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Transcription Factors in Plant Gene Expression Regulation
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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: 20 February 2025 | Viewed by 4780

Special Issue Editor

Dr. Piotr Szymczyk

E-Mail Website
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

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Published Papers (5 papers)

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Research

16 pages, 14657 KiB  
Article
Genome-Wide Identification and Role of the bHLH Gene Family in Dendrocalamus latiflorus Flowering Regulation
by Mei-Yin Zeng, Peng-Kai Zhu, Yu Tang, Yu-Han Lin, Tian-You He, Jun-Dong Rong, Yu-Shan Zheng and Ling-Yan Chen
Int. J. Mol. Sci. 2024, 25(19), 10837; https://doi.org/10.3390/ijms251910837 - 9 Oct 2024
Viewed by 382
Abstract
The basic helix–loop–helix (bHLH) gene family is a crucial regulator in plants, orchestrating various developmental processes, particularly flower formation, and mediating responses to hormonal signals. The molecular mechanism of bamboo flowering regulation remains unresolved, limiting bamboo breeding efforts. In this study, [...] Read more.
The basic helix–loop–helix (bHLH) gene family is a crucial regulator in plants, orchestrating various developmental processes, particularly flower formation, and mediating responses to hormonal signals. The molecular mechanism of bamboo flowering regulation remains unresolved, limiting bamboo breeding efforts. In this study, we identified 309 bHLH genes and divided them into 23 subfamilies. Structural analysis revealed that proteins in specific DlbHLH subfamilies are highly conserved. Collinearity analysis indicates that the amplification of the DlbHLH gene family primarily occurs through segmental duplications. The structural diversity of these duplicated genes may account for their functional variability. Many DlbHLHs are expressed during flower development, indicating the bHLH gene’s significant role in this process. In the promoter region of DlbHLHs, different homeopathic elements involved in light response and hormone response co-exist, indicating that DlbHLHs are related to the regulation of the flower development of D. latiflorus. Full article
(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation)
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19 pages, 5162 KiB  
Article
The AtMINPP Gene, Encoding a Multiple Inositol Polyphosphate Phosphatase, Coordinates a Novel Crosstalk between Phytic Acid Metabolism and Ethylene Signal Transduction in Leaf Senescence
by Xiaoyun Peng, Haiou Li, Wenzhong Xu, Qian Yang, Dongming Li, Tingting Fan, Bin Li, Junhui Ding, Wenzhen Ku, Danyi Deng, Feiying Zhu, Langtao Xiao and Ruozhong Wang
Int. J. Mol. Sci. 2024, 25(16), 8969; https://doi.org/10.3390/ijms25168969 - 17 Aug 2024
Viewed by 721
Abstract
Plant senescence is a highly coordinated process that is intricately regulated by numerous endogenous and environmental signals. The involvement of phytic acid in various cell signaling and plant processes has been recognized, but the specific roles of phytic acid metabolism in Arabidopsis leaf [...] Read more.
Plant senescence is a highly coordinated process that is intricately regulated by numerous endogenous and environmental signals. The involvement of phytic acid in various cell signaling and plant processes has been recognized, but the specific roles of phytic acid metabolism in Arabidopsis leaf senescence remain unclear. Here, we demonstrate that in Arabidopsis thaliana the multiple inositol phosphate phosphatase (AtMINPP) gene, encoding an enzyme with phytase activity, plays a crucial role in regulating leaf senescence by coordinating the ethylene signal transduction pathway. Through overexpressing AtMINPP (AtMINPP–OE), we observed early leaf senescence and reduced chlorophyll contents. Conversely, a loss-of-function heterozygous mutant (atminpp/+) exhibited the opposite phenotype. Correspondingly, the expression of senescence-associated genes (SAGs) was significantly upregulated in AtMINPP–OE but markedly decreased in atminpp/+. Yeast one-hybrid and chromatin immunoprecipitation assays indicated that the EIN3 transcription factor directly binds to the promoter of AtMINPP. Genetic analysis further revealed that AtMINPP–OE could accelerate the senescence of ein3–1eil1–3 mutants. These findings elucidate the mechanism by which AtMINPP regulates ethylene-induced leaf senescence in Arabidopsis, providing insights into the genetic manipulation of leaf senescence and plant growth. Full article
(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation)
