Proteomic Analysis of In Vitro Plant Tissues (Coffea canephora): A Case of Study.

Since the term proteomics was coined by Marc Wilkins in 1994, there has been an explosion in the number of articles reporting the use of the proteomics technique. As the layers of biological organization and their regulation increase, the complexity of living beings increases. Thus, we go from the genome to tissues, cells, cellular compartments, and phenotypes and the complexity of the tools used to study this complexity also increases. Unlike the genome study, in the case of the proteome, we have a more complex panorama. We have a spatial and temporal proteome. Proteomics helps to answer complex biological questions since proteins' function depends on their molecular structure, subcellular localization, and posttranslational modifications. In this protocol, we describe a methodology to extract proteins using different methods, separating proteins by electrophoresis in double-dimensional gels and analyzing the gels using specialized software that allows obtaining information on the number and abundance of the proteins from the gels.

Lipophilic and Hydrophilic Metabolites as Descriptors of Different Coffee Beverages.

Coffee is a widely consumed beverage rich in bioactive phytochemicals. This study investigated the effect of brewing method on the profile of potential bioactive compounds in different coffee beverages using metabolomics and lipidomics based on UHPLC-MS/QTOF. The oil contents of the espresso coffee (EC), pot coffee (PC), instant coffee (IC), and filter coffee (FC) beverages studied were 0.13% ± 0.002, 0.12% ± 0.001, 0.04% ± 0.002, and 0.03% ± 0.003, respectively. Univariate analysis indicated significant differences (P < 0.001) in oil content when EC and PC beverages were compared with IC and FC beverages. Principal component analysis revealed similarities in the lipid profiles of FC and EC beverages and the hydrophilic profiles of PC and FC beverages. The EC beverage had the highest intensity of hydrophilic compounds such as adenine, theobromine, chlorogenic acid, and caffeine. The PC beverage was the most abundant in triglycerides, phosphatidylcholine, and diterpenes. Cafestol and kahweol esters, but not their free forms, were the most abundant diterpenes in the PC beverage. This work provides information on the differences in the profile of potentially bioactive compounds in four commonly consumed coffee beverage types and, thus, on the possible differences in the health effects of these coffee beverage types.

Transcriptomic Analyses Reveal That Coffea arabica and Coffea canephora Have More Complex Responses under Combined Heat and Drought than under Individual Stressors.

Increasing exposure to unfavorable temperatures and water deficit imposes major constraints on most crops worldwide. Despite several studies regarding coffee responses to abiotic stresses, transcriptome modulation due to simultaneous stresses remains poorly understood. This study unravels transcriptomic responses under the combined action of drought and temperature in leaves from the two most traded species: Coffea canephora cv. Conilon Clone 153 (CL153) and C. arabica cv. Icatu. Substantial transcriptomic changes were found, especially in response to the combination of stresses that cannot be explained by an additive effect. A large number of genes were involved in stress responses, with photosynthesis and other physiologically related genes usually being negatively affected. In both genotypes, genes encoding for protective proteins, such as dehydrins and heat shock proteins, were positively regulated. Transcription factors (TFs), including MADS-box genes, were down-regulated, although responses were genotype-dependent. In contrast to Icatu, only a few drought- and heat-responsive DEGs were recorded in CL153, which also reacted more significantly in terms of the number of DEGs and enriched GO terms, suggesting a high ability to cope with stresses. This research provides novel insights into the molecular mechanisms underlying leaf Coffea responses to drought and heat, revealing their influence on gene expression.

Targeted metabolomics and transcript profiling of methyltransferases in three coffee species.

