Pyridine nucleotide cycle and trigonelline (N-methylnicotinic acid) synthesis in developing leaves and fruits of Coffea arabica

We examined the biosynthesis of trigonelline in leaves and fruits of Arabica coffee ( Coffea arabica ) plants. [³H]Quinolinic acid, which is an intermediate of de novo pyridine nucleotide synthesis, and [¹⁴C]nicotinamide and [¹⁴C]nicotinic acid, which are degradation products of NAD, were converted to trigonelline and pyridine nucleotides. These tracer experiments suggest that the pyridine nucleotide cycle, nicotinamide → nicotinic acid → nicotinic acid mononucleotide (NaMN) → nicotinic acid adenine dinucleotide (NaAD) → NAD → nicotinamide mononucleotide (NMN) → nicotinamide, operates in coffee plants, and trigonelline is synthesized from nicotinic acid formed in the cycle. Trigonelline accumulated up to 18 µmol per leaf in developed young leaves, and then decreased with age. Although the biosynthetic activity of trigonelline from exogenously supplied [¹⁴C]nicotinamide was observed in aged leaves, the endogenous supply of nicotinamide may be limited, reducing the contents in these leaves. Trigonelline is synthesized and accumulated in fruits during development. The trigonelline synthesis in pericarps is much higher than that in seeds, but its content in seeds is higher than pericaps, so that some of the trigonelline synthesized in the pericarps may be transported to seeds. Trigonelline in seeds may be utilized during germination, as its content decreases. Trigonelline synthesis from [¹⁴C]nicotinamide was also found in Theobroma cacao plants, but instead of trigonelline, nicotinic acid-glucoside was synthesized from [¹⁴C]nicotinamide in Camellia sinensis plants.     

A Role for Trigonelline During Imbibition and Germination of Coffee Seeds

Abstract: Trigonelline was investigated as an NAD reserve during germination of coffee ( Coffea arabica L.) seeds. Seeds were germinated on filter paper moistened with water or in agar and the endogenous content of trigonelline, nicotinic acid and NAD investigated in the endosperm, embryo and germination medium. Seeds were also fed with [ carboxyl -¹⁴C]trigonelline and the distribution of the radioactivity in these compounds was investigated. In addition, trigonelline demethylase was detected in coffee for the first time, showing a K_m of 1.13 mM. The activity increased with germination. These data clearly show that in seeds there is a significant conversion of trigonelline to NAD, although a concomitant biosynthesis of the alkaloid is also observed. It is concluded that trigonelline is indeed a reserve molecule for NAD biosynthesis but this function may be limited to the very early stages of germination or restricted to specific tissues, such as the embryo.     

Wild coffee management and plant diversity in the montane rainforest of southwestern Ethiopia

Coffea arabica occurs naturally in the montane rainforests of Ethiopia, but large areas of these unique forests have been converted to other land-uses. In the remaining forest, wild coffee is managed and harvested with increasing intensity because of rising coffee prices in the world market. This study evaluated the impact of coffee management on wild coffee populations and the forest vegetation as a basis for conservation planning in southwestern Ethiopia. Vegetation surveys and yield assessments were carried out in unmanaged natural forest and in managed semi-forest coffee (SFC) systems. Analyses show that wild coffee density and coffee yields were low in natural forest (max. 15 kg ha⁻¹ year⁻¹). In SFC systems, 30% of the canopy trees and most undergrowth vegetation were removed. This stimulated wild coffee growth and strongly enhanced yields (max. 54 kg ha⁻¹ year⁻¹), but severely disturbed forest structure. Species richness increased by 26% because of an increase in species of ruderal and secondary vegetation; however, species richness and abundance of typical forest species declined. Conservation of the natural forest therefore requires the control of wild coffee management. Wild coffee certification is discussed as one tool to reconcile conservation measures and the interests of local farmers.     

