Regulation of galactomannan biosynthesis in coffee seeds

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.

Changes in structure and physicochemical properties of Sophora japonica f. pendula galactomannan in late growth stage

Galactomannan (GM) has been widely applied in food and other fields due to its appealing physicochemical properties. In this work, considering the changes in structural and physicochemical properties of Sophora japonica f. pendula (SJ-GM) with very high mannose to galactose (M/G) ratio in the late deposition stage, extensive exploration is conducted. The core of structural change is the change of M/G ratio (4.94-5.68), which is caused by the loss of galactose side residues modulated by α-d-galactosidase during seed maturation. Afterwards, the more compact conformation, the higher molecular weight, the increased hydrophobicity, and the greater solution viscosity of SJ-GM can be caused. Notably, the gel strength of SJ-GM with the highest M/G surpasses other GMs, including fenugreek gum (M/G = 1.20), guar gum (M/G = 1.80), Gleditsia microphylla gum (M/G = 2.77), and LBG (M/G = 4.00). Finally, SJ-GM is proven to be an attractive alternative to other GMs.

Glucomannan in Dendrobium catenatum: Bioactivities, Biosynthesis and Perspective

Dendrobium catenatum is a classical and precious dual-use plant for both medicine and food in China. It was first recorded in Shen Nong’s Herbal Classic, and has the traditional functions of nourishing yin, antipyresis, tonifying the stomach, and promoting fluid production. The stem is its medicinal part and is rich in active polysaccharide glucomannan. As an excellent dietary fiber, glucomannan has been experimentally confirmed to be involved in anti-cancer, enhancing immunity, lowering blood sugar and blood lipids, etc. Here, the status quo of the D. catenatum industry, the structure, bioactivities, biosynthesis pathway and key genes of glucomannan are systematically described to provide a crucial foundation and theoretical basis for understanding the value of D. catenatum and the potential application of glucomannan in crop biofortification.

Genomic and physiological evaluation of two root associated Pseudomonas from Coffea arabica

Many Pseudomonas species promote plant growth and colonize a wide range of environments. The annotation of a Coffea arabica ESTs database revealed a considerable number of Pseudomonas sequences. To evaluate the genomic and physiology of Pseudomonas that inhabit coffee plants, fluorescent Pseudomonas from C. arabica root environment were isolated. Two of them had their genomes sequenced; one from rhizospheric soil, named as MNR3A, and one from internal part of the root, named as EMN2. In parallel, we performed biochemical and physiological experiments to confirm genomic analyses results. Interestingly, EMN2 has achromobactin and aerobactin siderophore receptors, but does not have the genes responsible for the production of these siderophores, suggesting an interesting bacterial competition strategy. The two bacterial isolates were able to degrade and catabolize plant phenolic compounds for their own benefit. Surprisingly, MNR3A and EMN2 do not contain caffeine methylases that are responsible for the catabolism of caffeine. In fact, bench experiments confirm that the bacteria did not metabolize caffeine, but were resistant and chemically attracted to it. Furthermore, both bacteria, most especially MNR3A, were able to increase growth of lettuce plants. Our results indicate MNR3A as a potential plant growth promoting bacteria.

Modern mannan: a hemicellulose's journey

Hemicellulosic polysaccharides built of β-1,4-linked mannose units have been found throughout the plant kingdom and have numerous industrial applications. Here, I review recent advances in the biosynthesis and modification of plant β-mannans. These matrix polymers can associate with cellulose bundles to impact the mechanical properties of plant fibers or biocomposites. In certain algae, mannan microfibrils even replace cellulose as the dominant structural component of the cell wall. Conversely, patterned galactoglucomannan found in Arabidopsis thaliana seed mucilage significantly modulates cell wall architecture and abiotic stress tolerance despite its relatively low content. I also discuss the subcellular requirements for β-mannan biosynthesis, the increasing number of carbohydrate-active enzymes involved in this process, and the players that continue to be puzzling. I discuss how cellulose synthase-like enzymes elongate (gluco)mannans in orthogonal hosts and highlight the discoveries of plant enzymes that add specific galactosyl or acetyl decorations. Hydrolytic enzymes such as endo-β-1,4-mannanases have recently been involved in a wide range of biological contexts including seed germination, wood formation, heavy metal tolerance, and defense responses. Synthetic biology tools now provide faster tracks to modulate the increasingly-relevant mannan structures for improved plant traits and bioproducts.