Coffee plants contain well-known xanthines as caffeine. Three Coffea species grown in a controlled greenhouse environment were the focus of this research. Coffea arabica and C. canephora are two first principal commercial species and commonly known as arabica and robusta, respectively. Originating in Central Africa, C. anthonyi is a novel species with small leaves. The xanthine metabolites in flower, fruit and leaf extracts were compared using both targeted and untargeted metabolomics approaches. We evaluated how the xanthine derivatives and FQA isomers relate to the expression of biosynthetic genes encoding N- and O-methyltransferases. Theobromine built up in leaves of C. anthonyi because caffeine biosynthesis was hindered in the absence of synthase gene expression. Despite this, green fruits expressed these genes and they produced caffeine. Given that C. anthonyi evolved successfully over time, these findings put into question the defensive role of caffeine in leaves. An overview of the histolocalisation of xanthines in the different flower parts of Coffea arabica was also provided. The gynoecium contained more theobromine than the flower buds or petals. This could be attributed to increased caffeine biosynthesis before fructification. The presence of theophylline and the absence of theobromine in the petals indicate that caffeine is catabolized more in the petals than in the gynoecium.

Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L.

To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.

Characterization of yeast mutant strains for starter culture in Arabica coffee fermentation.

Arabica coffee is the most popular and best-selling type of coffee. During coffee fermentation, microorganisms are essential for the production of metabolites and volatile compounds that affect coffee flavor quality. This work aimed to study the mutation, selection, and characterization of the Wickerhamomyces anomalus strain YWP1-3 as a starter culture to enhance the flavor quality of Arabica coffee. The results revealed that six mutants could produce relatively high levels of the pectinase enzyme on pectin agar media and exhibited high activity levels, ranging from 332.35 to 415.88 U/ml in mucilage broth. Strains UV22-2, UV22-3, UV41-1 and UV32-1 displayed higher levels of amylase activity than did the wild type. The UV22-2 and UV22-3 mutants exhibited the highest pectin degradation indices of 49.22% and 45.97%, respectively, and displayed significantly enhanced growth rates in nitrogen yeast base media supplemented with various sugars; thus, these mutants were evaluated for their ability to serve as a starter for fermentation of Arabica coffee. The cupping scores of coffees derived from UV22-2 and UV22-3 were 83.5 ± 1.5 and 82.0 ± 2.14, respectively. The volatile compounds in the roasted coffee fermented by UV22-2 were analyzed by GC‒MS, which revealed higher levels of furfuryl alcohol and furfuryl acetate than did the other samples. These findings suggested that UV22-2 could be an influential starter culture for Arabica coffee fermentation.

Coffee Husk By-Product as Novel Ingredients for Cascara Kombucha Production.

Kombucha, a fermented beverage, is gaining popularity due to its numerous beneficial health effects. Various substrates such as herbs, fruits, flowers, and vegetables, have been used for kombucha fermentation in order to enhance the flavor, aroma, and nutritional composition. This study aims to investigate the potential suitability of cascara as a novel ingredient for kombucha production. Our findings suggested that cascara is a suitable substrate for kombucha production. Fermentation elevated the total phenolic and flavonoid content in cascara, which enhanced the antioxidant, antibacterial, and prebiotic characteristics of the product. Furthermore, the accumulation of acetic acid-induced the pH lowering reached 2.7 after 14 days of fermentation, which achieved the microbiological safety of the product. Moreover, 14 days of fermentation resulted in a balanced amalgamation of acidity, sweetness, and fragrance according to sensory evaluation. Our findings not only highlight the potential of cascara kombucha as a novel substrate for kombucha production but also contribute to repurposing coffee by-products, promoting environmentally friendly and sustainable agricultural development.

Inhibition of pancreatic lipase by coffee leaves-derived polyphenols: A mechanistic study.

The suppression of pancreatic lipase has been employed to mitigate obesity. This study explored the mechanism of coffee leaf extracts to inhibit pancreatic lipase. The ethyl acetate fraction derived from coffee leaves (EAC) exhibited the highest inhibitory capacity with a half-maximal inhibitory concentration (IC50) of 0.469 mg/mL and an inhibitor constant (Ki) of 0.185 mg/mL. This fraction was enriched with 3,5-dicaffeoylquinic acid (3,5-diCQA, 146.50 mg/g), epicatechin (87.51 mg/g), and isoquercetin (48.29 mg/g). EAC inhibited lipase in a reversible and competitive manner, and quenched its intrinsic fluorescence through a static mechanism. Molecular docking revealed that bioactive compounds in EAC bind to key amino acid residues (HIS-263, PHE-77, and SER-152) located within the active cavity of lipase. Catechin derivatives play a key role in the lipase inhibitory activity within EAC. Overall, our findings highlight the promising potential of coffee leaf extract as a functional ingredient for alleviating obesity through inhibition of lipase.

