

...

Keyword(s):

Transcription Factor ◽

Graphene Oxide ◽

Gene Regulatory Network ◽

Regulatory Network ◽

Target Gene ◽

Microrna Target ◽

Gene Regulatory

Download Full-text

A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation

FEBS Letters ◽

10.1002/1873-3468.12713 ◽

2017 ◽

Vol 591 (13) ◽

pp. 2019-2031 ◽

Cited By ~ 4

Author(s):

Hirotaka Sugino ◽

Takanori Usui ◽

Tomohiro Shimada ◽

Masahiro Nakano ◽

Hiroshi Ogasawara ◽

...

Keyword(s):

Transcription Factor ◽

Biofilm Formation ◽

Master Regulator

Download Full-text

Class I TCP transcription factors regulate trichome branching and cuticle development in Arabidopsis

Journal of Experimental Botany ◽

10.1093/jxb/eraa257 ◽

2020 ◽

Vol 71 (18) ◽

pp. 5438-5453

Author(s):

Alejandra Camoirano ◽

Agustín L Arce ◽

Federico D Ariel ◽

Antonela L Alem ◽

Daniel H Gonzalez ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factor ◽

Transcription Factors ◽

Regulatory Network ◽

Class I ◽

Branch Number ◽

Plant Organ ◽

Cuticle Formation ◽

Cuticle Development ◽

Different Levels

Abstract Trichomes and the cuticle are two specialized structures of the aerial epidermis that are important for plant organ development and interaction with the environment. In this study, we report that Arabidopsis thaliana plants affected in the function of the class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 show overbranched trichomes in leaves and stems and increased cuticle permeability. We found that TCP15 regulates the expression of MYB106, a MIXTA-like transcription factor involved in epidermal cell and cuticle development, and overexpression of MYB106 in a tcp14 tcp15 mutant reduces trichome branch number. TCP14 and TCP15 are also required for the expression of the cuticle biosynthesis genes CYP86A4, GPAT6, and CUS2, and of SHN1 and SHN2, two AP2/EREBP transcription factors required for cutin and wax biosynthesis. SHN1 and CUS2 are also targets of TCP15, indicating that class I TCPs influence cuticle formation acting at different levels, through the regulation of MIXTA-like and SHN transcription factors and of cuticle biosynthesis genes. Our study indicates that class I TCPs are coordinators of the regulatory network involved in trichome and cuticle development.

Download Full-text