Control of Arabidopsis Leaf Morphogenesis Through Regulation of the <i>YABBY</i> and <i>KNOX</i> Families of Transcription Factors

Ha, Chan Man; Jun, Ji Hyung; Fletcher, Jennifer

doi:10.1534/genetics.110.118703

Cited by 49 publications

(53 citation statements)

References 39 publications

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“…The ankyrin repeat is a very common protein–protein interaction motif in nature and occurs in a large number of functionally diverse proteins. The results agree with previous studies that showed this gene interacts with other genes to control leaf and/or flower development 47–49…”

Section: Resultssupporting

confidence: 93%

Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

et al. 2012

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Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non-DNA-binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes with unknown functions are found to be DNA-binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA-binding and regulatory functions from structural perspective. All structural models of TFs are deposited in the online database for public usage at http://sysbio.unl.edu/AthTF.

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Section: Resultssupporting

confidence: 93%

Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

et al. 2012

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“…Given that pan loss-of-function did not reproduce the RIM- phenotype (Figure 5a) other genes, perhaps TGAs , are involved in this phenotype, as shown for SA perception [23]. Given that BOPs play both positive and negative roles in transcriptional regulation of the KNOX (Knotted1-like homeobox) gene KNAT6 [46], we also tested if RIM was affected by knat6 loss-of-function, but again, no difference was observed (Figure 5a). This may reflect redundancy with other KNOX genes, or more likely, that BOP regulation of RIM is independent of KNAT6.…”

Section: Discussionmentioning

confidence: 99%

The BLADE-ON-PETIOLE genes of Arabidopsis are essential for resistance induced by methyl jasmonate

Canet

Dobón

Fajmonová³

et al. 2012

BMC Plant Biol

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BackgroundNPR1 is a gene of Arabidopsis thaliana required for the perception of salicylic acid. This perception triggers a defense response and negatively regulates the perception of jasmonates. Surprisingly, the application of methyl jasmonate also induces resistance, and NPR1 is also suspected to be relevant. Since an allelic series of npr1 was recently described, the behavior of these alleles was tested in response to methyl jasmonate.ResultsThe response to methyl jasmonate of different npr1s alleles and NPR1 paralogs null mutants was measured by the growth of a pathogen. We have also tested the subcellular localization of some npr1s, along with the protein-protein interactions that can be measured in yeast. The localization of the protein in npr1 alleles does not affect the response to methyl jasmonate. In fact, NPR1 is not required. The genes that are required in a redundant fashion are the BOPs. The BOPs are paralogs of NPR1, and they physically interact with the TGA family of transcription factors.ConclusionsSome npr1 alleles have a phenotype in this response likely because they are affecting the interaction between BOPs and TGAs, and these two families of proteins are responsible for the resistance induced by methyl jasmonate in wild type plants.

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“…This situation is the case for the C2H2 Zn-Finger encoding gene JAGGED (JAG; Dinneny et al, 2004;Ohno et al, 2004), and for the closely related YABBY1 (YAB1) group genes FILAMENTOUS FLOWER (FIL, Chen et al, 1999;Sawa et al, 1999) and YABBY3 (YAB3, Siegfried et al, 1999). These genes were identified initially for their roles in repressing meristematic activities in lateral organ primordia and for controlling abaxial-adaxial polarity of the leaf (Chen et al, 1999;Sawa et al, 1999;Siegfried et al, 1999;Kumaran et al, 2002;Dinneny et al, 2004;Ohno et al, 2004;Ha et al, 2010). Most recently, it has been proposed that along the medio-lateral axis of the ovary, JAG, FIL and YAB3 act redundantly in a gradient of activity (known as JAG/FIL activity) to promote valve and valve margin formation (Dinneny et al, 2005;Alonso-Cantabrana et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…In addition to its role in the replum, RPL has been also shown to regulate meristem maintenance of the SAM by interacting genetically and molecularly with members of the class I KNOX, including BP and SHOOTMERISTEM-LESS (STM, Endrizzi et al, 1996;Long et al, 1996;Byrne et al, 2003;Smith and Hake, 2003;Bhatt et al, 2004;Smith et al, 2004;Cole et al, 2006;Kanrar et al, 2006;Scofield et al, 2007;Rutjens et al, 2009). However, members of the JAG/FIL activity act antagonistically to meristematic genes including BP (Kumaran et al, 2002;Ha et al, 2010). Similarly in the fruit, JAG/FIL genes negatively regulate the expression of RPL and BP (Dinneny et al, 2004;Alonso-Cantabrana et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit

et al. 2012

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SUMMARYThe Arabidopsis fruit forms a seedpod that develops from the fertilized gynoecium. It is mainly comprised of an ovary in which three distinct tissues can be differentiated: the valves, the valve margins and the replum. Separation of cells at the valve margin allows for the valves to detach from the replum and thus dispersal of the seeds. Valves and valve margins are located in lateral positions whereas the replum is positioned medially and retains meristematic properties resembling the shoot apical meristem (SAM). Members of the WUSCHEL-related homeobox family have been involved in stem cell maintenance in the SAM, and within this family, we found that WOX13 is expressed mainly in meristematic tissues including the replum. We also show that wox13 loss-of-function mutations reduce replum size and enhance the phenotypes of mutants affected in the replum identity gene RPL. Conversely, misexpression of WOX13 produces, independently from BP and RPL, an oversized replum and valve defects that closely resemble those of mutants in JAG/FIL activity genes. Our results suggest that WOX13 promotes replum development by likely preventing the activity of the JAG/FIL genes in medial tissues. This regulation seems to play a role in establishing the gradient of JAG/FIL activity along the medio-lateral axis of the fruit critical for proper patterning. Our data have allowed us to incorporate the role of WOX13 into the regulatory network that orchestrates fruit patterning.

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Control of Arabidopsis Leaf Morphogenesis Through Regulation of the YABBY and KNOX Families of Transcription Factors

Cited by 49 publications

References 39 publications

Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

The BLADE-ON-PETIOLE genes of Arabidopsis are essential for resistance induced by methyl jasmonate

The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit

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