Review on factors affecting coffee volatiles: from seed to cup.

The objective of this review is to evaluate the influence of six factors on coffee volatiles. At present, the poor aroma from robusta or low-quality arabica coffee can be significantly improved by advanced technology, and this subject will continue to be further studied. On the other hand, inoculating various starter cultures in green coffee beans has become a popular research direction for promoting coffee aroma and flavor. Several surveys have indicated that shade and altitude can affect the content of coffee aroma precursors and volatile organic compounds (VOCs), which remain to be fully elucidated. The emergence of the new roasting process has greatly enriched the aroma composition of coffee. Cold-brew coffee is one of the most popular trends in coffee extraction currently, and its influence on coffee aroma is worthy of in-depth and detailed study. Omics technology will be one of the most important means to analyze coffee aroma components and their quality formation mechanism. A better understanding of the effect of each parameter on VOCs would assist coffee researchers and producers in the optimal selection of post-harvest parameters that favor the continuous production of flavorful and top-class coffee beans and beverages. © 2021 Society of Chemical Industry.

The complete chloroplast genome of Coffea liberica (Gentianales: Rubiaceae).

Coffee is one of the most popular beverages around the world. As one of the best-known coffee species, Liberian coffee (Coffea liberica Bull ex Hiern 1876) has a high resistance to leaf rust, a devasting disease caused by Hemileia vastatrix. However, there are few reports on the systematic position and phylogenetic relationship of C. liberica at the chloroplast (cp) genome level. Thus, we successfully assembled its cp genome. The full length is 154,799 bp with a GC content of 37.48%. We have further annotated the cp genome and predicted 85 protein-coding genes together with 8 rRNAs and 37 tRNAs. Furthermore, a large single copy region (LSC), a small single copy region (SSC), an inverted repeat region a (IRa) and an inverted repeat region b (IRb) are identified with lengths of 84,868 bp, 18,121 bp, 25,905 bp and 25,905 bp, respectively. The phylogenetic tree indicates that C. liberica is closely related to C. canephora, which is consistent with a previous result obtained from genotyping-by-sequencing.

Metabolite Profiling and Transcriptome Analysis Revealed the Conserved Transcriptional Regulation Mechanism of Caffeine Biosynthesis in Tea and Coffee Plants.

Caffeine is a characteristic bioactive compound in tea and coffee plants, which is synthesized and accumulated extensively in leaves and seeds. However, little is known about the regulatory mechanism of caffeine synthesis in plants. This study compared the caffeine metabolite between tea and coffee plants. We found that tea leaves contained significantly higher caffeine than coffee leaves, which is perhaps due to more members of N-methyltransferase (NMT) genes as well as higher expression levels in tea plants. Substantial numbers of transcription factors were predicted to be involved in caffeine biosynthesis regulation, combining weighted gene co-expression network analysis and the cis-element of NMT promoter analysis in tea and coffee plants. Furthermore, analysis of the transcription factors from the caffeine-related modules suggested that the regulatory mechanism of caffeine biosynthesis was probably partly conservative in tea and coffee plants. This study provides an essential resource for the regulatory mechanism of caffeine biosynthesis in plants.

Chemical ingredients characterization basing on 1H NMR and SHS-GC/MS in twelve cultivars of Coffea arabica roasted beans.

This work aimed to study the composition differences of roasted beans between 12 coffee cultivars (Catimor 7963, HIBRIDO DE TIMOR, Ruiru 11, Castillo, DTARI 296, DTARI 366, DTARI 392, DTARI 585, SL28, SL34, Catuai-Amarelo and Catuai-Vermelho) from Bourbon-Typica group and Introgressed group under subtropical humid monsoon climate. The water-soluble compounds of roasted coffee beans were characterized by proton nuclear magnetic resonance spectroscopy (1H NMR), and the aroma components were analyzed by static headspace gas chromatography mass spectrometry (SHS-GC/MS). In total, 20 water soluble compounds and 43 volatile compounds were identified. Both water-soluble and volatile compounds are rich in acidic substances, and the content varied depending on the cultivars. Furthermore, principal component analysis (PCA) clustered 12 coffee cultivars into four groups. The four different chemically defined clusters of Arabica cultivars produced by chemical differences cannot reflect the traditional grouping based on introgressed, and it is one-sided to judge coffee quality based on lineage. These results give further insight into the quality characteristics of different coffee cultivars, which is of great significance for guiding the adjustment of cultivars' structure and the breeding of new cultivars.

Synergistic effect of chlorogenic acid and levofloxacin against Klebsiella pneumonia infection in vitro and in vivo.