Unveiling the bioactivity and bioaccessibility of phenolic compounds from organic coffee husks using an in vitro digestion model.

BACKGROUND: The large quantities of by-products generated in the coffee industry are a problem. Studies related to the biological potential of organic coffee husks are still limited. The aim of this work was to investigate the occurrence of phenolic compounds in organic coffee husks and to evaluate their potential as a source of bioactive dietary components. RESULTS: To achieve this objective, three extracts were prepared, namely extractable polyphenols (EPs), hydrolyzable non-extractable polyphenols (H-NEPs), and non-extractable polyphenols (NEPs). These extracts were characterized and evaluated for their bioactive properties after simulated gastrointestinal digestion. The results show that the extraction process affected the occurrence of phenols from coffee peels, especially for caffeic acid, gallic acid, and chlorogenic acid. The free and bound polyphenols found in the extracts and digests not only showed antioxidant properties against 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals but were also strongly bioavailable and had good anticoagulant potential. CONCLUSION: These results highlight the potential health benefits of phytochemicals from coffee husks and open new perspectives for the use of such compounds in dietary supplements. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Coffee Leaf Tea Extracts Improve Hyperuricemia Nephropathy and Its Associated Negative Effect in Gut Microbiota and Amino Acid Metabolism in Rats.

Hyperuricemia nephropathy (HN) is a metabolic disease characterized by tubular damage, tubulointerstitial fibrosis, and uric acid kidney stones and has been demonstrated to be associated with hyperuricemia. Coffee leaf tea is drunk as a functional beverage. However, its prevention effects on HN remain to be explored. This study showed that coffee leaf tea extracts (TE) contain 19 polyphenols, with a total content of 550.15 ± 27.58 mg GAE/g. TE decreased serum uric acid levels via inhibiting XOD activities and modulating the expression of urate transporters (GLUT9, OAT3, and ABCG2) in HN rats. TE prevented HN-induced liver and kidney damage and attenuated renal fibrosis. Moreover, it upregulated the abundance of SCFA-producing bacteria (Phascolarctobacterium, Alloprevotella, and Butyricicoccus) in the gut and reversed the amino acid-related metabolism disorder caused by HN. TE also decreased the circulating LPS and d-lactate levels and increased the fecal SCFA levels. This study supported the preliminary and indicative effect of coffee leaf tea in the prevention of hyperuricemia and HN.

Functional Characterization of ent-Copalyl Diphosphate Synthase and Kaurene Synthase Genes from Coffea arabica L.

The biochemical profile of coffee beans translates directly into quality traits, nutraceutical and health promoting properties of the coffee beverage. Ent-kaurene is the ubiquitous precursor for gibberellin biosynthesis in plants, but it also serves as an intermediate in specialized (i.e., secondary) diterpenoid metabolism that leads to a diversity of more than 1,000 different metabolites. Nutraceutical effects on human health attributed to diterpenes include antioxidant, anticarcinogenic, and anti-inflammatory properties. Cafestol (CAF) and kahweol (KAH) are two diterpenes found exclusively in the Coffea genus. Our objective was to identify and functionally characterize genes involved in the central step of ent-kaurene production. We identified 17 putative terpene synthase genes in the transcriptome of Coffea arabica. Two ent-copalyl diphosphate synthase (CaCPS) and three kaurene synthase (CaKS) were selected and manually annotated. Transcript expression profiles of CaCPS1 and CaKS3 best matched the CAF and KAH metabolite profiles in different tissues. CaCPS1 and CaKS3 proteins were heterologously expressed and functionally characterized. CaCPS1 catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to ent-copalyl diphosphate (ent-CPP), which is converted to ent-kaurene by CaKS3. Knowledge about the central steps of diterpene formation in coffee provides a foundation for future characterization of the subsequent enzymes involved in CAF and KAH biosynthesis.

