Abstract
In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins. Most F-box proteins are shown to be an integral part of SCF complexes, which carry out the degradation of proteins and regulate diverse important biological processes. Anthers and pollen development have a huge importance in crop breeding. Despite the vast diversity of FBPs in Arabidopsis male reproductive organs, their role in anther and pollen development is not much explored. Moreover, a standard nomenclature for naming FBPs is also lacking. Here, we propose a standard nomenclature for naming the FBPs of Arabidopsis thaliana uniformly and carry out a systematic analysis of sperm cell-specific FBP gene, i.e., 3p.AtFBP113 due to its reported high and preferential expression, for detailed functional annotation. The results revealed that 3p.AtFBP113 is located on the small arm of chromosome and encodes 397 amino acid long soluble, stable, and hydrophilic protein with the possibility of localization in various cellular compartments. The presence of the C-terminal F-box associated domain (FBA) with immunoglobulin-like fold anticipated its role in protein binding. Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination. Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold. Thus, the outcomes of the study will be useful in developing a better understating of the function of 3p.AtFBP113 during the process of pollen development, which will be helpful for targeting the gene for manipulation of male fertility that has immense importance in hybrid breeding.
Highlights
In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins, which control diverse biological processes from growth to development (Gagne et al, 2002; Xu et al, 2009; Abd-Hamid et al, 2020)
The schematic representation of standardized nomenclature, which is proposed here for naming the FBP genes, exemplifying gene of interest is shown in Figure 4A, while Arabidopsis FBP gene family nomenclature is provided in Supplementary Table S1
The ePlant chromosome viewer used for determining the location of the genes revealed that our target gene is residing on the short arm (p) of chromosome 3 (Figure 4B) and according to the nomenclature our gene of interest is as 3p.AtFBP113
Summary
F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins, which control diverse biological processes from growth to development (Gagne et al, 2002; Xu et al, 2009; Abd-Hamid et al, 2020). Human, fruit fly, and Caenorhabditis elegans genomes contain only 38, 23 and 326 FBP genes, respectively, where C. elegans is the only one among all animal species whose genome contains the largest number of FBP genes (Kipreos and Pagano, 2000). F-box proteins are usually characterized by the presence of 50-60 amino acid long, conserved F-box motif present at their N-terminal regions (Kipreos and Pagano, 2000) and, named as F-box proteins after its first discovery in a human protein Cyclin F (Bai et al, 1996). C terminal regions of FBPs contain protein-protein interaction domains that are mostly of diverse types and classify FBPs into different subfamilies (Bai et al, 1996; Gagne et al, 2002). Some of the commonly known subfamilies in plants are leucine-rich repeats (LRRs), Kelch repeats, WD-40, TUB, actin, F-box associated (FAB), Armadillo (Am), tetratricopeptide repeats (TPRs), Jumonji (JmjC), and DEAD-like helicase (de Pozo and Estelle, 2000; Kipreos and Pagano, 2000; Gagne et al, 2002; Xu et al, 2009)
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