The study aimed to investigate the antibacterial effect and potential mechanisms of chlorogenic acid (CA) in Klebsiella pneumonia (KPN) induced infection in vitro and in vivo. 62 KPN strains were collected from the First People's Hospital of Yunnan Province. CA and CA combined Levofloxacin (LFX) were detected for KPN biofilm (BF) formation in vitro. The lung infection mice model were established by KPN. The effect of CA (500 mg/kg), LFX (50 mg/kg) and CA combined LFX (250 mg/kg + 25 mg/kg) were evaluated through the survival of mice, the changes of inflammation factors of tumor necrosis factor-alpha (TNF-α), interleukin (IL)-1ß and IL-6 in serum, the histopathological analysis of lung and the protein expression of NLRP3 signaling pathway in vivo. A total of 62 KPNs were isolated and identified, of which 13 (21%) strains were BF positive. 8 (13%) strains were extended spectrum ß-lactamase strains (ESBLs), and 20 (32%) strains are ESBLs biofilm positive. In vitro study, CA and LFX showed a synergistic effect on KPN biofilm formation. In vivo mice experiment, CA, especially CA + LFX treated group significantly decreased the serum levels of TNF-α, IL-1ß and IL-6, improved the survival ratio and lung pathology changes, and also reduced the protein expression of ASC, caspase 1 p20, IL-1ß and phosphor NF-κB p65. CA could effectively alleviate lung infection of KPN infected mice, and the antibacterial effection is strengthened by combined with LFX. The study provide a theroy basis for making rational and scientific antibacterial therapy strategy in clinic.

Genome-Wide Analysis of the PIN Auxin Efflux Carrier Gene Family in Coffee.

Coffee is one of the most popular beverages around the world, which is mainly produced from the allopolyploid Coffea arabica. The genomes of C. arabica and its two ancestors C. canephora and C. eugenioides have been released due to the development of next generation sequencing. However, few studies on C. arabica are related to the PIN-FORMED (PIN) auxin efflux transporter despite its importance in auxin-mediated plant growth and development. In the present study, we conducted a genome-wide analysis of the PIN gene family in the three coffee species. Totals of 17, 9 and 10 of the PIN members were characterized in C. Arabica, C. canephora and C. eugenioides, respectively. Phylogenetic analysis revealed gene loss of PIN1 and PIN2 homologs in C. arabica, as well as gene duplication of PIN5 homologs during the fractionation process after tetraploidy. Furthermore, we conducted expression analysis of PIN genes in C. arabica by in silico and qRT-PCR. The results revealed the existence of gene expression dominance in allopolyploid coffee and illustrated several PIN candidates in regulating auxin transport and homeostasis under leaf rust fungus inoculation and the tissue-specific expression pattern of C. arabica. Together, this study provides the basis and guideline for future functional characterization of the PIN gene family.

Molecular cloning and characterization of a novel isoflavone reductase-like gene (FcIRL) from high flavonoids-producing callus of Fagopyrum cymosum.

Lignans are important defensive compounds in plants and have good biological activities protecting human health. In order to study the medicinal secondary metabolism of Fagopyrum cymosum (Trev.) Meisn, a traditional Chinese medicine with anti-tumor effect, a novel isoflavone reductase-like gene, FcIRL, was cloned using RACE strategy from a cDNA library of high flavonoids-producing callus. The full-length cDNA of the FcIRL was 1 217 bp (accession no. EU116032), which contained a 942 bp open reading frame (ORF) encoding a 313 amino acid protein. Two stop codons (TAG) and a putative polyadenylation signal ATAAA at 24 bp upstream from the polyadenylation site was found in 5' and 3' UTR, separately. And no intron was found in the genomic sequence yet. FcIRL contained a predicted N-terminal acetylation site (M1-K5) and a NADPH-binding motif (G10-G-T-G13-Y-I-G16) in the N-terminal region, a conserved NmrA (nitrogen metabolite repression regulator) domain (V6-N244), multi-phosphorylation sites and one conserved N-glycosylation site (N214). Sequence homology comparison, phylogenetic analysis and advanced structures prediction all suggested that FcIRL belonged to the class of pinoresinol-lariciresinol reductase (PLR), which is a key enzyme in synthetic pathway of 8-8'-linked lignans, with function in catalyzing reduction of pinoresinol and lariciresinol into secoisolariciresinol, and medicinal secondary metabolism and resistance in F. cymosum.

[Cloning and molecular characteristics analysis of a MYB gene from Fagopyrum dibotrys].

Using RACE with a Fagopyrum dibotrys callus cDNA library, one clone, named FdMYBP1, encoding a putative R2R3 MYB protein was identified. FdMYBP1 appeared to be a full-length cDNA of 1159 bp encoding a protein of 265 amino acids. Through structure and property analysis of FdMYBPI with bioinformational methods, it was found that the amino acid sequence of FdMYBP1 showed great homology to other MYBP with the R2R3 repeat region in the N-terminus. Southern blot analysis indicated that FdMYBP1 belongs to a single copy gene in F. dibotrys genomes. The FdMYBP1 gene has the same classic characters with other MYBP and probably involved in the pathway of flavonoid metabolisms.