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Transcription Factors in Plant Gene Expression Regulation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 525

Special Issue Editor


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Guest Editor
Department of Biology and Pharmaceutical Botany, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland
Interests: medicinal plant molecular biology; medicinal plant genetics; promoter structure and function; plant secondary metabolites; protein homology modeling

Special Issue Information

Dear Colleagues,

Plant transcription factors play a decisive role in the regulation of gene expression. Their interactions with promoter and enhancer regions are pivotal for the building of the RNA polymerase preinitiation complex. The activation and degradation of plant trans-factors are precisely regulated by post-translational modifications in response to diverse events occurring within plant cells or outside of the plant body as biotic or abiotic stress factors. The plant trans-factors interact with oligo DNA sequences known as cis-active elements. Although the position weight matrices for plant cis-active elements are characterized in plentiful databases, the binding of trans-factors in in vivo conditions is dependent on interactions that are often imperfect, weak, and protein- or DNA modification-dependent. Numerous trans-factors require to undergo dimerization or oligomerization to achieve their active state, adding another control stratum to gene expression regulation. Building functional dimers or oligomers of trans-factors may be dependent on the closely localized cis-elements confined within the promoter sequence. Usually, cis-active elements that are important for gene regulation are not distributed statistically but concentrated within evolutionary conserved promoter fragments known as modules. Original research and reviews articles from experts in the field are welcome.

Dr. Piotr Szymczyk
Guest Editor

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Keywords

  • plant trans-factor
  • cis-active sequence
  • post-translational modification
  • dimerization and oligomerization
  • DNA modules

Published Papers (1 paper)

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Research

17 pages, 3480 KiB  
Article
Evolutionary Conservation in Protein–Protein Interactions and Structures of the Elongator Sub-Complex ELP456 from Arabidopsis and Yeast
by Sang Eun Jun, Kiu-Hyung Cho, Raffael Schaffrath and Gyung-Tae Kim
Int. J. Mol. Sci. 2024, 25(8), 4370; https://doi.org/10.3390/ijms25084370 - 15 Apr 2024
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Abstract
The Elongator complex plays a pivotal role in the wobble uridine modification of the tRNA anticodon. Comprising two sets of six distinct subunits, namely, Elongator proteins (ELP1-ELP6) and associated proteins, the holo-Elongator complex demonstrates remarkable functional and structural conservation across eukaryotes. However, the [...] Read more.
The Elongator complex plays a pivotal role in the wobble uridine modification of the tRNA anticodon. Comprising two sets of six distinct subunits, namely, Elongator proteins (ELP1-ELP6) and associated proteins, the holo-Elongator complex demonstrates remarkable functional and structural conservation across eukaryotes. However, the precise details of the evolutionary conservation of the holo-Elongator complex and its individual sub-complexes (i.e., ELP123; ELP456) in plants remain limited. In this study, we conducted an in vivo analysis of protein–protein interactions among Arabidopsis ELP4, ELP5, and ELP6 proteins. Additionally, we predicted their structural configurations and performed a comparative analysis with the structure of the yeast Elp456 sub-complex. Protein–protein interaction analysis revealed that AtELP4 interacts with AtELP6 but not directly with AtELP5. Furthermore, we found that the Arabidopsis Elongator-associated protein, Deformed Roots and Leaves 1 (DRL1), did not directly bind to AtELP proteins. The structural comparison of the ELP456 sub-complex between Arabidopsis and yeast demonstrated high similarity, encompassing the RecA-ATPase fold and the positions of hydrogen bonds, despite their relatively low sequence homology. Our findings suggest that Arabidopsis ELP4, ELP5, and ELP6 proteins form a heterotrimer, with ELP6 serving as a bridge, indicating high structural conservation between the ELP456 sub-complexes from Arabidopsis and yeast. Full article
(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation)
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