The r2r3-myb gene family in arabidopsis thaliana

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.

/pdf/genome-wide-analysis-of-the-erf-gene-family-in-arabidopsis-33fkj4btth.pdf

Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice

Elicitor signal transduction leading to production of plant secondary metabolites.

Many plants, including Arabidopsis, increase in freezing tolerance in response to low, nonfreezing temperatures, a phenomenon known as cold acclimation. Previous studies established that cold acclimation involves rapid expression of the CBF transcriptional activators (also known as DREB1 proteins) in response to low temperature followed by induction of the CBF regulon (CBF-targeted genes), which contributes to an increase in freezing tolerance. Here, we present the results of transcriptome-profiling experiments indicating the existence of multiple low-temperature regulatory pathways in addition to the CBF cold response pathway. The transcript levels of ∼8000 genes were determined at multiple times after plants were transferred from warm to cold temperature and in warm-grown plants that constitutively expressed CBF1, CBF2, or CBF3. A total of 306 genes were identified as being cold responsive, with transcripts for 218 genes increasing and those for 88 genes decreasing threefold or more at one or more time points during the 7-day experiment. These results indicate that extensive downregulation of gene expression occurs during cold acclimation. Of the cold-responsive genes, 48 encode known or putative transcription factors. Two of these, RAP2.1 and RAP2.6, were activated by CBF expression and thus presumably control subregulons of the CBF regulon. Transcriptome comparisons indicated that only 12% of the cold-responsive genes are certain members of the CBF regulon. Moreover, at least 28% of the cold-responsive genes were not regulated by the CBF transcription factors, including 15 encoding known or putative transcription factors, indicating that these cold-responsive genes are members of different low-temperature regulons. Significantly, CBF expression at warm temperatures repressed the expression of eight genes that also were downregulated by low temperature, indicating that in addition to gene induction, gene repression is likely to play an integral role in cold acclimation.

https://bioinformatics.cs.vt.edu/~easychair/FowlerThomashow_PlantCell_2002.pdf

Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway

Despite the recognition of H2O2 as a central signaling molecule in stress and wounding responses, pathogen defense, and regulation of cell cycle and cell death, little is known about how the H2O2 signal is perceived and transduced in plant cells We report here that H2O2 is a potent activator of mitogen-activated protein kinases (MAPKs) in Arabidopsis leaf cells Using epitope tagging and a protoplast transient expression assay, we show that H2O2 can activate a specific Arabidopsis mitogen-activated protein kinase kinase kinase, ANP1, which initiates a phosphorylation cascade involving two stress MAPKs, AtMPK3 and AtMPK6 Constitutively active ANP1 mimics the H2O2 effect and initiates the MAPK cascade that induces specific stress-responsive genes, but it blocks the action of auxin, a plant mitogen and growth hormone The latter observation provides a molecular link between oxidative stress and auxin signal transduction Finally, we show that transgenic tobacco plants that express a constitutively active tobacco ANP1 orthologue, NPK1, display enhanced tolerance to multiple environmental stress conditions without activating previously described drought, cold, and abscisic acid signaling pathways Thus, manipulation of key regulators of an oxidative stress signaling pathway, such as ANP1/NPK1, provides a strategy for engineering multiple stress tolerance that may greatly benefit agriculture

/pdf/functional-analysis-of-oxidative-stress-activated-mitogen-4fommzy9to.pdf

Functional analysis of oxidative stress-activated mitogen-activated protein kinase cascade in plants.

Transcription factors containing a conserved DNA-binding domain similar to that of the proto-oncogene c-myb have been identified in nearly all eukaryotes. MYB-related proteins from plants generally contain two related helix-turn-helix motifs, the R2 and R3 repeats. It was estimated that Arabidopsis thaliana contains more than 100 R2R3-MYB genes. The few cases where functional data are available suggest an important role of these genes in the regulation of secondary metabolism, the control of cell shape, disease resistance, and hormone responses. To determine the full regulatory potential of this large family of regulatory genes, a systematic search for the function of all genes of this family was initiated. Sequence data for more than 90 different A. thaliana R2R3-MYB genes have been obtained. Sequence comparison revealed conserved amino acid motifs shared by subgroups of R2R3-MYB genes in addition to the characteristic DNA-binding domain. No significant clustering of the genes was detected, although they are not uniformly distributed throughout the A. thaliana genome.

