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      Functional studies of plant transcription factors and their relevance in the plant root-knot nematode interaction

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          Abstract

          Root-knot nematodes are polyphagous parasitic nematodes that cause severe losses in the agriculture worldwide. They enter the root in the elongation zone and subtly migrate to the root meristem where they reach the vascular cylinder and establish a feeding site called gall. Inside the galls they induce a group of transfer cells that serve to nurture them along their parasitic stage, the giant cells. Galls and giant cells develop through a process of post-embryogenic organogenesis that involves manipulating different genetic regulatory networks within the cells, some of them through hijacking some molecular transducers of established plant developmental processes, such as lateral root formation or root regeneration. Galls/giant cells formation involves different mechanisms orchestrated by the nematode´s effectors that generate diverse plant responses in different plant tissues, some of them include sophisticated mechanisms to overcome plant defenses. Yet, the plant-nematode interaction is normally accompanied to dramatic transcriptomic changes within the galls and giant cells. It is therefore expected a key regulatory role of plant-transcription factors, coordinating both, the new organogenesis process induced by the RKNs and the plant response against the nematode. Knowing the role of plant-transcription factors participating in this process becomes essential for a clear understanding of the plant-RKNs interaction and provides an opportunity for the future development and design of directed control strategies. In this review, we present the existing knowledge of the TFs with a functional role in the plant-RKN interaction through a comprehensive analysis of current scientific literature and available transcriptomic data.

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          Genome-wide analysis of the ERF gene family in Arabidopsis and rice.

          Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.
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            MYB transcription factors in Arabidopsis.

            The MYB family of proteins is large, functionally diverse and represented in all eukaryotes. Most MYB proteins function as transcription factors with varying numbers of MYB domain repeats conferring their ability to bind DNA. In plants, the MYB family has selectively expanded, particularly through the large family of R2R3-MYB. Members of this family function in a variety of plant-specific processes, as evidenced by their extensive functional characterization in Arabidopsis (Arabidopsis thaliana). MYB proteins are key factors in regulatory networks controlling development, metabolism and responses to biotic and abiotic stresses. The elucidation of MYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general. Copyright © 2010 Elsevier Ltd. All rights reserved.
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              DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression.

              DRE/CRT is a cis-acting element that is involved in gene expression responsive to drought and low-temperature stress in higher plants. DREB1A/CBF3 and DREB2A are transcription factors that specifically bind to DRE/CRT in Arabidopsis. We precisely analyzed the DNA-binding specificity of DREBs. Both DREBs specifically bound to six nucleotides (A/GCCGAC) of DRE. However, these proteins had different binding specificities to the second or third nucleotides of DRE. Gel mobility shift assay using mutant DREB proteins showed that the two amino acids, valine and glutamic acid conserved in the ERF/AP2 domains, especially valine, have important roles in DNA-binding specificity. In the Arabidopsis genome, 145 DREB/ERF-related proteins are encoded. These proteins were classified into five groups-AP-2 subfamily, RAV subfamily, DREB subfamily, ERF subfamily, and others. The DREB subfamily included three novel DREB1A- and six DREB2A-related proteins. We analyzed expression of novel genes for these proteins and discuss their roles in stress-responsive gene expression.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/395720Role: Role: Role: Role: Role: Role: Role: Role: Role: Role:
                Role: Role: Role:
                URI : https://loop.frontiersin.org/people/126997Role: Role: Role: Role: Role: Role: Role: Role: Role: Role:
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                08 May 2024
                2024
                : 15
                : 1370532
                Affiliations
                [1] 1Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha , Toledo, Spain
                [2] 2Centro de Biotecnologia y Genomica de Plantas (CBGP), Universidad Politecnica de Madrid and Instituto de Investigacion y Tecnologia Agraria y Alimentaria-Consejo Superior de investigaciones Cientificas (UPM-INIA/CSIC) , Madrid, Spain
                Author notes

                Edited by: Andressa Machado, Agronema, Brazil

                Reviewed by: Muhammad Shahzad Anjam, Swedish University of Agricultural Sciences, Sweden

                Robert Malinowski, Polish Academy of Sciences, Poland

                *Correspondence: Carolina Escobar, carolina.escobar@ 123456uclm.es

                †These authors have contributed equally to this work

                Article
                10.3389/fpls.2024.1370532
                11113014
                38784063
                ae58e589-d69f-437f-ad7f-92339bd752d2
                Copyright © 2024 Domínguez-Figueroa, Gómez-Rojas and Escobar

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 14 January 2024
                : 10 April 2024
                Page count
                Figures: 2, Tables: 1, Equations: 0, References: 116, Pages: 20, Words: 9794
                Funding
                Funded by: Ministerio de Ciencia e Innovación , doi 10.13039/501100004837;
                Award ID: PID2019-105924RB-I00, PID2022-138989OB-I00, CPP2021-008347. 2022-2024
                Funded by: Junta de Comunidades de Castilla-La Mancha , doi 10.13039/501100011698;
                Award ID: SBPLY/17/180501/000287, SBPLY/21/180501/000033
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Spanish Government (PID2019-105924RB-I00 and PID2022-138989OB-I00, Ministerio de Ciencia e Innovacion, MCIN/AEI/10.13039/501100011033 FEDER, UE), CPP2021-008347. 2022-2024. MICIN/AEI/10.13039/501100011033 and by the European Union Next Generation EU/PRTR, by the Castilla-La Mancha Government (SBPLY/17/180501/000287; SBPLY/21/180501/000033), to CE. AG-R was a recipient of a grant from Plan Propio I+D+I of UCLM co-financed by FSE [2019/5964] and JD-F received funding from Ministerio de Universidades-European Union in the frame of NextGenerationEU RD 289/2021 (Universidad Politécnica de Madrid).
                Categories
                Plant Science
                Review
                Custom metadata
                Plant Pathogen Interactions

                Plant science & Botany
                plant-rkns interaction,galls,giant cells,transcription factors,new organogenesis,plant defense,plant-development

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