Journal:MicroPubl Biol:000670

Gossypium hirsutum gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulation

Jonathan Zirkel, Amanda M. Hulse-Kemp, Amanda R. Storm ^[1]

Molecular Tour
Genomic sequencing of cotton species identified thousands of uncharacterized proteins (Chen et al., 2020^[2]). One encoded by the gene LOC107943309, termed ‘light-dependent short hypocotyls 4-like’ (NCBI: XP_016732548, Uniprot: A0A1U8MC48) or GhLSH4L-A0A1U8MC48, was shown to be part of the ALOG (Arabidopsis LSH1 (light-dependent short hypocotyl) and Oryza G1) family and contains the necessary sequence and structure for localization to the nucleus and subsequent DNA-binding.

The ALOG family is largely found in flowering plants with over 80% belonging to dicots (Iyer and Aravind, 2012^[3]). Members of the ALOG family appear to be involved in tissue and organ development in plants with evidence that some function as transcription factors, regulating the expression of particular sets of genes. The 125-residue ALOG domain may be derived from the N-terminal DNA-binding domain (DBD) of viral recombinases and integrases, proteins that rearrange DNA segments (Iyer and Aravind, 2012^[3]). One of these proteins, CRE recombinase, has been crystalized bound to DNA (PDB 1crx, Guo et al., 1997^[4]) through a core four helix-bundle where three helices interact with DNA through the major groove with a fourth helix located near the C-terminal. . ALOG domains in plants also have a four helix bundle but are set apart by a Zinc-Ribbon region inserted between helices 2 and 3 that is proposed to chelate a Zinc ion.

An AlphaFold model of GhLSH4L-A0A1U8MC48 predicted a high level of confidence in the ALOG domain region from amino acid 55 to 193, which consists of a bundle of four alpha helices characteristic of ALOG proteins (Iyer and Aravind, 2012^[3]).

(PDB 1crx, red), showing very similar helical arrangement and this overlay allowed DNA (shown in white and grey) to be modeled onto the structure of GhLSH4L-A0A1U8MC48 (pink). Helices 1 and 3 are positioned to form contacts deep in the DNA major groove. The position of DNA binding residues in structural analogs (Iyer and Aravind, 2012^[3]) were highlighted in the structure and these residues cluster around the modeled DNA binding site. . Although there is almost no conservation in sequence with CRE recombinase, all these predicted DNA binding residues were highly conserved between the plant orthologs suggesting that they have a distinct DNA recognition site.

The UCSF ChimeraX electrostatic potential tool showed this (Anionic (-) / Cationic (+)). The conservation of predicted DNA binding residues, electrostatic surface potentials, structural similarity to recombinase DBDs, along with a predicted nuclear localization, support GhLSH4L-A0A1U8MC48 functioning as a transcription factor or a recruiter of chromatin remodeling that binds to DNA and alters gene expression, likely as an important step in early plant development.

References

1. ↑ doi: https://dx.doi.org/10.17912/micropub.biology.000670
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. ↑ ^{3.0 3.1 3.2 3.3} Iyer LM, Aravind L. ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons. Biol Direct. 2012 Nov 12;7:39. doi: 10.1186/1745-6150-7-39. PMID:23146749 doi:http://dx.doi.org/10.1186/1745-6150-7-39
4. ↑ Guo F, Gopaul DN, van Duyne GD. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature. 1997 Sep 4;389(6646):40-6. PMID:9288963 doi:10.1038/37925