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The ALOG domain defines a new family of plant-specific Transcription Factors acting during Arabidopsis flower development.

ABSTRACT: Analysis of the transcriptome of the reproductive meristems of Arabidopsis thaliana Col-0. We compared the transcriptome obtained from lsh1 lsh3 lsh4 triple mutant to a wild type control

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE247357 | GEO | 2024/02/06

REPOSITORIES: GEO

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The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

Project description:The ALOGs (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1) are Transcription Factors (TFs) from an evolutionarily conserved plant-specific family shown to play critical roles in meristem identity, inflorescence architecture and organ boundaries in diverse species from mosses to higher flowering plants. However, the DNA binding-specificity and molecular determinants of protein-DNA interactions of this family were uncharacterized. Using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato and rice. In order to determine the amino acids responsible for DNA-binding specificity, we solved the 2.1Å structure of the ALOG DNA binding domain in complex with its cognate DNA. The ALOG DBD is an all-alpha helical domain with a structural zinc ribbon insertion and an N-terminal disordered NLS. The NLS sequence forms an integral part of the DNA binding domain and contributes to direct base read-out. To define the function of a group of redundant ALOG proteins in the model plant Arabidopsis thaliana, we generated a series of alog mutants and uncovered their participation in a gene regulatory network involving the other floral regulators LEAFY, BLADE-ON-PETIOLE and PUCHI, all active in defining boundary regions between reproductive meristems and repressing bracts development. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in defining organ boundaries in Arabidopsis.

2024-02-06 | GSE235674 | GEO

The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

Project description:The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

| PRJNA986886 | ENA

The ALOG domain defines a new family of plant-specific Transcription Factors acting during Arabidopsis flower development.

Project description:The ALOG domain defines a new family of plant-specific Transcription Factors acting during Arabidopsis flower development.

| PRJNA1037151 | ENA

The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis.

Project description:APETALA2 (AP2) plays an important role in the control of Arabidopsis flower and seed development and encodes a putative transcription factor that is distinguished by a novel DNA binding motif referred to as the AP2 domain. In this study we show that the AP2 domain containing or RAP2 (related to AP2) family of proteins is encoded by a minimum of 12 genes in Arabidopsis. The RAP2 genes encode two classes of proteins, AP2-like and EREBP-like, that are defined by the number of AP2 domains in each polypeptide as well as by two sequence motifs referred to as the YRG and RAYD elements that are located within each AP2 domain. RAP2 genes are differentially expressed in flower, leaf, inflorescence stem, and root. Moreover, the expression of at least three RAP2 genes in vegetative tissues are controlled by AP2. Thus, unlike other floral homeotic genes, AP2 is active during both reproductive and vegetative development.

| S-EPMC21287 | biostudies-literature

The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.

Project description:The PWWP domain is a weakly conserved sequence motif found in > 60 eukaryotic proteins, including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids 223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a five-helix bundle. The two halves are packed against each other to form a single structural module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2 protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds DNA more strongly than Delta369, which lacks the PWWP domain.

| S-EPMC4035047 | biostudies-literature

The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice

Project description:Analysis of the transcriptome of the early developmental stages of the reproductive meristems of Oryza sativa ssp. Japonica cv Nipponbare. We compared the transcriptome obtained from osg1l2 single mutant to a wild type control

2023-05-31 | GSE227706 | GEO

The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the ?-tent fold.

Project description:Despite having caused one of the greatest medical catastrophies of the last century through its teratogenic side-effects, thalidomide continues to be an important agent in the treatment of leprosy and cancer. The protein cereblon, which forms an E3 ubiquitin ligase compex together with damaged DNA-binding protein 1 (DDB1) and cullin 4A, has been recently indentified as a primary target of thalidomide and its C-terminal part as responsible for binding thalidomide within a domain carrying several invariant cysteine and tryptophan residues. This domain, which we name CULT (cereblon domain of unknown activity, binding cellular ligands and thalidomide), is also found in a family of secreted proteins from animals and in a family of bacterial proteins occurring primarily in ?-proteobacteria. Its nearest relatives are yippee, a highly conserved eukaryotic protein of unknown function, and Mis18, a protein involved in the priming of centromeres for recruitment of CENP-A. Searches for distant homologs point to an evolutionary relationship of CULT, yippee, and Mis18 to proteins sharing a common fold, which consists of two four-stranded ?-meanders packing at a roughly right angle and coordinating a zinc ion at their apex. A ?-hairpin inserted into the first ?-meander extends across the bottom of the structure towards the C-terminal edge of the second ?-meander, with which it forms a cradle-shaped binding site that is topologically conserved in all members of this fold. We name this the ?-tent fold for the striking arrangement of its constituent ?-sheets. The fold has internal pseudosymmetry, raising the possibility that it arose by duplication of a subdomain-sized fragment.

| S-EPMC4287342 | biostudies-literature

Flower development

Project description:Wild type and mutanat Arabiposis plants grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0) Landsberg erecta (Ler) leafy-12 (lfy-12, in Col-0) constans-2 (co-2, in Ler) flowering locus T-2 (ft-2, in Ler) Time points: 0, 3, 5, and 7 days after shift to long days Keywords = flowering Keywords: time-course

2003-08-06 | GSE576 | GEO

Synchronization of flowering transition by the tomato TERMINATING FLOWER gene

Project description:We sequenced mRNA from late vegetative meristems of tomato mutant TERMINARING FLOWER as well as the wild type progenitor to see genome-wide expression changes affected by the mutation. Meristems from multiple plants at the same developmental stages were collected for both mutants and wild types. The meristems were pooled together for mRNA extractions. Two biological replicates for each genotypes were prepared for mRNA extraction and sequencing library construction.

2012-09-13 | E-GEOD-40854 | biostudies-arrayexpress

Characterization of a broad-specificity ?-glucanase acting on ?-(1,3)-, ?-(1,4)-, and ?-(1,6)-glucans that defines a new glycoside hydrolase family.

Project description:Here we report the cloning of the Pa_3_10940 gene from the coprophilic fungus Podospora anserina, which encodes a C-terminal family 1 carbohydrate binding module (CBM1) linked to a domain of unknown function. The function of the gene was investigated by expression of the full-length protein and a truncated derivative without the CBM1 domain in the yeast Pichia pastoris. Using a library of polysaccharides of different origins, we demonstrated that the full-length enzyme displays activity toward a broad range of ?-glucan polysaccharides, including laminarin, curdlan, pachyman, lichenan, pustulan, and cellulosic derivatives. Analysis of the products released from polysaccharides revealed that this ?-glucanase is an exo-acting enzyme on ?-(1,3)- and ?-(1,6)-linked glucan substrates and an endo-acting enzyme on ?-(1,4)-linked glucan substrates. Hydrolysis of short ?-(1,3), ?-(1,4), and ?-(1,3)/?-(1,4) gluco-oligosaccharides confirmed this striking feature and revealed that the enzyme performs in an exo-type mode on the nonreducing end of gluco-oligosaccharides. Excision of the CBM1 domain resulted in an inactive enzyme on all substrates tested. To our knowledge, this is the first report of an enzyme that displays bifunctional exo-?-(1,3)/(1,6) and endo-?-(1,4) activities toward beta-glucans and therefore cannot readily be assigned to existing Enzyme Commission groups. The amino acid sequence has high sequence identity to hypothetical proteins within the fungal taxa and thus defines a new family of glycoside hydrolases, the GH131 family.

| S-EPMC3502917 | biostudies-literature

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