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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #397934
Research Project: Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

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

Author
item ZIRKEL, JONATHAN - Western Carolina University
item Hulse-Kemp, Amanda
item STORM, AMANDA - Western Carolina University

Submitted to: microPublication Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2023
Publication Date: 9/25/2023
Citation: Zirkel, J., Hulse-Kemp, A.M., Storm, A.R. 2023. Gossypium hirsutum gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulation. microPublication Biology. https://doi.org/10.17912/micropub.biology.000670.
DOI: https://doi.org/10.17912/micropub.biology.000670

Interpretive Summary: Multiple high-quality genomes are available for cotton, the most important producer of natural fibers for textiles. Genes identified in these genomes have been computationally identified, but determining the function of the genes has been difficult and a large number of these (approximately 20%) remain classified as unknown function. Manual curation and investigation of one gene of unknown function has identified a potential function of a gene involved in regulation of other genes at the DNA level during plant development This investigation was performed as a part of a collaborative effort of USDA-ARS with Western Carolina University undergraduate students as the topic of a semester research project.

Technical Abstract: A protein of unknown function GhLSH4L-A0A1U8MC48, encoded by gene Gohir.A02G039501.1 in Gossypium hirsutum, was studied using sequence and structure bioinformatic tools leading to its proposed function as a nuclear, DNA-binding ALOG protein involved in gene regulation during organ boundary specification and maintenance. The encoded protein contains a predicted nuclear localization sequence, an ALOG domain with conserved residues in the modeled DNA-binding regions and nearly identical sequence identity to Arabidopsis homologs involved in development of organ boundaries at the shoot apical meristem. The GhLSH4L-A0A1U8MC48 protein was modeled by AlphaFold2 to have a four-helix bundle that is structurally analogous to DNA-binding domains of XerC/D-like recombinases.