scholarly journals Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
M. S. Krasnikova ◽  
I. A. Milyutina ◽  
V. K. Bobrova ◽  
L. V. Ozerova ◽  
A. V. Troitsky ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Experimental Approach ◽  
Single Copy ◽  
Small Interfering Rnas ◽  
Database Analysis ◽  
Plant Genomes ◽  
Target Sites ◽  
Number Of Genes ◽  
Conservation Pattern

TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor inArabidopsis thalianais controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the5′-terminal miR390 target site.

scholarly journals Interactions among Plant Transcription Factors Regulating Expression of Stress-responsive Genes

2014 ◽  
Vol 8 ◽  
pp. BBI.S16313 ◽  
Author(s):  
Sony Malhotra ◽  
R. Sowdhamini
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Molecular Docking ◽  
Stress Responses ◽  
Binding Sites ◽  
Spatial Proximity ◽  
Number Of Genes ◽  
Stress Responsive Genes ◽  
Interface Parameters ◽  
Plant Arabidopsis Thaliana

Plants are simultaneously subjected to a variety of stress conditions in the field and are known to combat the hostile conditions by up/downregulating number of genes. There exists a significant level of cross-talk between different stress responses in plants. In this study, we predict the interacting pairs of transcription factors that regulate the multiple abiotic stress-responsive genes in the plant Arabidopsis thaliana. We identified the interacting pair(s) of transcription factors (TFs) based on the spatial proximity of their binding sites. We also examined the interactions between the predicted pairs of TFs using molecular docking. Subsequent to docking, the best interaction pose was selected using our scoring scheme DockScore, which ranks the docked solutions based on several interface parameters and aims to find optimal interactions between proteins. We analyzed the selected docked pose for the interface residues and their conservation.

Identification of a single-copy gene encoding a Type I chlorophyll a/b-binding polypeptide of photosystem I in Arabidopsis thaliana

1992 ◽  
Vol 84 (4) ◽  
pp. 561-567 ◽  
Author(s):  
Poul E. Jensen ◽  
Michael Kristensen ◽  
Tine Hoff ◽  
Jan Lehmbeck ◽  
Bjarne M. Stummann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Chlorophyll A ◽  
Photosystem I ◽  
Single Copy ◽  
Type I ◽  
Single Copy Gene ◽  
Gene Encoding ◽  
Copy Gene

IRON MAN interacts with BRUTUS to maintain iron homeostasis in Arabidopsis

2021 ◽  
Vol 118 (39) ◽  
pp. e2109063118
Author(s):  
Yang Li ◽  
Cheng Kai Lu ◽  
Chen Yang Li ◽  
Ri Hua Lei ◽  
Meng Na Pu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Iron Homeostasis ◽  
Fe Deficiency ◽  
Small Peptides ◽  
Interaction Domain ◽  
C Terminus ◽  
Positive Regulators ◽  
Fe Homeostasis ◽  
And Function

IRON MAN (IMA) peptides, a family of small peptides, control iron (Fe) transport in plants, but their roles in Fe signaling remain unclear. BRUTUS (BTS) is a potential Fe sensor that negatively regulates Fe homeostasis by promoting the ubiquitin-mediated degradation of bHLH105 and bHLH115, two positive regulators of the Fe deficiency response. Here, we show that IMA peptides interact with BTS. The C-terminal parts of IMA peptides contain a conserved BTS interaction domain (BID) that is responsible for their interaction with the C terminus of BTS. Arabidopsis thaliana plants constitutively expressing IMA genes phenocopy the bts-2 mutant. Moreover, IMA peptides are ubiquitinated and degraded by BTS. bHLH105 and bHLH115 also share a BID, which accounts for their interaction with BTS. IMA peptides compete with bHLH105/bHLH115 for interaction with BTS, thereby inhibiting the degradation of these transcription factors by BTS. Genetic analyses suggest that bHLH105/bHLH115 and IMA3 have additive roles and function downstream of BTS. Moreover, the transcription of both BTS and IMA3 is activated directly by bHLH105 and bHLH115 under Fe-deficient conditions. Our findings provide a conceptual framework for understanding the regulation of Fe homeostasis: IMA peptides protect bHLH105/bHLH115 from degradation by sequestering BTS, thereby activating the Fe deficiency response.

scholarly journals Genome wide analysis of stress responsive WRKY transcription factors in Arabidopsis thaliana

2016 ◽  
Vol 4 (4) ◽  
pp. 279 ◽  
Author(s):  
Shaiq Sultan ◽  
Muhammad Amjid Ali ◽  
Rana Muhammad Atif ◽  
Farrukh Azeem ◽  
Habibullah Nadeem ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Chromosomal Localization ◽  
Evolutionary Relationship ◽  
Wrky Transcription Factors ◽  
Specific Sequence ◽  
Multiple Sequence ◽  
Genome Wide Analysis ◽  
Functional Homology ◽  
Genome Wide

WRKY transcription factors are a class of DNA-binding proteins that bind with a specific sequence C/TTGACT/C known as W-Box found in promoters of genes which are regulated by these WRKYs. From previous studies, 43 different stress responsive WRKY transcription factors in Arabidopsis thaliana, identified and then categorized in three groups viz., abiotic, biotic and both of these stresses. A comprehensive genome wide analysis including chromosomal localization, gene structure analysis, multiple sequence alignment, phylogenetic analysis and promoter analysis of these WRKY genes was carried out in this study to determine the functional homology in Arabidopsis. This analysis led to the classification of these WRKY family members into 3 major groups and subgroups and showed evolutionary relationship among these groups on the base of their functional WRKY domain, chromosomal localization and intron/exon structure. The proposed groups of these stress responsive WRKY genes and annotation based on their position on chromosomes can also be explored to determine their functional homology in other plant species in relation to different stresses. The result of the present study provides indispensable genomic information for the stress responsive WRKY transcription factors in Arabidopsis and will pave the way to explain the precise role of various AtWRKYs in plant growth and development under stressed conditions.

WRKY transcription factors down-regulate the expression of H 2 S-generating genes, LCD and DES in Arabidopsis thaliana

2015 ◽  
Vol 60 (11) ◽  
pp. 995-1001 ◽  
Author(s):  
Zhiqiang Liu ◽  
Huihui Fang ◽  
Yanxi Pei ◽  
Zhuping Jin ◽  
Liping Zhang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Wrky Transcription Factors

Unravelling the role of DRIF transcription factors in Arabidopsis thaliana

2018 ◽  
Vol 120 ◽  
pp. S116
Author(s):  
Ana Maria Cunha ◽  
Sara Laranjeira ◽  
Shweta Singh ◽  
João Raimundo ◽  
Rómulo Sobral ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors

DREB2 Family Transcription Factors Promote the Expression of Phytocystatin1 in Arabidopsis thaliana During Seed Germination

2020 ◽  
Author(s):  
Taeyoon Kim ◽  
Trang Thi Nguyen ◽  
Juwan Baek ◽  
Young Hun Song ◽  
Jong Chan Hong ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Seed Germination
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