An Intermediate Category of Seed Storage Behaviour?II. EFFECTS OF PROVENANCE, IMMATURITY, AND IMBIBITION ON DESICCATION-TOLERANCE IN COFFEE

Seeds of four cultivars of arabica coffee (Coffea arabica L.)received from three continents survived desiccation to between7-2% and 11-3% moisture content (wet basis), i.e. to seed waterpotentials of –90 MPa to –150 MPa, but further desiccationreduced germination (criterion, normal seedling development)in all seed lots. Only a few individuals from four of the lotsgerminated after being dried to 4–5% moisture content.Differences in desiccation sensitivity were apparent among lotswithin each cultivar. Desiccation sensitivity in these lotswas similar to that observed in seeds of orthodox species whichhave begun to germinate. Seeds extracted from fruits of intermediatematurity (yellow) were able to tolerate greater desiccationthan those from either ripe (red) or immature (green) fruits.Imbibed storage increased desiccation sensitivity. The resultsare compatible with the view that arabica coffee seeds are unableto tolerate extreme desiccation because germination has beeninitiated before harvest.     

An Intermediate Category of Seed Storage Behaviour?: I. COFFEE

Seeds of four cultivars of arabica coffee (Coffea arabica L.)were tested for germination following hermetic storage for upto 12 months at several different combinations of temperaturesbetween –20 °C and 15 °C and moisture contentsbetween 5% and 10% (wet basis). Most of the seeds from one cultivarwithstood desiccation to between 5% and 6% moisture content,a seed water potential of approximately –250 MPa, butthose of the remaining three cultivars were much more sensitiveto desiccation damage. Moreover, in all four cultivars, seedlongevity at cool and sub-zero temperatures, and at low moisturecontents did not conform with orthodox seed storage behaviour:viability was lost more rapidly under these conditions thanat either warmer temperatures or higher moisture contents. Theresults confirm that coffee seeds fail to satisfy the definitionsof either typical orthodox or recalcitrant seed storage behaviour.These results, therefore, point to the possibility of a thirdcategory of storage behaviour intermediate between those oforthodox and recalcitrant seeds. One of the main features ofthis category is that dry seeds are injured by low temperatures. Key words: coffee, Coffea arabica L., seed storage, seed longevity, desiccation, temperature     

Biochemical and molecular characterization and expression of the 11S-type storage protein from Coffea arabica endosperm

In order to define better the endosperm protein content of commercial coffee species Coffea arabica (Arabica) and C. canephora (Robusta), the principal storage protein of coffee grains has been analysed by 2-dimensional electrophoresis (2DE) and amino acid microsequencing. The most abundant polypeptide spots observed on mature coffee grain 2DE profiles were found to be subunits of the same protein, which exists as multiple isoforms with varying pIs. Strong sequence similaritywas found to the 11S family of plant storage proteins. The structure is typical of the 11S type, which occurs as a precursor of 55 kDa, and is observed under denaturing and reducing conditions on 2DE profiles in the form of cleavage products at approximately 20 kDa (β arms) and 32 kDa (α arms). Differences between Arabica and Robusta 2DE profiles indicate a secondary 11S protein family in some varieties of the latter. The existence of multiple pI forms may indicate that a multigene family encodes for these proteins. We estimate that the protein accounts for approximately 45 % of total grain protein. A cloned full-length cDNA of 1 706 bp coding for one of the isoforms is described and discussed in relation to other coffee storage protein sequences.     

Equivalent pore radii of hydrophilic foliar uptake routes in stomatous and astomatous leaf surfaces – further evidence for a stomatal pathway

