Journal:MicroPubl Biol:000669

Gossypium hirsutum gene Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site

Emma R. Smith, Lauryn R. Caulley, Amanda M. Hulse-Kemp, Amanda R Storm, Angela K. Stoeckman ^[1]

Molecular Tour
Based on our analyses, the uncharacterized Gossypium hirsutum protein (UniProt A0A1U8N485; NCBI XP_016732659) here referred to as GhVAB-A0A1U8N485, identified as a gene of unknown function in cotton species (Chen et al., 2020^[2]), contains two domains: a VAN3-binding protein-like, auxin canalisation domain (domain of unknown function, DUF828) and a pleckstrin homology (PH) domain. The specific function of these domains is unknown but they are often found together in proteins of the VAN3-binding (VAB) protein family, also known as the FORKED-like (FL) family. It is proposed that members of this plant-specific family in Arabidopsis are involved in aiding asymmetrical localization of PIN1 (PINFORMED) an auxin transport protein responsible for establishing vein patterns and numbers in leaves (Hou et al., 2010^[3]). GhVAB-A0A1U8N485 is most similar in sequence to the Group 3 FL proteins in Arabidopsis, FL5-7, which appear to be localized to the Golgi apparatus and decrease leaf size when mutated.

The AlphaFold structure model for GhVAB-A0A1U8N485 predicted two distinct folding regions with high confidence from Gly111-Arg224 and Gln259-Val366. The first region (colored in blue), from residues 111-224, consists primarily of four alpha helices and contains most of the DUF828 domain. The second region (in green) contains the PH domain residues 259-366 and consists of a single alpha helix and seven anti-parallel beta sheets. Although VAB proteins are only found in plants, the PH domain structure is found in proteins across kingdoms of life. PH domains often localize to membranes, contain a conserved set of secondary structures and commonly bind phosphatidylinositol phosphates involved in signaling pathways (Le Huray et al., 2022^[4]). From published structures of other PH domains (Saccharomyces cerevisiae Avo1, PDB 3ulb and human protein kinase B/Akt, PDB 1h10), the core of the PH domain is shown to be a seven-stranded anti-parallel beta-sandwich closed at its C-terminus by an alpha-helix. At the N-terminus of this beta-sandwich are three variable loops containing positively charged residues forming a pocket of basic residues that bind negatively-charged phosphoinositides.

When the PH domain of human protein kinase B/Akt (in pink) containing a bound phosphatidylinositol trisphosphate ligand (shown in ball-in-sticks; PDB [[1h10]]) was overlaid with the GhVAB-A0A1U8N485 PH domain (in orange), a deep binding pocket accommodating the phosphoinositide ligand was observed in the structure. Indeed, this GhVAB-A0A1U8N485 binding pocket is lined with positively-charged amino acids that could interact with the negatively-charge phosphate groups (Anionic (-) / Cationic (+)) and residues within this pocket are highly-conserved based on ConSurf analysis.

A structure-based alignment between GhVAB-A0A1U8N485 and human protein kinase B/Akt indicated that two of the five ligand-binding residues in B/Akt are completely conserved in GhVAB-A0A1U8N485, with two others being conservative substitutions (Thomas et al., 2002^[5]). Evidence from sequence and structure features support that GhVAB-A0A1U8N485 is part of the VAN3-binding protein family. Furthermore, based on functional reports of other VAN3-binding proteins as well as structural analysis of our protein, GhVAB-A0A1U8N485 might be involved in regulating leaf size or vein development in cotton plants by binding phosphoinositides as part of an auxin signaling pathway.

References

1. ↑ Smith, ER; Caulley, LR; Storm, AR; Hulse-Kemp, AM; Stoeckman, AK (2023). Gossypium hirsutum gene of unknown function Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site. microPublication Biology. doi:https://dx.doi.org/10.17912/micropub.biology.000669
2. ↑ 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
3. ↑ Hou H, Erickson J, Meservy J, Schultz EA. FORKED1 encodes a PH domain protein that is required for PIN1 localization in developing leaf veins. Plant J. 2010 Sep;63(6):960-73. doi: 10.1111/j.1365-313X.2010.04291.x. PMID:20626652 doi:http://dx.doi.org/10.1111/j.1365-313X.2010.04291.x
4. ↑ Le Huray KIP, Wang H, Sobott F, Kalli AC. Systematic simulation of the interactions of pleckstrin homology domains with membranes. Sci Adv. 2022 Jul 8;8(27):eabn6992. doi: 10.1126/sciadv.abn6992. Epub 2022 Jul 6. PMID:35857458 doi:http://dx.doi.org/10.1126/sciadv.abn6992
5. ↑ Thomas CC, Deak M, Alessi DR, van Aalten DM. High-resolution structure of the pleckstrin homology domain of protein kinase b/akt bound to phosphatidylinositol (3,4,5)-trisphosphate. Curr Biol. 2002 Jul 23;12(14):1256-62. PMID:12176338