Tags

Type your tag names separated by a space and hit enter

Identification, analysis, and modeling of the YUCCA protein family genome-wide in Coffea canephora.
Proteins. 2022 04; 90(4):1005-1024.P

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.

Links

Publisher Full Text (DOI)

Authors+Show Affiliations

Uc-Chuc MA
Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Mexico.
Kú-González ÁF
Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Mexico.
Jiménez-Ramírez IA
Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Mexico.
Loyola-Vargas VM
Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Mexico.

MeSH

ArabidopsisArabidopsis ProteinsCoffeaFlavin-Adenine DinucleotideIndoleacetic AcidsMolecular Docking SimulationNADPPhylogenyYucca

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34890079

Citation

Uc-Chuc, Miguel A., et al. "Identification, Analysis, and Modeling of the YUCCA Protein Family Genome-wide in Coffea Canephora." Proteins, vol. 90, no. 4, 2022, pp. 1005-1024.
Uc-Chuc MA, Kú-González ÁF, Jiménez-Ramírez IA, et al. Identification, analysis, and modeling of the YUCCA protein family genome-wide in Coffea canephora. Proteins. 2022;90(4):1005-1024.
Uc-Chuc, M. A., Kú-González, Á. F., Jiménez-Ramírez, I. A., & Loyola-Vargas, V. M. (2022). Identification, analysis, and modeling of the YUCCA protein family genome-wide in Coffea canephora. Proteins, 90(4), 1005-1024. https://doi.org/10.1002/prot.26293
Uc-Chuc MA, et al. Identification, Analysis, and Modeling of the YUCCA Protein Family Genome-wide in Coffea Canephora. Proteins. 2022;90(4):1005-1024. PubMed PMID: 34890079.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification, analysis, and modeling of the YUCCA protein family genome-wide in Coffea canephora. AU - Uc-Chuc,Miguel A, AU - Kú-González,Ángela F, AU - Jiménez-Ramírez,Irma A, AU - Loyola-Vargas,Víctor M, Y1 - 2021/12/17/ PY - 2021/11/04/revised PY - 2021/03/16/received PY - 2021/12/02/accepted PY - 2021/12/11/pubmed PY - 2022/4/22/medline PY - 2021/12/10/entrez KW - Coffea canephora KW - FMO KW - IPyA KW - YUCCA KW - auxin KW - docking KW - yucasin SP - 1005 EP - 1024 JF - Proteins JO - Proteins VL - 90 IS - 4 N2 - 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. SN - 1097-0134 UR - https://www.unboundmedicine.com/medline/citation/34890079/Identification_analysis_and_modeling_of_the_YUCCA_protein_family_genome_wide_in_Coffea_canephora_ DB - PRIME DP - Unbound Medicine ER -