Coffee cell walls—composition, influence on cup quality and opportunities for coffee improvements

The coffee beverage is the second most consumed drink worldwide after water. In coffee beans, cell wall storage polysaccharides (CWSPs) represent around 50 per cent of the seed dry mass, mainly consisting of galactomannans and arabinogalactans. These highly abundant structural components largely influence the organoleptic properties of the coffee beverage, mainly due to the complex changes they undergo during the roasting process. From a nutritional point of view, coffee CWSPs are soluble dietary fibers shown to provide numerous health benefits in reducing the risk of human diseases. Due to their influence on coffee quality and their health-promoting benefits, CWSPs have been attracting significant research attention. The importance of cell walls to the coffee industry is not restricted to beans used for beverage production, as several coffee by-products also present high concentrations of cell wall components. These by-products include cherry husks, cherry pulps, parchment skin, silver skin, and spent coffee grounds, which are currently used or have the potential to be utilized either as food ingredients or additives, or for the generation of downstream products such as enzymes, pharmaceuticals, and bioethanol. In addition to their functions during plant development, cell walls also play a role in the plant’s resistance to stresses. Here, we review several aspects of coffee cell walls, including chemical composition, biosynthesis, their function in coffee’s responses to stresses, and their influence on coffee quality. We also propose some potential cell wall–related biotechnological strategies envisaged for coffee improvements.

Comparative transcriptome and metabolome profiling in the maturing seeds of contrasting cluster bean (Cyamopsis tetragonoloba L. Taub) cultivars identified key molecular variations leading to increased gum accumulation

Cluster bean (Guar) is the major source of industrial gum. Knowledge on the molecular events regulating galactomannan gum accumulation in guar will pave way for accelerated development of gummy guar genotypes. RNA Seq analysis in the immature seeds of contrasting cluster bean genotypes HGS 563 (gum type) and Pusa Navbahar (vegetable type) resulted in the generation of 19,855,490 and 21,488,472 quality reads. Data analysis identified 4938 differentially expressed genes between the gummy vs vegetable genotypes. A set of 2241 genes were up-regulated and 2587 genes were down-regulated in gummy guar. Significant up-regulation of genes involved in the biosynthesis of galactomannan and cell wall storage polysaccharides was observed in the gummy HGS 563. Genes involved in carotenoids, flavonoids, non mevalonic acid, terpenoids, and wax metabolism were also up-regulated in HGS 563. Mannose and galactose were the major nucleotide sugars in Pusa Navbahar and HGS 563 immature seeds. Immature seeds of HGS 563 showed high concentration of mannose and galactose accumulation compared to Pusa Navbahar. qRT-PCR analysis of selected genes confirmed the findings of transcriptome data.

Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa

Caulerpa is an unusual algal genus from Caulerpaceae (Chlorophyta, Bryopsidales). Species from this family produce a wide range of metabolites suitable for biotechnology applications. Among these, sulfated polysaccharides (SPs) are often highly desirable for pharmaceutical and nutraceutical applications. Here, we provide a classification of sulfotransferases from Caulerpa; these important enzymes catalyze the nodal step for the biosynthesis of SPs. For this, we performed phylogenetic, genomic, expression analyses and prediction of the protein structure on sulfotransferases from Caulerpa. Sequences, domains and structures of sulfotransferases generally shared common characteristics with other plants and algae. However, we found an extensive duplication of sulfotransferase gene family, which is unique among the green algae. Expression analysis revealed specific transcript abundance in the pinnae and rachis of the alga. The unique genomic features could be utilized for the production of complex SPs, which require multiple and specific sulfation reactions. The expansion of this gene family in Caulerpaceae would have resulted in a number of proteins characterizing the unique SPs found in these algae. We provide a putative biosynthetic pathway of SPs, indicating the unique characteristics of this pathway in Caulerpa species. These data may help in the future selection of Caulerpa species for both commercial applications and genetic studies to improve the synthesis of valuable products from Caulerpa.

Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora

The endosperm cell walls of mature coffee seeds accumulate large amounts of mannan storage polysaccharides, which serve as nutrient reserve for embryo and contribute to beverage quality. Our study investigated the evolutionary patterns of key galactomannan (GM) biosynthesis genes using d N/d S ratio, synteny, and phylogenetic analysis and detected heterogeneity in rate of evolution among gene copies. Selection ratio index revealed evidence of positive selection in the branch editing gene Coffea canephora alpha (α) galactosidase (Cc-alpha Gal) at Cc11_g15950 copy (ω = 1.12), whereas strong purifying selection on deleterious mutations was observed in the Coffea canephora uridine diphosphate (UDP)-glucose 4'-epimerase (Cc-UG4E) and Coffea canephora mannose-1P guanylytransferase (Cc-MGT) genes controlling the crucial nucleotide carbon sugar building blocks flux in the pathway. Relatively low sequence diversity and strong syntenic linkages were detected in all GM pathway genes except in Cc-alpha Gal, which suggests a correlation between selection pressure and nucleotide diversity or synteny analysis. In addition, phylogenetic analysis revealed independent evolution or expansion of GM pathway genes in different plant species, with no obvious inferable clustering patterns according to either gene family or congruent with evolutionary plants lineages tested due to high dynamic nature and specific biochemical cell wall modification requirements. Altogether, our study shows a significant high rate of evolutionary variation among GM pathway genes in the diploid C. canephora and demonstrates the inherent variation in evolution of gene copies and their potential role in understanding selection rates in a homogenously connected metabolic pathway.

Global Gene Expression of Seed Coat Tissues Reveals a Potential Mechanism of Regulating Seed Size Formation in Castor Bean

The physiological and molecular basis of seed size formation is complex, and the development of seed coat (derived from integument cells) might be a critical factor that determines seed size formation for many endospermic seeds. Castor bean (Ricinus communis L.), a model system of studying seed biology, has large and persistent endosperm with a hard seed coat at maturity. Here, we investigated the potential molecular mechanisms underlying seed size formation in castor bean by comparing the difference between global gene expression within developing seed coat tissues between the large-seed ZB107 and small-seed ZB306. First, we observed the cell size of seed coat and concluded that the large seed coat area of ZB107 resulted from more cell numbers (rather than cell size). Furthermore, we found that the lignin proportion of seed coat was higher in ZB306. An investigation into global gene expression of developing seed coat tissues revealed that 815 genes were up-regulated and 813 were down-regulated in ZB306 relative to ZB107. Interestingly, we found that many genes involved in regulating cell division were up-regulated in ZB107, whereas many genes involved in regulating lignin biosynthesis (including several NAC members, as well as MYB46/83 and MYB58/63) and in mediating programmed cell death (such as CysEP1 and βVPE) were up-regulated in ZB306. Furthermore, the expression patterns of the genes mentioned above indicated that the lignification of seed coat tissues was enhanced and occurred earlier in the developing seeds of ZB306. Taken together, we tentatively proposed a potential scenario for explaining the molecular mechanisms of seed coat governing seed size formation in castor bean by increasing the cell number and delaying the onset of lignification in seed coat tissues in large-seed ZB107. This study not only presents new information for possible modulation of seed coat related genes to improve castor seed yield, but also provides new insights into understanding the molecular basis of seed size formation in endospermic seeds with hard seed coat.

Mechanistic insights from plant heteromannan synthesis in yeast

Heteromannan (HM) is one of the most ancient cell wall polymers in the plant kingdom, consisting of β-(1-4)-linked backbones of glucose (Glc) and mannose (Man) units. Despite the widespread distribution of HM polysaccharides, their biosynthesis remains mechanistically unclear. HM is elongated by glycosyltransferases (GTs) from the cellulose synthase-like A (CSLA) family. MANNAN-SYNTHESIS RELATED (MSR) putative GTs have also been implicated in (gluco)mannan synthesis, but their roles have been difficult to decipher in planta and in vitro. To further characterize the products of the HM synthases and accessory proteins, we chose a synthetic biology approach to synthesize plant HM in yeast. The expression of a CSLA protein in Pichia pastoris led to the abundant production of plant HM: up to 30% of glycans in the yeast cell wall. Based on sequential chemical and enzymatic extractions, followed by detailed structural analyses, the newly produced HM polymers were unbranched and could be larger than 270 kDa. Using CSLAs from different species, we programmed yeast cells to produce an HM backbone composed exclusively of Man or also incorporating Glc. We demonstrate that specific MSR cofactors were indispensable for mannan synthase activity of a coffee CSLA or modulated a functional CSLA enzyme to produce glucomannan instead of mannan. Therefore, this powerful platform yields functional insight into the molecular machinery required for HM biosynthesis in plants.

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.