Foliar uptake pathways for hydrophilic solutes were studied by the analysis of co-uptake of ¹⁵N-labelled urea, NH₄⁺ or NO₃⁻ and ¹³C-labelled sucrose across leaf surfaces of various plant species. Uptake of N (y) and sucrose (x) were strongly correlated. Curvilinear regression revealed significantly positive intercepts with the y-axis indicating the involvement of a sucrose-excluding pathway consisting of small pores with radii <0.5 nm. Depending on plant species, N source, leaf side and aperture of stomata, these small pores accounted for 6–62% of total N uptake. Regression analysis revealed that in stomatous leaf surfaces of Vicia faba L., Coffea arabica L. and Prunus cerasus L., the remaining N uptake occurred via another pathway with an estimated average pore radius (r_P) greater than 20 nm. This is two orders of magnitude greater than previous estimations of cuticular r_P, indicating that this pathway, which was only found in stomatous leaf surfaces, was probably not located in the cuticle but at the surfaces of the stomatal pores. In astomatous leaf surfaces of C. arabica and Populus × canadensis Moench, average r_P was 2.0 and 2.4 nm, respectively, which is four to eight times larger than previous estimations of cuticular r_P. These results indicate that for polar solutes, the size exclusion limits of plant surfaces can be considerably larger than previously estimated. The far-reaching implications of these findings are discussed.     

AFLP analysis of genetic diversity within and among Coffea arabica cultivars

Genetic diversity of Coffea arabica cultivars was estimated using amplified fragment length polymorphism (AFLP) markers. Sixty one Coffea accessions composed of six arabica cultivars, including Typica, Bourbon, Catimor, Catuai, Caturra and Mokka Hybrid, plus two diploid Coffea species, were analyzed with six EcoRI- MseI primer combinations. A total of 274 informative AFLP markers were generated and scored as binary data. These data were analyzed using cluster methods in the software package NTSYSpc. The differences among cultivars at the DNA level were small, with an average genetic similarity of 0.933. Most accessions within a cultivar formed a cluster, although deviant samples occurred in five of the six cultivars examined due to residual heterozygosity from ancestral materials. Among the six cultivars fingerprinted, the highest level of genetic diversity was found within the cultivar Catimor, with an average genetic similarity of 0.880. The lowest level was found within Caturra accessions, with an average genetic similarity of 0.993. Diversity between C. arabica and two other Coffea species, Coffea canephora and Coffea liberica, was also estimated with average genetic similarities of 0.540 and 0.413, respectively, suggesting that C. canephora is more closely related to C. arabica than is C. liberica. The genetic variation among arabica cultivars was similar to the variation within cultivars, and no cultivar-specific DNA marker was detected. Although arabica cultivars appear to have a narrow genetic base, our results show that sufficient polymorphism can be found among some arabica cultivars with a genetic similarity as low as 0.767 for genetic/QTL mapping and breeding. The assessment of genetic diversity among arabica cultivars provided the necessary information to estimate the potential for using marker-assisted breeding for coffee improvement.     

Legumin- and vicilin-like proteins from spores of the fern Matteuccia struthiopteris

Legumin- and vicilin-like proteins have been isolated from spores of the fern Matteuccia struthiopteris. Their relationship with seed legumin and vicilin was demonstrated by cross-reactivities of antibodies directed against respective storage globulins from Vicia faba as evidenced by Western blotting. The Matteuccia legumin-like protein was characterised as a 300-340 kDa holoprotein preferentially consisting of a 32 kDa alpha-chain and a 24 kDa beta-chain. Patterns of limited proteolysis of the spore legumin-like protein and seed legumins were similar as well. In contrast to seed legumins, the Matteuccia legumin-like protein is devoid of disulfide bridges between alpha- and beta-chains. A 52 kDa polypeptide of the Matteuccia vicilin-like protein, first detected by SDS gel electrophoresis, is probably encoded by a vicilin-like gene specifically expressed in Matteuccia struthiopteris spores (Shutov et al. 1998). The vicilin-like holoprotein was found to form a complex of 600 kDa apparent molecular mass, presumably composed of four vicilin-like trimers.     

N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species

Cells of Geobacter metallireducens , Magnetospirillum strain AMB-1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N₂-dependent growth, the first anaerobically with Fe(III) as the electron acceptor, and the latter three species microaerobically in semi-solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N₂ under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5 ± 5.9 nmol C₂H₄ produced min⁻¹ mg⁻¹ cell protein) while growing with Fe(III) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi-solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease-digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum , indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal-metabolizing genera, Geobacter and Magnetospirillum , fix atmospheric dinitrogen.     

