scholarly journals Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 752
Author(s):  
Changhai Chen ◽  
Yanjun Li ◽  
Hehong Zhang ◽  
Qiang Ma ◽  
Zhongyan Wei ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Virus Infection ◽  
Rice Genome ◽  
Rice Stripe Virus ◽  
Response Patterns ◽  
Chromosomal Distribution ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Genome Wide ◽  
Transcription Factor Genes

The RAV family is part of the B3 superfamily and is one of the most abundant transcription factor families in plants. Members have highly conserved B3 or AP2 DNA binding domains. Although the RAV family genes of several species have been systematically identified from genome-wide studies, there has been no comprehensive study to identify rice RAV family genes. Here, we identified 15 genes of the RAV family in the rice genome and analyzed their phylogenetic relationships, gene structure, conserved domains, and chromosomal distribution. Based on domain similarity and phylogenetic topology, rice RAV transcription factors were phylogenetically clustered into four groups. qRT-PCR analyses showed that expression of these RAV genes was significantly up-regulated or down-regulated by plant hormone treatments, including BL, NAA, IAA, MeJA, and SA. Most of the rice RAV genes were dramatically down-regulated in response to rice stripe virus (RSV) and mostly up-regulated in response to Southern rice black-streaked dwarf virus (SRBSDV). These results suggest that the rice RAV genes are involved in diverse signaling pathways and in varied responses to virus infection.

Dimeric transcription factor families: it takes two to tango but who decides on partners and the venue?

1992 ◽  
Vol 103 (1) ◽  
pp. 9-14 ◽  
Author(s):  
K.A. Lee
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Experimental Evidence ◽  
Cdna Cloning ◽  
Transcriptional Activation ◽  
Effector Functions ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Elements

Dimeric transcription factors that bind to DNA are often grouped into families on the basis of dimerization and DNA-binding specificities. cDNA cloning studies have established that members of the same family have structurally related dimerisation and DNA-binding domains but diverge in other regions that are important for transcriptional activation. These features lead to the straightforward suggestion that although all members of a family bind to similar DNA elements, individual members exhibit distinct transcriptional effector functions. This simple view is now supported by experimental evidence from those systems that have proved amenable to study. There are however some largely unaddressed questions that concern the mechanisms that allow family members to go about their business without interference from their highly related siblings. Here I will discuss some insights from studies of the bZIP class of transcription factors.

scholarly journals The PAX3-FKHR fusion protein created by the t(2;13) translocation in alveolar rhabdomyosarcomas is a more potent transcriptional activator than PAX3.

1995 ◽  
Vol 15 (3) ◽  
pp. 1522-1535 ◽  
Author(s):  
W J Fredericks ◽  
N Galili ◽  
S Mukhopadhyay ◽  
G Rovera ◽  
J Bennicelli ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Fusion Protein ◽  
Target Genes ◽  
Transcriptional Activator ◽  
Wild Type ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Pediatric Solid Tumors ◽  
Single Polypeptide

Alveolar rhabdomyosarcomas are pediatric solid tumors with a hallmark cytogenetic abnormality: translocation of chromosomes 2 and 13 [t(2;13) (q35;q14)]. The genes on each chromosome involved in this translocation have been identified as the transcription factor-encoding genes PAX3 and FKHR. The NH2-terminal paired box and homeodomain DNA-binding domains of PAX3 are fused in frame to COOH-terminal regions of the chromosome 13-derived FKHR gene, a novel member of the forkhead DNA-binding domain family. To determine the role of the fusion protein in transcriptional regulation and oncogenesis, we identified the PAX3-FKHR fusion protein and characterized its function(s) as a transcription factor relative to wild-type PAX3. Antisera specific to PAX3 and FKHR were developed and used to examine PAX3 and PAX3-FKHR expression in tumor cell lines. Sequential immunoprecipitations with anti-PAX3 and anti-FKHR sera demonstrated expression of a 97-kDa PAX3-FKHR fusion protein in the t(2;13)-positive rhabdomyosarcoma Rh30 cell line and verified that a single polypeptide contains epitopes derived from each protein. The PAX3-FKHR protein was localized to the nucleus in Rh30 cells, as was wild-type PAX3, in t(2;13)-negative A673 cells. In gel shift assays using a canonical PAX binding site (e5 sequence), we found that DNA binding of PAX3-FKHR was significantly impaired relative to that of PAX3 despite the two proteins having identical PAX DNA-binding domains. However, the PAX3-FKHR fusion protein was a much more potent transcriptional activator than PAX3 as determined by transient cotransfection assays using e5-CAT reporter plasmids. The PAX3-FKHR protein may function as an oncogenic transcription factor by enhanced activation of normal PAX3 target genes.

scholarly journals Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4172 ◽  
Author(s):  
Bernard Kinuthia Karanja ◽  
Liang Xu ◽  
Yan Wang ◽  
Everlyne M’mbone Muleke ◽  
Bashir Mohammed Jabir ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Hormone Signaling ◽  
Preferential Expression ◽  
Genome Wide ◽  
Raphanus Sativus L ◽  
Transcription Factor Genes ◽  
Membrane Bound ◽  
Polymerase Chain

NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.

scholarly journals Recurrent evolution of vertebrate transcription factors by transposase capture

Science ◽  
2021 ◽  
Vol 371 (6531) ◽  
pp. eabc6405 ◽  
Author(s):  
Rachel L. Cosby ◽  
Julius Judd ◽  
Ruiling Zhang ◽  
Alan Zhong ◽  
Nathaniel Garry ◽  
...  
Keyword(s):  
Fusion Proteins ◽  
Regulatory Elements ◽  
Exon Shuffling ◽  
Cellular Functions ◽  
Protein Coding ◽  
Regulatory Domains ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Genome Wide ◽  
Tetrapod Evolution

Genes with novel cellular functions may evolve through exon shuffling, which can assemble novel protein architectures. Here, we show that DNA transposons provide a recurrent supply of materials to assemble protein-coding genes through exon shuffling. We find that transposase domains have been captured—primarily via alternative splicing—to form fusion proteins at least 94 times independently over the course of ~350 million years of tetrapod evolution. We find an excess of transposase DNA binding domains fused to host regulatory domains, especially the Krüppel-associated box (KRAB) domain, and identify four independently evolved KRAB-transposase fusion proteins repressing gene expression in a sequence-specific fashion. The bat-specific KRABINER fusion protein binds its cognate transposons genome-wide and controls a network of genes and cis-regulatory elements. These results illustrate how a transcription factor and its binding sites can emerge.

scholarly journals Genome-wide RNA-seq Analysis of Differentially Expressed Transcription Factor Genes Against Bacterial Leaf Pustule in Soybean

2015 ◽  
Vol 3 (3) ◽  
pp. 197-207 ◽  
Author(s):  
Kil Hyun Kim ◽  
Yang Jae Kang ◽  
Sangrea Shim ◽  
Min-Jung Seo ◽  
Seong-Bum Baek ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Genome Wide ◽  
Transcription Factor Genes
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