A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences

Nagano, Yukio; Furuhashi, Hirofumi; Inaba, Tomoki; Sasaki, Yukiko

doi:10.1093/nar/29.20.4097

Cited by 82 publications

(88 citation statements)

References 23 publications

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“…This observation, however, represents an underestimate of the total number of transcription factors, given that, at present, approximately 40% of the proteins predicted from the genome sequence cannot be assigned to functional categories on the basis of sequence similarity to proteins of known biochemical function (Lin et al, 1999;Mayer et al, 1999; Arabidopsis Genome Initiative, 2000;Salanoubat et al, 2000;Tabata et al, 2000;Theologis et al, 2000). Some of those uncharacterized proteins are expected to be transcriptional regulators and, in fact, novel classes of transcription factors are still being discovered (for example: Boggon et al, 1999;Schauser et al, 1999;Kawaoka et al, 2000;Nagano et al, 2001;Windhövel et al, 2001). Therefore, the total number of transcription factor genes present in Arabidopsis (as well as, for the same reasons, in any other of the sequenced eukaryotic genomes) will be uncertain for some time.…”

Section: Transcription Factor Gene Content Of the Arabidopsis Genomementioning

confidence: 99%

Transcriptional Regulation: a Genomic Overview

Riechmann

2002

The Arabidopsis Book

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The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription. Introduction. The Arabidopsis Book ©2002 American Society of Plant BiologistsFirst published on April 4, 2002 doi: 10.1199/tab.0085 : e0085. The Arabidopsis Book 2 of 46In addition, gene expression profiling technologies, such as DNA microarrays, allow monitoring transcription factor activity at a genome-wide level. These studies should eventually lead to an understanding of the interplay of the transcription factors with the genome whose expression they control.This chapter intends to provide a genomic perspective on transcriptional regulation in Arabidopsis. The first section briefly reviews the different types of proteins directly involved in transcription in eukaryotes, and our current understanding on how they function. The following sections consist of a description of the Arabidopsis complement of genes and proteins involved in transcriptional control, in particular sequence-specific DNA-binding transcription factors and chromatin-related proteins. Transcriptional regulators often act in a combinatorial fashion, and this mode of action is reviewed in the context of Arabidopsis promoters and cis-regulatory sequences, and of protein-protein interactions. Finally, genome-wide functional analyses of transcription factors, the characterization of the Arabidopsis promoterome, and of the transcriptome by gene expression profiling experiments, are considered. The availability of the genome sequence of different prokaryotic and eukaryotic organisms has provided for new ways of searching for unity and diversity among biological systems, and given birth to the field of comparative genomics. Although the subject of this book is Arabidopsis, reference is made in this chapter to other eukaryotic organisms, in order to situate the Arabidopsis genome information in a broader biological context. Transcription machinery: concepts, components, and mechanismsIn eukaryotic organisms, regulation of gene expression proceeds ...

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Section: Transcription Factor Gene Content Of the Arabidopsis Genomementioning

confidence: 99%

Transcriptional Regulation: a Genomic Overview

Riechmann

2002

The Arabidopsis Book

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“…PLATZ family proteins are a novel class of plant-specific zincdependent DNA binding proteins and are classified as transcription factors (TFs) in plant TF databases (Nagano et al, 2001); however, none have yet been genetically characterized to regulate (H) No signal was seen when a 12-DAP kernel section was hybridized with a sense probe. NU, nucellus; En, endosperm; asterisk, embryo; SE, starchy endosperm; SA, subaleurone ; A, aleurone.…”

Section: Fl3 Binds Nonspecifically To A/t-rich Sequencesmentioning

confidence: 99%

“…PLATZ1 isolated from pea (Pisum sativum) binds nonspecifically to A/T-rich sequences and is believed to function in transcriptional repression (Nagano et al, 2001). To investigate the DNA element recognized by FL3, we performed a random binding site selection experiment.…”

Section: Fl3 Binds Nonspecifically To A/t-rich Sequencesmentioning

confidence: 99%

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The Maize Imprinted Gene Floury3 Encodes a PLATZ Protein Required for tRNA and 5S rRNA Transcription through Interaction with RNA Polymerase III

Wang

et al. 2017

Plant Cell

118

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Maize (Zea mays) floury3 (fl3) is a classic semidominant negative mutant that exhibits severe defects in the endosperm but fl3 plants otherwise appear normal. We cloned the fl3 gene and determined that it encodes a PLATZ (plant AT-rich sequence and zinc binding) protein. The mutation in fl3 resulted in an Asn-to-His replacement in the conserved PLATZ domain, creating a dominant allele. Fl3 is specifically expressed in starchy endosperm cells and regulated by genomic imprinting, which leads to the suppressed expression of fl3 when transmitted through the male, perhaps as a consequence the semidominant behavior. Yeast two-hybrid screening and bimolecular luciferase complementation experiments revealed that FL3 interacts with the RNA polymerase III subunit 53 (RPC53) and transcription factor class C 1 (TFC1), two critical factors of the RNA polymerase III (RNAPIII) transcription complex. In the fl3 endosperm, the levels of many tRNAs and 5S rRNA that are transcribed by RNAPIII are significantly reduced, suggesting that the incorrectly folded fl3 protein may impair the function of RNAPIII. The transcriptome is dramatically altered in fl3 mutants, in which the downregulated genes are primarily enriched in pathways related to translation, ribosome, misfolded protein responses, and nutrient reservoir activity. Collectively, these changes may lead to defects in endosperm development and storage reserve filling in fl3 seeds.

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“…Plant-specific transcription factors play diverse and vital roles in the process of plant development (Kusano et al 1995;Nagano et al 2001;Singh et al 2002). NAC domain proteins have been identified as a novel class of transcriptional regulators recently.…”

Section: Introductionmentioning

confidence: 99%

Molecular Cloning and Characterization of a NAC-like Gene in “Navel” Orange Fruit Response to Postharvest Stresses

et al. 2007

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A cDNA subtraction library had been constructed to identify differentially expressed genes in peel pitting of citrus fruit. Based on the sequence of a cDNA fragment homologous to NAC gene family, the full-length cDNA of 1,203 nucleotides was cloned from "navel" orange by rapid amplification of cDNA ends. It was designated as CsNAC, encoding a protein of 305 amino acids. The calculated molecular weight of the CsNAC protein was 35.2 kDa, and theoretical isoelectric point was 6.72. Sequence comparison showed that the CsNAC protein had a strikingly conserved region at the N terminus, which is considered as the characteristic of the NAC protein family. CsNAC protein was orthologous to Arabidopsis thaliana ATAF1. Phylogenetic analysis confirmed CsNAC belonged to the ATAF subfamily, which plays an important role in response to stress stimuli. RNA gel blot analysis showed that the expression of CsNAC gene was rapidly and strongly induced by stresses such as wounding and no oxygen. Low temperature (4°C) and exposure to ethylene also increased the expression level of CsNAC gene. However, its expression was suppressed by high temperature (40°C) but not affected by low oxygen (3%). Our results may provide the basis for future research of NAC-like gene's role in stress-induced citrus peel pitting.

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A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences

Cited by 82 publications

References 23 publications

Transcriptional Regulation: a Genomic Overview

Transcriptional Regulation: a Genomic Overview

The Maize Imprinted Gene Floury3 Encodes a PLATZ Protein Required for tRNA and 5S rRNA Transcription through Interaction with RNA Polymerase III

Molecular Cloning and Characterization of a NAC-like Gene in “Navel” Orange Fruit Response to Postharvest Stresses

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