Yeasts are essential for mucilage degradation of coffee beans during wet fermentation.

During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been proposed. The aim of this work was to improve our understanding of the kinetics of mucilage breakdown. Pulped coffee beans were wet fermented with seven different treatments for 36 h. Endogenous bacteria and yeasts are selectively suppressed, and pectinases or lactic acid are added. They also involve maintaining the beans at pH 7 throughout fermentation and using spontaneous fermentation without additives as a control. During spontaneous fermentation, yeast and lactic acid bacteria were detected and significantly increased to 5.5 log colony-forming units (CFU)/mL and 5.2 log CFU/mL, respectively. In the first 12 h of fermentation, there was a significant degree of endogenous pectinolytic activity, which resulted in partly destroyed beans in the absence of microorganisms. By adding pectinase and lactic acid to the fermentation mass, the breakdown process was accelerated in less than 8 h. When yeast was present throughout the fermentation, complete degradation was achieved. Bacteria played no critical role in the degradation. Klebsiella pneumoniae and Erwinia soli were found in a lower population and showed weaker pectinolytic activities compared to Hanseniaspora uvarum and Pichia kudriavzevii. During wet fermentation, mucilage degradation appears to be mediated by endogenous enzymes at the early stage, whereas microbial contributions, mainly yeasts, occur subsequently. H. uvarum and P. kudriavzevii may be promising candidates to be tested in future studies as coffee starter cultures to better control the mucilage degradation process.

Potassium Phosphite Activates Components Associated with Constitutive Defense Responses in Coffea arabica Cultivars.

Phosphites have been used as inducers of resistance, activating the defense of plants and increasing its ability to respond to the invasion of the pathogen. However, the mode of action of phosphites in defense responses has not yet been fully elucidated. The objective of this study was to evaluate the effect of potassium phosphite (KPhi) in coffee cultivars with different levels of resistance to rust to clarify the mechanism by which KPhi activates the constitutive defense of plants. To this end, we studied the expression of genes and the activity of enzymes involved in the defense pathway of salicylic acid (SA) and reactive oxygen species (ROS), in addition to the levels of total soluble phenolic compounds and soluble lignin. Treatment with KPhi induced constitutive defense responses in cultivars resistant and susceptible to rust. The results suggest that KPhi acts in two parallel defense pathways, SA and ROS, which are essential for the induction of systemic acquired resistance (SAR) when activated simultaneously. The activation of the mechanisms associated with defense routes demonstrates that KPhi is a potential inducer of resistance in coffee plants.

Liposomal stem cell extract formulation from Coffea canephora shows outstanding anti-inflammatory activity, increased tissue repair, neocollagenesis and neoangiogenesis.

Coffea canephora plant stem cells can have bioactive compounds with tissue repairing and anti-inflammatory action. This study aimed to develop a liposomal stem cell extract formulation obtained from the leaves of C. canephora (LSCECC) and to investigate its capacity to contribute to the dynamic mechanisms of tissue repair. The liposome cream was developed and characterized through the dynamic light scattering technique, atomic force microscopy, and transmission electron microscopy. The excisional full-thickness skin wound model was used and daily topically treated with the LSCECC formulation or vehicle control. On days 2, 7, 14, and 21 after wounding, five rats from each group were euthanized and the rates of wound closure and re-epithelialization were evaluated using biochemical and histological tests. LSCECC resulted in faster re-epithelialization exhibiting a significant reduction in wound area of 36.4, 42.4, and 87.5% after 7, 10, and 14 days, respectively, when compared to vehicle control. LSCECC treated wounds exhibited an increase in granular tissue and a proper inflammatory response mediated by the reduction of pro-inflammatory cytokines like TNF-α and IL-6 and an increase of IL-10. Furthermore, wounds treated with LSCECC showed an increase in the deposition and organization of collagen fibers at the wound site and improved scar tissue quality due to the increase in transforming growth factor-beta and vascular endothelial growth factor. Our data showed that LSCECC improves wound healing, the formation of extracellular matrix, modulates inflammatory response, and promotes neovascularization being consider a promising bioactive extract to promote and support healthy skin. The graphical presents the action of LSCECC in all four phases of wound healing and tissue repair. The LSCECC can reduce the inflammatory infiltrate in the inflammatory phase by decreasing the pro-inflammatory cytokines like IL-6 and TNF-α, in addition to maintaining this modulation through lesser activation and recruitment of macrophages. The LSCECC can also increase the release of IL-10, an anti-inflammatory cytokine, decreasing local edema. The increase in VEGF provides neovascularization and the supply of nutrients to newly repaired tissue. Finally, signaling via TGF-ß increases the production and organization of collagen fibers in the remodeling phase.

A Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja.

Terpenoids are a class of compounds that are found in all living organisms. In plants, some terpenoids are part of primary metabolism, but most terpenes found in plants are classified as specialized metabolites, encoded by terpene synthases (TPS). It is not obvious how to assign the putative product of a given TPS using bioinformatics tools. Phylogenetic analyses easily assign TPS into families; however members of the same TPS family can synthetize more than one terpenoid-and, in many biotechnological applications, researchers are more interested in the product of a given TPS rather than its phylogenetic profile. Automated protein annotation can be used to classify TPS based on their products, despite the family they belong to. Here, we implement an automated bioinformatics method, search_TPS, to identify TPS proteins that synthesize mono, sesqui and diterpenes in Angiosperms. We verified the applicability of the method by classifying wet lab validated TPS and applying it to find TPS proteins in Coffea arabica, C. canephora, C. eugenioides, and Quillaja saponaria. Search_TPS is a computational tool based on PERL scripts that carries out a series of HMMER searches against a curated database of TPS profile hidden Markov models. The tool is freely available at https://github.com/liliane-sntn/TPS .

SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm.

BACKGROUND: Coffee quality is an important selection criterion for coffee breeding. Metabolite profiling and Genome-Wide Association Studies (GWAS) effectively dissect the genetic background of complex traits such as metabolites content (caffeine, trigonelline, and 5-caffeoylquinic acid (5-CQA)) in coffee that affect quality. Therefore, it is important to determine the metabolic profiles of Coffea spp. genotypes. This study aimed to identify Single Nucleotide Polymorphisms (SNPs) within Coffea spp. genotypes through GWAS and associate these significant SNPs to the metabolic profiles of the different genotypes. METHODS AND RESULTS: A total of 1,739 SNP markers were obtained from 80 genotypes using the DArTseq™ method. Caffeine, trigonelline, and 5-CQA content were determined in coffee leaves using Ultra-Performance Liquid Chromatography/tandem mass spectrometry (UPLC-MS/MS) analyses. The GWAS was carried out using the Genome Association and Prediction Integrated Tool (GAPIT) software and a compressed mixed linear model. Finally, a total of three significant SNP markers out of ten were identified. One SNP, located in the coffee chromosome (Chr) 8, was significantly associated with caffeine. The two remaining SNPs, located in Chr 4 and 5, were significantly associated with trigonelline and six SNPs markers were associated with 5-CQA in Chr 1, 5 and 10, but these six markers were not significant. CONCLUSIONS: These significant SNP sequences were associated with protein ubiquitination, assimilation, and wall receptor kinases. Therefore, these SNPs might be useful hits in subsequent quality coffee breeding programs.

LysM receptors in Coffea arabica: Identification, characterization, and gene expression in response to Hemileia vastatrix.