Farm to Consumer: Factors Affecting the Organoleptic Characteristics of Coffee. II: Postharvest Processing Factors

The production and consumption of coffee are increasing despite the roadblocks to its agriculture and global trade. The unique, refreshing, and stimulating final cupping quality of coffee is the only reason for this rising production and consumption. Coffee quality is a multifaceted trait and is inevitably influenced by the way it is successively processed after harvesting. Reportedly, 60% of the quality attributes of coffee are governed by postharvest processing. The current review elaborates and establishes for the first time the relationship between different methods of postharvest processing of coffee and its varying organoleptic and sensory quality attributes. In view of the proven significance of each processing step, this review has been subdivided into three sections, secondary processing, primary processing, and postprocessing variables. Secondary processing addresses the immediate processing steps on the farm after harvest and storage before roasting. The primary processing section adheres specifically to roasting, grinding and brewing/extraction, topics which have been technically addressed more than any others in the literature and by industry. The postprocessing attribute section deals generally with interaction of the consumer with products of different visual appearance. Finally, there are still some bottlenecks which need to be addressed, not only to completely understand the relationship of varying postharvest processing methods with varying in-cup quality attributes, but also to devise the next generation of coffee processing technologies.

V. AM, Solanke AU, Singh NK, Sharma TR, Gaikwad K. Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Owing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC-936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP- D-glucose 4-epimerase) and validated as targets for three novel miRNAs, that is Ct-miR3130, Ct-miR3135 and Ct-miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan-producing species.

Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds

The 'intermediate seed' category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage and has implications for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone contents, and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis, and respiration, and the up-regulation of genes coding for late-embryogenesis abundant (LEA) proteins, heat-shock proteins (HSPs), and antioxidant enzymes. Analysis of the heat-stable proteome in mature coffee seeds confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggested a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ, and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.

Infant food applications of complex carbohydrates: Structure, synthesis, and function

Professional health bodies such as the World Health Organization (WHO), the American Academy of Pediatrics (AAP), and the U.S. Department of Health and Human Services (HHS) recommend breast milk as the sole source of food during the first year of life. This position recognizes human milk as being uniquely suited for infant nutrition. Nonetheless, most neonates in the West are fed alternatives by 6 months of age. Although inferior to human milk in most aspects, infant formulas are able to promote effective growth and development. However, while breast-fed infants feature a microbiota dominated by bifidobacteria, the bacterial flora of formula-fed infants is usually heterogeneous with comparatively lower levels of bifidobacteria. Thus, the objective of any infant food manufacturer is to prepare a product that results in a formula-fed infant developing a breast-fed infant-like microbiota. The goal of this focused review is to discuss the structure, synthesis, and function of carbohydrate additives that play a role in governing the composition of the infant microbiome and have other health benefits.

Advances in genomics for the improvement of quality in coffee

Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programmes. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. © 2016 Society of Chemical Industry.

Seed germination and seedling development in response to submergence in tree species of the Central Amazonian floodplains

Successful germination and seedling establishment are crucial steps for maintenance and expansion of plant populations and recovery from perturbations. Every year the Amazon River and its tributaries overflow and flood the adjacent forest, exerting a strong selective pressure on traits related to seedling recruitment. We examined seed characteristics, stored reserves, germination, seedling development and survival under water of eight representative tree species from the lower portions of the flood-level gradient to identify adaptive strategies that contribute to their regeneration in this extreme ecosystem. Submerged seedlings were assessed for longevity and survival until they showed symptoms of injury. At this point, the remaining healthy seedlings were planted in unsaturated soil to monitor recovery after re-exposure to air over 30 days. All small (seed mass ≤0.17 g) seeds had epigeal phanerocotylar-type germination, a trait that would allow plants to acquire light and CO2 in the shortest time. Cell wall storage polysaccharide was a major component of all seeds, suggesting plant investment in structural reserves. Seven of the eight species germinated and formed healthy seedlings under water that endured submersion without any apparent injury for periods of 20-115 days, depending on the species. Seedlings of some species changed the direction of root growth and grew towards the surface of the water, which might have increased the uptake of oxygen to the tissues. Only one of the seven species did not survive re-exposure to air. Species able to germinate and produce seedlings under submersion, which subsequently are able to establish in aerated soils, would have more time available for terrestrial growth. This is critical for colonization of lower portions of the flood-level gradient where establishment is constrained by the short terrestrial phase that precedes the next flood.