Sepallata 3

Background Information

Other names: SEP3, AGAMOUS-LIKE 9, AGL9
Locus: AT1G24260

genomic sequence
protein sequence

Using a reverse genetics approach I will use the bioinformatics databases available online to find information on the genetic and structural basis of SEP3

Functional Predictions

Yanofsky et.al. 2000 shows that SEPALLATA3 (SEP3) has been shown to bind to SEPALLATA1 and SEPALLATA2, and binds to the CArG box (CC [A/T]6 GG) motif. SEP3 is redundant with SEP1 and 2 and flowers of SEP1/2/3 triple mutants show a conversion of petals and stamens to sepals. This suggests that SEP1, 2 and 3 act together to ensure proper development of petals, stamens and carpels and to prevent the indeterminate growth of the flower meristem.

InterPro predicts that SEPALLATA3 (SEP3) contains a MADs box and a K-box transcription factor and the associated GO terms suggest that SEP3 is capable of DNA binding and localises to the nucleus.

Building a Genetic Tree

NCBI BLAST searches of both the genomic and protein sequence of SEP3 returned the following results: nBLAST, pBLAST. The Mobyle portal was used to produce a Clustral Multiple Sequence Alignment for the genomic sequence and for the protein sequence. The Archaeopteryx plugin was used to produce a genetic tree for each.
Amino Acid Sequence Tree

Protein Sequence Tree

Gene Structure

GENSCAN (left) predicts that the SEP3 genomic sequence will produce the following. When the predicted protein is used in a BLAST search the SEP3 protein is the first hit. However whilst the identity is 100%, the coverage is only 80% as the first 17 predicted amino acids are not present in the real protein. Augustus (right) correctly predicts the protein sequence of SEP3.


The gene model Augustus builds also fits well with what is know about the exon/intron patters of SEP3. Here is the gene structure produced by Augustus and below is the structure of SEP3 as shown on the Tair database

Motifs

xxMotif was used to search the genomic secuence of SEP3 for motifs. Here is the full readout of SEP3 motifs found by xxMotif. However, the most common motif is .
The diagram below shows how the motif is distributed within the gene.

Protein Structure

The protein prediction database UniProt shows that SEP3 has two helical structures separated by a turn. The two helicies sit roughly a right angles to each other.

ExPASy's Swiss Model


The Protein Data Bank has a crystal structure for a homotetramer of SEP3 that was produced by Zubieta et.al. 2014. Here is the cartoon model as well as a ball and stick model.

Genetic Variation

The NCBI SNP database was used to discover all the reported single nucleotide polymorphisms within SEP3. It can be seen that the SNP at position 165 would result in the incorporation of a threonine rather than an alanine.
sep3_snps.jpg

b2gof15/students/sepottin/final_project.txt · Last modified: 2015/11/02 22:37 by sepottin
 
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