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13 pages, 16054 KiB  
Article
Expression of Iron Metabolism Genes Is Potentially Regulated by DOF Transcription Factors in Dendrocalamus latiflorus Leaves
by Peng-Kai Zhu, Mei-Xia Lin, Mei-Yin Zeng, Yu Tang, Xin-Rui Li, Tian-You He, Yu-Shan Zheng and Ling-Yan Chen
Int. J. Mol. Sci. 2024, 25(15), 8114; https://doi.org/10.3390/ijms25158114 - 25 Jul 2024
Viewed by 676
Abstract
Transcription factors (TFs) are crucial pre-transcriptional regulatory mechanisms that can modulate the expression of downstream genes by binding to their promoter regions. DOF (DNA binding with One Finger) proteins are a unique class of TFs with extensive roles in plant growth and development. [...] Read more.
Transcription factors (TFs) are crucial pre-transcriptional regulatory mechanisms that can modulate the expression of downstream genes by binding to their promoter regions. DOF (DNA binding with One Finger) proteins are a unique class of TFs with extensive roles in plant growth and development. Our previous research indicated that iron content varies among bamboo leaves of different colors. However, to our knowledge, genes related to iron metabolism pathways in bamboo species have not yet been studied. Therefore, in the current study, we identified iron metabolism related (IMR) genes in bamboo and determined the TFs that significantly influence them. Among these, DOFs were found to have widespread effects and potentially significant impacts on their expression. We identified specific DOF members in Dendrocalamus latiflorus with binding abilities through homology with Arabidopsis DOF proteins, and established connections between some of these members and IMR genes using RNA-seq data. Additionally, molecular docking confirmed the binding interactions between these DlDOFs and the DOF binding sites in the promoter regions of IMR genes. The co-expression relationship between the two gene sets was further validated using q-PCR experiments. This study paves the way for research into iron metabolism pathways in bamboo and lays the foundation for understanding the role of DOF TFs in D. latiflorus. Full article
(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation)
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17 pages, 5106 KiB  
Article
The Characterization of a Novel PrMADS11 Transcription Factor from Pinus radiata Induced Early in Bent Pine Stem
by Tamara Méndez, Joselin Guajardo, Nicolás Cruz, Rodrigo A. Gutiérrez, Lorena Norambuena, Andrea Vega, María A. Moya-León and Raúl Herrera
Int. J. Mol. Sci. 2024, 25(13), 7245; https://doi.org/10.3390/ijms25137245 - 30 Jun 2024
Viewed by 1028
Abstract
A novel MADS-box transcription factor from Pinus radiata D. Don was characterized. PrMADS11 encodes a protein of 165 amino acids for a MADS-box transcription factor belonging to group II, related to the MIKC protein structure. PrMADS11 was differentially expressed in the stems of [...] Read more.
A novel MADS-box transcription factor from Pinus radiata D. Don was characterized. PrMADS11 encodes a protein of 165 amino acids for a MADS-box transcription factor belonging to group II, related to the MIKC protein structure. PrMADS11 was differentially expressed in the stems of pine trees in response to 45° inclination at early times (1 h). Arabidopsis thaliana was stably transformed with a 35S::PrMADS11 construct in an effort to identify the putative targets of PrMADS11. A massive transcriptome analysis revealed 947 differentially expressed genes: 498 genes were up-regulated, and 449 genes were down-regulated due to the over-expression of PrMADS11. The gene ontology analysis highlighted a cell wall remodeling function among the differentially expressed genes, suggesting the active participation of cell wall modification required during the response to vertical stem loss. In addition, the phenylpropanoid pathway was also indicated as a PrMADS11 target, displaying a marked increment in the expression of the genes driven to the biosynthesis of monolignols. The EMSA assays confirmed that PrMADS11 interacts with CArG-box sequences. This TF modulates the gene expression of several molecular pathways, including other TFs, as well as the genes involved in cell wall remodeling. The increment in the lignin content and the genes involved in cell wall dynamics could be an indication of the key role of PrMADS11 in the response to trunk inclination. Full article
(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation)
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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
Viewed by 857
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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