Modification of the basic subunits of pea legumin on storage

Basic subunits of legumin of Pisum sativum undergo a modification on storage of dry seeds which increases their apparent MW on SDS-polyacrylamide gel electrophoresis and decreases their pI values.     

RAPD markers of mitochondrial origin exhibit lower population diversity and higher differentiation than RAPDs of nuclear origin in Douglas fir

We developed a method of screening RAPD markers for the presence of organelle DNA products using enriched organelle DNA probes, then used these markers to compare the structure of nuclear and mitochondrial RAPD diversity in Douglas fir. Of 237 screened RAPD fragments from 25 primers, 16% were identified as originating in the mitochondrial genome and 3% in the chloroplast genome. The mitochondrial DNA probe correctly distinguished fragments with known maternal inheritance (which is exclusive for the mitochondrial genome in the Pinaceae), and neither of the organelle probes hybridized to biparentally inherited fragments. Mitochondrial RAPD markers exhibited low diversity within populations compared to nuclear RAPD diversity ( H _S = 0.03 and 0.22, respectively), but were much more highly differentiated than were fragments of nuclear origin at both the population ( G _ST = 0.18 and 0.05, respectively) and racial levels ( G _ST = 0.72 and 0.25, respectively). Both nuclear and mitochondrial DNA based phylogenetic analyses identified the varieties as monophyletic groups; the nuclear RAPD markers further separated the north and south interior races.     

Cloning and antigenic expression of two genes from Chlamydia psittaci avian strain

Abstract: Genes from Chlamydia psittaci P-1041 were cloned into the Bam HI site of pUC19 and were transformed to host Escherichia coli JM109. Two recombinant plasmids that expressed protein antigens of Chlamydia were isolated. The sizes of the DNA fragments were 1350 and 1710 bp, and encoded for polypeptides of M _r 25 and 42 kilodaltons (kDa), respectively. The 25-kDa protein had cross-reactivity with antisera to ten C. psittaci strains and two C. trachomatis strains, whereas the 42-kDa protein reacted only with homologous antiserum to the C. psittaci P-1041 strain. Furthermore, in Southern hybridization analysis these two fragments as probes hybridized with DNA of ten C. psittaci strains and four C. trachomatis strains. These results indicated that the two fragments shared a DNA sequence common to the chlamydial genus.     

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.).

Fluorescence in situ hybridization (FISH) was used to study the presence of alien chromatin in interspecific hybrids and one introgressed line (S.288) derived from crosses between the cultivated species Coffea arabica and the diploid relatives C. canephora and C. liberica. In situ hybridization using genomic DNA from C. canephora and C. arabica as probes showed elevated cross hybridization along the hybrid genome, confirming the weak differentiation between parental genomes. According to our genomic in situ hybridization (GISH) data, the observed genomic resemblance between the modern C. canephora genome (C) and the C. canephora-derived subgenome of C. arabica (Ca) appears rather considerable. Poor discrimination between C and Ca chromosomes supports the idea of low structural modifications of both genomes since the C. arabica speciation, at least in the frequency and distribution of repetitive sequences. GISH was also used to identify alien chromatin segments on chromosome spreads of a C. liberica-introgressed line of C. arabica. Further, use of GISH together with BAC-FISH analysis gave us additional valuable information about the physical localization of the C. liberica fragments carrying the SH3 factor involved in resistance to the coffee leaf rust. Overall, our results illustrate that FISH analysis is a complementary tool for molecular cytogenetic studies in coffee, providing rapid localization of either specific chromosomes or alien chromatin in introgressed genotypes derived from diploid species displaying substantial genomic differentiation from C. arabica.     

Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)

Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.     

