Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily
Michael Allen, Amanda M. Hulse-Kemp, Amanda R. Storm [1]
Molecular Tour
Genomic sequencing of five Gossypium allopolyploid species, included the two agricultural species of upland (G. hirsutum) and Pima (G. barbadense) cotton [2], revealed thousands of encoded uncharacterized proteins that were shared across all five species. Functional characterization of these proteins will contribute to a richer annotation of the cotton genomes and could identify proteins of interest for important agricultural traits. A protein of unknown function (UniProt: A0A1U8MGX4) encoded by gene Gohir.A02G044702.1 in Gossypium hirsutum, was studied using sequence and structure bioinformatic tools leading to a proposed function as a nuclear, DNA-binding B3 transcription factor of the REM subfamily.
pLDDT coloring scheme
- Very low (pLDDT < 50) orange
- Low (70 > pLDDT > 50) yellow
- Confident (90 > pLDDT > 70) cyan
- Very high (pLDDT > 90) blue
|
An AlphaFold model of the protein predicted a high confidence structure for the DUF313 domain region of the protein. The region of highest confidence is between residue 111-241 which includes the entire predicted DUF 313.
The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. A structural overlay of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB 6j9c), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated positively charged residues surrounding the DNA-binding site (Anionic (-) / Cationic (+)) that could interact with the negatively charged DNA backbone.
Mapping of the level of conservation for each residue showed that
the residues within this site were all highly conserved among homologs of this protein, as determined by the ConSurf program.
Remember to drag the structures with the mouse to rotate them.
References
- ↑ Allen M, Hulse-Kemp AM, Storm AR. Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily. MicroPubl Biol. 2022 Aug 6;2022. doi: 10.17912/micropub.biology.000574., eCollection 2022. PMID:35996691 doi:http://dx.doi.org/10.17912/micropub.biology.000574
- ↑ Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J, Schmutz J. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet. 2020 May;52(5):525-533. doi: 10.1038/s41588-020-0614-5. Epub 2020 Apr , 20. PMID:32313247 doi:http://dx.doi.org/10.1038/s41588-020-0614-5
