Summary: Floricaula / Leafy protein SAM domain
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Leafy Edit Wikipedia article
LEAFY is involved in floral meristem identity.
LEAFY encodes a plant-specific transcription factor, is found in all land plants and in charophytes and one of its exons have been used extensively in phylogenetic work on spermatophytes. When the gene is overexpressed, the plant is less sensitive to environmental signals and flowers earlier.
The LEAFY protein has two conserved domains: the DNA binding domain, a Helix-Turn-Helix motif buried inside a unique 7-helix fold and a Sterile Alpha Motif. It binds DNA as a dimer and its binding site has been identified both in vivo and in vitro.
- Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM (1992). "LEAFY controls floral meristem identity in Arabidopsis". Cell. 69 (5): 843–859. doi:10.1016/0092-8674(92)90295-N. PMID 1350515.
- Sayou, Camille; Monniaux, Marie; Nanao, Max H.; Moyroud, Edwige; Brockington, Samuel F.; Thévenon, Emmanuel; Chahtane, Hicham; Warthmann, Norman; Melkonian, Michael (2014-02-07). "A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity". Science. 343 (6171): 645–648. doi:10.1126/science.1248229. ISSN 1095-9203. PMID 24436181.
- Peter M. Hollingsworth; Richard M. Bateman; R. J. Gornall (1999). Molecular Systematics and Plant Evolution. CRC Press. p. 242. ISBN 0-7484-0908-4.
- Weigel D, Nilsson O (1995). "A developmental switch sufficient for flower initiation in diverse plants". Nature. 377 (6549): 495–500. doi:10.1038/377495a0. PMID 7566146.
- Hamès, Cécile; Ptchelkine, Denis; Grimm, Clemens; Thevenon, Emmanuel; Moyroud, Edwige; Gérard, Francine; Martiel, Jean-Louis; Benlloch, Reyes; Parcy, François (2008-10-08). "Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins". The EMBO Journal. 27 (19): 2628–2637. doi:10.1038/emboj.2008.184. ISSN 1460-2075. PMC . PMID 18784751.
- Sayou, Camille; Nanao, Max H.; Jamin, Marc; Posé, David; Thévenon, Emmanuel; Grégoire, Laura; Tichtinsky, Gabrielle; Denay, Grégoire; Ott, Felix (2016-04-21). "A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor". Nature Communications. 7: 11222. doi:10.1038/ncomms11222. ISSN 2041-1723. PMC . PMID 27097556.
- Moyroud, Edwige; Minguet, Eugenio Gómez; Ott, Felix; Yant, Levi; Posé, David; Monniaux, Marie; Blanchet, Sandrine; Bastien, Olivier; Thévenon, Emmanuel (2011-04-01). "Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor". The Plant Cell. 23 (4): 1293–1306. doi:10.1105/tpc.111.083329. ISSN 1532-298X. PMC . PMID 21515819.
- Winter, Cara M.; Austin, Ryan S.; Blanvillain-Baufumé, Servane; Reback, Maxwell A.; Monniaux, Marie; Wu, Miin-Feng; Sang, Yi; Yamaguchi, Ayako; Yamaguchi, Nobutoshi (2011-04-19). "LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response". Developmental Cell. 20 (4): 430–443. doi:10.1016/j.devcel.2011.03.019. ISSN 1878-1551. PMID 21497757.
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Floricaula / Leafy protein SAM domain Provide feedback
This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species .
Sayou C, Nanao MH, Jamin M, Pose D, Thevenon E, Gregoire L, Tichtinsky G, Denay G, Ott F, Peirats Llobet M, Schmid M, Dumas R, Parcy F;, Nat Commun. 2016;7:11222.: A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor. PUBMED:27097556 EPMC:27097556
This tab holds annotation information from the InterPro database.
InterPro entry IPR035079
FLO and LFY proteins are floral meristem identity proteins [PUBMED:1350515, PUBMED:9259553]. Mutations in the sequences of these proteins affect flower and leaf development. LFY has been shown to bind semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DNA-binding domain (DBD). In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). Crystallographic structure determination shows that LFY-N is a sterile alpha motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFY-binding sites and to access closed chromatin regions. Experiments revealed that altering the capacity of LFY to oligomerize compromised floral function. It has been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species [PUBMED:27097556].
This entry represents a SAM domain found in various plant proteins which are homologues of floricaula (FLO) and Leafy (LFY).
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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SAM domains are found in a diverse set of proteins, which include scaffolding proteins, transcription regulators, translational regulators tyrosine kinases and serine/threonine kinases [1-3]. SAM domains are found in all eukaryotes and some bacteria  . Structures of SAM domains reveal a common five helical structure. The SAM domain is involved in a variety of functions. The most widespread function is in domain-domain interactions. The SAM domain performs domain-domain interactions using multifarious arrangements of the SAM domain. More recently, the SAM domain within the Smaug protein has been demonstrated to bind to the Nanos 3' UTR translation control element (Rfam:RF00161) . This clan currently only represents the diverse SAM domain family and does not contain the more divergent SAM/Pointed family (Pfam:PF02198).
The clan contains the following 12 members:IGR NCD1 SAM_1 SAM_2 SAM_3 SAM_4 SAM_DrpA SAM_Exu SAM_KSR1 SAM_LFY SAM_PNT SAM_Ste50p
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Seed source:||Pfam-B_1633 (release 4.1)|
|Previous IDs:||FLO_LFY; LFY_SAM;|
|Author:||Bashton M , Bateman A|
|Number in seed:||8|
|Number in full:||106|
|Average length of the domain:||79.00 aa|
|Average identity of full alignment:||64 %|
|Average coverage of the sequence by the domain:||20.31 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SAM_LFY domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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