Pathogen-associated molecular patterns (PAMPs) are recognized by pattern recognition receptors (PRRs) localized on the host plasma membrane. These receptors activate a broad-spectrum and durable defense, which are desired characteristics for disease resistance in plant breeding programs. In this study, candidate sequences for PRRs with lysin motifs (LysM) were investigated in the Coffea arabica genome. For this, approaches based on the principle of sequence similarity, conservation of motifs and domains, phylogenetic analysis, and modulation of gene expression in response to Hemileia vastatrix were used. The candidate sequences for PRRs in C. arabica (Ca1-LYP, Ca2-LYP, Ca1-CERK1, Ca2-CERK1, Ca-LYK4, Ca1-LYK5 and Ca2-LYK5) showed high similarity with the reference PRRs used: Os-CEBiP, At-CERK1, At-LYK4 and At-LYK5. Moreover, the ectodomains of these sequences showed high identity or similarity with the reference sequences, indicating structural and functional conservation. The studied sequences are also phylogenetically related to the reference PRRs described in Arabidopsis, rice, and other plant species. All candidates for receptors had their expression induced after the inoculation with H. vastatrix, since the first time of sampling at 6 hours post-inoculation (hpi). At 24 hpi, there was a significant increase in expression, for most of the receptors evaluated, and at 48 hpi, a suppression. The results showed that the candidate sequences for PRRs in the C. arabica genome display high homology with fungal PRRs already described in the literature. Besides, they respond to pathogen inoculation and seem to be involved in the perception or signaling of fungal chitin, acting as receptors or co-receptors of this molecule. These findings represent an advance in the understanding of the basal immunity of this species.

Unusual ent-Kaurane Diterpenes from the Coffea Cultivar S288 Coffee Beans and Molecular Docking to α-Glucosidase.

A total of 11 new (1-11) and 2 known (12 and 13) ent-kaurane diterpene derivatives were identified from the roasted beans of Coffea cultivar S288. Their structures were established by extensive spectroscopic analysis, including one- and two-dimensional nuclear magnetic resonance (heteronuclear single-quantum correlation, heteronuclear multiple-bond correlation, correlation spectroscopy, and rotating-frame Overhauser enhancement spectroscopy), high-resolution electrospray ionization mass spectrometry, and X-ray analyses. Cafespirone acid A (1) represents the first example of diterpene featuring a spirocyclic skeleton constructed from a 6/6/5 tricyclic system. Cafeane acid A (2) possesses a 6/6/6/5 tetracyclic system as a result of the C/D ring rearrangement. Furthermore, compounds 1-12 were evaluated for their α-glucosidase inhibitory activity. The results showed that compounds 2, 4, 5, 6, 7, 10, and 11 had a moderate inhibitory effect on α-glucosidase, and half-maximal inhibitory concentration values of compounds 4, 6, 7, and 10 were 18.76 ± 1.46, 4.88 ± 0.03, 12.35 ± 0.91, and 12.64 ± 0.59 µM, respectively, compared to the positive control acarbose (60.71 ± 16.45 µM). Additionally, the molecular docking experiments showed that the carbonyl group at C-19 of compounds 4, 6, and 7 formed strong hydrogen bonds with ARG315, which may make them have moderate inhibitory activity.

Screening coffee genotypes for brown eye spot resistance in Brazil.

Several researchers have attempted to develop coffee plants that are resistant to brown eye spot (BES); however, no coffee cultivars are resistant to the disease. In the present study, a blend of strains from Cercospora coffeicola was inoculated into 19 Brazilian commercial cultivars and 41 accessions from the Germplasm Collection of Minas Gerais to evaluate the genetic resistance ability within the population and select superior genotypes for the breeding program. After predicting the genotypic values of the estudied material, the evaluations number necessary for selecting genotypes with accuracy and efficiency was determined based on the data of severity to BES. The action of defense mechanisms plant was also investigated by assessing the levels of total soluble phenolic compounds and soluble lignin in contrasting genotypes for disease susceptibility. Based on the results, the accession MG 1207 Sumatra, had an intrinsic genetic capacity to maintain low levels of severity to BES. The genotype MG 1207 Sumatra can substantially contribute to the development of new cultivars, which may lead to the reduced use of pesticides. According to the accuracy and efficiency results obtained, four evaluations BES severity are sufficient to achieve accuracy, providing expressive genetic gains. Finally, the levels of lignin and phenolic compounds were not found to be associated with the resistance of coffee genotypes to BES.

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

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.