Functional Modules in the Meristems: “Tinkering” in Action

Kuznetsova, Ksenia; Efremova, Elena; Dodueva, Irina; Lebedeva, Maria; Lutova, Ludmila

doi:10.3390/plants12203661

Cited by 3 publications

(3 citation statements)

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“…Meristem regulators are known to be involved in the control of the plant cell division plan, and have been shown to be involved in the development of numerous examples of plant tumours [ 4 ]. The balance between cell division and differentiation in various plant meristems is controlled by the WOX-CLAVATA system, a highly conserved regulatory module [ 21 ], consisting of CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides; the protein kinase receptors that bind CLEs; and the targets of CLE action, the WUSCHEL-RELATED HOMEOBOX (WOX) homeodomain transcription factors [ 22 , 23 , 24 ].…”

Section: Resultsmentioning

confidence: 99%

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Kuznetsova,

Dodueva,

Afonin

et al. 2024

IJMS

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Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

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Section: Resultsmentioning

confidence: 99%

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Kuznetsova,

Dodueva,

Afonin

et al. 2024

IJMS

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“…To search for probable candidate regulators of spontaneous tumour formation among genes containing selected SNVs in the line 19, we amplified the corresponding gene regions of several other tumour (12,13,14,16,20,21,32) and non-tumour (3, 5, 6, 8, 9, 23, 25, 26, 27, 28, 29, 30, 37, 39) lines of the radish genetic collection.…”

Section: Search For the Presence Of Identified Snvs In The Tumour And...mentioning

confidence: 99%

“…Meristem regulators are known to be involved in the control of the plant cell division plan, and they was shown to participate in the development of numerous examples of plant tumours [4]. The balance between cell division and differentiation in various plant meristems is under control of WOX-CLAVATA system, a highly conserved regulatory module [21], which consists of CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides, the protein kinase receptors that bind CLEs, and the targets of CLE action, the WUSCHEL-RELATED HOMEOBOX (WOX) homeodomain transcription factors [22][23][24].…”

Section: Identification and Chromosomal Localisation Of Wox And Cle G...mentioning

confidence: 99%

Whole Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Kuznetsova,

Dodueva,

Afonin

et al. 2024

Preprint

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Spontaneous tumours in higher plants can develop depending on plant genotype without any pathogen invasion. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this work, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We have identified numerous single nucleotide variants (amino acid substitutions, insertions or deletions) that are likely to be associated with the spontaneous tumour formation. Furthermore, we performed the identification of CLE and WOX genes the genomic sequences of the radish inbred lines and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

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The homeodomain of the Raphanus sativus WOX4 binds to the promoter of the LOG3 cytokinin biosynthesis gene

Kuznetsova,

Dodueva,

Lutova

2024

Ecological genetics

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Background The WOX4 transcription factor plays a crucial role in maintaining the organisation of cambium meristem during secondary growth, but its direct targets are unknown. The objectives of our work were to study the effect of WOX4 overexpression on the root development and gene expression in radish (Raphanus sativus L.), a root crop related to Arabidopsis thaliana, and to search for direct targets of the WOX4 in radish. Materials and methods Radish line 19 of the St. Petersburg State University radish genetic collection was used. Plants were grown on Murashige-Skoog medium and then in soil at 23оС and 16 h of daylight. Total DNA was extracted from radish seedlings using the CTAB method. The PCR-amplified full-length RsWOX4-2 gene, gene fragments or homeobox sequence were cloned into the vectors for overexpression (pB7WG2D), RNA interference (pH7GWIWG2) and yeast one-hybrid assay (pDEST22), respectively, using the Gateway system. The vectors for overexpression and RNA interference of RsWOX4-2 were transformed into Escherichia coli DH10B and then into Agrobacteium rhizogenes Arqua chemically competent cells. Radish seedlings were transformed transformation with A. rhizogenes containing vectors for overexpression and RNA interference of RsWOX4-2, and GUS-overexpressing A. rhizogenes was used as a control. Total RNA from transgenic radish roots was extracted with Trizol reagent. RNA reverse transcription was performed using dT-18 primers and RevertAid reverse transcriptase. qPCR was performed using the Eva Green reagent kit on a CFX96 thermocycler with fluorescence detection system. Results were processed using the 2-ΔΔCT method. Yeast transformation with competent Saccharomyces cerevisiae of Y2H Gold strain cells and yeast one-hybrid assay were performed as described in the article. The obtained yeast colonies transformed with plasmids containing TF homeodomain sequence and promoter regions of genes were grown on DDO and TDO selective media with different concentrations of 3-amino-1,2,4-triazole. Statistical processing based on Student's t-test and graphing were performed using the ggplot2 package for the R programming language (v.4.0.2). Results Overexpression of the RsWOX4-2 gene affects the structure of the radish root stele and alters the number of vessels and cambium cells. Overexpression and RNA interference of the RsWOX4-2 causes changes in the expression levels of putative target genes with the WOX family transcription factor conserved binding sites in their promoters. Using the yeast one-hybrid assay, we have shown that the DNA-binding homeodomain of RsWOX4-2 interacts with the TAATCC site in the promoter of the RsLOG3 gene, which encodes the enzyme for cytokinin biosynthesis. Conclusion We have demonstrated the effect of RsWOX4-2 overexpression on radish root stele and gene expression and identified the RsLOG3 as the putative direct target of the WOX4 transcription factor in radish.

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Functional Modules in the Meristems: “Tinkering” in Action

Cited by 3 publications

References 289 publications

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Whole Genome Sequencing and Analysis of Tumour-Forming Radish (<em>Raphanus sativus</em> L.) Line

The homeodomain of the <i>Raphanus sativus</i> WOX4 binds to the promoter of the <i>LOG3</i> cytokinin biosynthesis gene

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