Towards functional characterisation of the members of the R2R3‐MYB gene family from Arabidopsis thaliana

Transcript levels of the Arabidopsis R2R3-AtMYB102 transcription factor gene, previously named AtM4, are rapidly induced by osmotic stress or abscisic acid (ABA) treatment. Reporter gene expression studies revealed that in addition, wounding is required for full induction of the gene. Histochemical analysis showed a local beta-glucuronidase induction around the wounding site, especially in veins. In ABA-treated plants, wounding-induced beta-glucuronidase activity could be mimicked by the wound signaling compound methyl jasmonate. In silico studies of the AtMYB102 promoter sequence and its close homolog AtMYB74 demonstrated several conserved putative stress regulatory elements such as an ABA-responsive element, its coupling element 1 (CE1), and a W box. Interestingly, further studies showed that the 5'-untranslated region is essential for the osmotic stress and wounding induced expression of the AtMYB102 gene. This 5'-untranslated region contains putative conserved regulatory elements such as a second W box and an overlapping MYB-binding element. These studies suggest that AtMYB102 expression depends on and integrates signals derived from both wounding and osmotic stress.

Integration of Wounding and Osmotic Stress Signals Determines the Expression of the AtMYB102 Transcription Factor Gene

More than 92 genes encoding MYB transcription factors of the R2R3 class have been described in Arabidopsis. The functions of a few members of this large gene family have been described, indicating important roles for R2R3 MYB transcription factors in the regulation of secondary metabolism, cell shape, and disease resistance, and in responses to growth regulators and stresses. For the majority of the genes in this family, however, little functional information is available. As the first step to characterizing these genes functionally, the sequences of >90 family members, and the map positions and expression profiles of >60 members, have been determined previously. An important second step in the functional analysis of the MYB family, through a process of reverse genetics that entails the isolation of insertion mutants, is described here. For this purpose, a variety of gene disruption resources has been used, including T-DNA-insertion populations and three distinct populations that harbor transposon insertions. We report the isolation of 47 insertions into 36 distinct MYB genes by screening a total of 73 genes. These defined insertion lines will provide the foundation for subsequent detailed functional analyses for the assignment of specific functions to individual members of the R2R3 MYB gene family.

http://www.plantcell.org/content/plantcell/11/10/1827.full.pdf

Function Search in a Large Transcription Factor Gene Family in Arabidopsis: Assessing the Potential of Reverse Genetics to Identify Insertional Mutations in R2R3 MYB Genes

In Arabidopsis thaliana the R2R3-MYB transcription factor family consists of over 100 members and is implicated in many biological processes, such as plant development, metabolism, senescence, and defense. The R2R3-MYB transcription factor gene AtMYB102 has been shown to respond to salt stress, ABA, JA, and wounding, suggesting that AtMYB102 plays a role in the response of plants to dehydration after wounding. Here, we studied the role of AtMYB102 in the response of A. thaliana to feeding by larvae of the white cabbage butterfly Pieris rapae. A. thaliana reporter lines expressing GUS under control of the AtMYB102 promoter revealed that AtMYB102 is expressed locally at the feeding sites of herbivore-damaged leaves, but not systemically in uninfested plant parts. Knockout AtMYB102 transposon-insertion mutant plants (myb102) allowed a faster development of P. rapae caterpillars than wild-type Col-0 plants. Moreover, the number of caterpillars that had developed into pupae within 14 days was significantly higher on myb102, indicating that in wild-type plants AtMYB102 contributes to basal resistance against P. rapae feeding. Microarray analysis of wild-type Col-0 and AtMYB102 overexpressing 35S::MYB102 plants revealed a large number of differentially expressed genes. Besides several defense-related genes, a relatively large number of genes is associated with cell wall modifications.

https://web.science.uu.nl/pmi/publications/PDF/2006/PSB-DeVos-2006.pdf

Marten Denekamp

Papers

Towards functional characterisation of the members of the R2R3‐MYB gene family from Arabidopsis thaliana

Integration of Wounding and Osmotic Stress Signals Determines the Expression of the AtMYB102 Transcription Factor Gene

Function Search in a Large Transcription Factor Gene Family in Arabidopsis: Assessing the Potential of Reverse Genetics to Identify Insertional Mutations in R2R3 MYB Genes

The Arabidopsis thaliana Transcription Factor AtMYB102 Functions in Defense Against the Insect Herbivore Pieris rapae.