Identification, analysis, and modeling of the YUCCA protein family genome‐wide in Coffea canephora

Abstract

Auxin is involved in almost every aspect of plant growth and development, from embryogenesis to senescence. Indole-3-acetic acid (IAA) is the main known natural auxin that is synthesized by enzymes tryptophan aminotransferase of arabidopsis (TAA) and YUCCA (YUC) of the flavin-containing monooxygenases family (FMO) from one of the tryptophan-dependent pathways. Genome-wide identification and comprehensive analysis of the YUC-protein family have been conducted in Coffea canephora in the present study. A total of 10 members CcYUC gene family were identified in C. canephora. Phylogenetic analysis revealed that the CcYUC protein family is evolutionarily conserved, and they consist of four groups. In contrast, bioinformatic analysis predicted a hydrophobic transmembrane helix (TMH) for one CcYUC (YUC10) member only. Isoelectric point (pI), molecular mass (Ms), signal peptide, subcellular localization, and phosphorylation sites were predicted for CcYUC proteins.YUC enzymes require the prosthetic group flavin adenine dinucleotide (FAD) and the cofactor nicotinamide adenine dinucleotide phosphate (NADPH) for their enzymatic activity. Therefore, we include the molecular docking for CcYUC2-FAD-NADPH-IPyA and yucasin, which is a specific inhibitor for YUC activity. The docking results showed FAD and NADPH binding at the big and small domain sites, respectively, in CcYUC2. IPyA binds very close to FAD along the big domain, and yucasin competes for the same site as IPA, blocking IAA production. Furthermore, in silico point mutations affect the stability of the CcYUC2-4 proteins.

Embryogenic abnormalities and genotoxicity induced by 2,4-dichlorophenoxyacetic acid during indirect somatic embryogenesis in Coffea

“…IAA is synthesized by the enzymes tryptophan aminotransferase of Arabidopsis (TAA) and YUCCA (YUC) from one of the tryptophandependent pathways. Uc-Chuc et al [27] identi ed 10 members of the CcYUC gene family in C. canephora. Quintana-Escobar et al [28] showed differences in the concentration of auxin homeostasis proteins in C. arabica, with a more signi cant accumulation of ABCs, GH3.17, UGT75C1 and IBR1 proteins.…”

Genome-Wide Analysis and Expression Profiling of YUCCA Gene Family in Developmental and Environmental Stress Conditions in Tea Plant (Camellia sinensis)

“…There are 11 CsYUC proteins that contain the NAD_binding_8 domain, including CsYUC2.1, -2.2, -6, -11.1, -11.2, -11.4, -11.5, -11.6, -11.7, -11.8, and -11.9. Previous reports have suggested that the FMO domain can bind FAD and NADPH, and these are its most prominent characteristics [8]. Thus, the FMO domain, acting as the FAD-and NADPHbinding sites, is essential for YUC enzymatic activities [3].…”

“…IAA is the richest and most predominant auxin in plants [5][6][7]. In plants, the central IAA biosynthetic pathway is the indole-3-pyruvic acid (IPyA) pathway (i.e., TAA/YUC pathway), which is essential for almost all the major developmental processes in plants [7][8][9]. YUCCA (YUC) enzymes catalyze the rate-limiting second step in the TAA/YUC pathway, which converts IPyA into IAA, and belong to a class of flavin-containing monooxygenases (FMOs) [1,[9][10][11].…”

SlPP2C2 interacts with FZY/SAUR and regulates tomato development via signaling crosstalk of ABA and auxin

“…Auxins are involved in the regulation of plant growth and development (Davies, 2010; Ge et al., 2019; Ross & Reid, 2010). Recently, a lot of information on the tryptamine pathway of IAA biosynthesis has been obtained because of the identification of flavin monooxygenases (YUC family) from Arabidopsis and maize, which have been demonstrated to catalyze the N ‐hydroxylation of tryptamine (Lu et al., 2023; Uc‐Chuc et al., 2022; Yamamoto et al., 2007). The flavin monooxygenase FZY is a YUC homolog from tomato and an important enzyme involved in a rate‐limiting step of IAA biosynthesis (Tivendale et al., 2010).…”