The nucleoside diphosphate kinase of Mycobacterium smegmatis: identification of proteins that modulate specificity of nucleoside triphosphate synthesis by the enzyme

We report the purification and characterization of the enzyme nucleoside diphosphate kinase (Ndk) from Mycobacterium smegmatis . The N-terminus of the enzyme was blocked but an internal sequence showed approx. 70% homology with the same enzymes from Pseudomonas aeruginosa and Escherichia coli . Immobilization of the mycobacterial nucleoside diphosphate kinase on a Sepharose 4B matrix and passing the total cell extract through it revealed four proteins (P₇₀, P₆₅, P₆₀, and P₅₀, respectively) of M _r 70 kDa, 65 kDa, 60 kDa and 50 kDa that were retained by the column. While the proteins of M _r 70 kDa and 50 kDa modulated the activity of Ndk directing it towards GTP synthesis, the 60 kDa protein channelled the specificity of Ndk entirely towards CTP synthesis. The 65 kDa protein modulated the specificity of Ndk directing it entirely towards UTP synthesis. The specificity for such mycobacterial proteins towards NTP synthesis is retained when they are complexed with P. aeruginosa Ndk. We further demonstrate that the P₇₀ protein is pyruvate kinase and that each of the four proteins forms a complex with Ndk and alters its substrate specificity. Given the ubiquitous nature of Ndk in the living cell and its role in maintaining correct ratios of intracellular nucleoside triphosphates, the implications of the occurrence of these complexes have been discussed in relation to the precursor pool for cell wall biosynthesis as well as RNA/DNA synthesis.     

Legumin and vicilin,storage proteins of legume seeds

The structure, location in the seed and distribution of the storage protein of legume seeds are described. Methods which have been employed for the extraction, purification and characterisation of seed globulins are reviewed in relation to modern biochemical practice. The physical, chemical and immunological characteristics of the classical legumin and vicilin preparations from Pisum sativum are summarised and the distributions of proteins with sedimentation coefficients and/or immunological determinants similar to those of legumin and vicilin, are tabulated. The structure and composition of various purified legumin and vicilin-type proteins from a variety of legumes, are compared.     

Characterization of polyphenol oxidase in coffee

Polyphenol oxidase (PPO) was characterized in partially purified extracts of leaves (PPO-L) and fruit endosperm (PPO-E) of coffee (Coffea arabica L.). PPO activity was higher in early developmental stages of both leaves and endosperm of fruits. Wounding or exposure of coffee leaves to methyl jasmonate increased PPO activity 1.5-4-fold. PPO was not latent and was not activated by protease treatment. PPO activity was stimulated 10-15% with sodium dodecyl sulphate (SDS) at 0.35-1.75 mM, but at higher concentrations activities were similar to the control samples, without detergent. Prolonged incubation of extracts with trypsin or proteinase K inhibited PPO activity but pepsin had no effect. Inhibition of PPO with proteinase K was increased in the presence of SDS. PPO activity from both tissues was optimal at pH 6-7 and at an assay temperature of 30 degrees C. Activity was highest with chlorogenic acid as substrate with a Km of 0.882 mM (PPO-L) and 2.27 mM (PPO-E). Hexadecyl trimethyl-ammonium bromide, polyvinylpyrrolidone 40. cinnamic acid and salicylhydroxamic acid inhibited PPO from both tissues. Both enzymes were inactivated by heat but the activity in endosperm extracts was more heat labile than that from leaves. The apparent Mr determined by gel filtration was 46 (PPO-L) and 50 kDa (PPO-E). Activity-stained SDS polyacrylamide gel electrophoresis (PAGE) gels and western blots probed with PPO antibodies suggested the existence of a 67 kDa PPO which is susceptible to proteolytic cleavage that generates a 45 kDa active form.     

Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross‐species amplifications

Genetic improvement of coffee (Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic make‐up of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic‐resolution becomes highly desirable. Here, we report the development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica. The developed microsatellites revealed robust cross‐species amplifications in 17 related species of coffee, and their Polymorphic Information Content varied from 0 to 0.6, 0 to 0.78 and 0.67 to 0.90 for the arabica, robusta genotypes and species representatives, respectively. The data thus suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee.     

Fumonisin B1 production by Fusarium proliferatum strains isolated from Allium fistulosum plants and seeds in Japan

Aims:  To test the fumonisin B₁ - producing ability of Fusarium proliferatum strains isolated from Welsh onion ( Allium fistulosum ) plants and seeds of commercial cultivars in Japan and to examine the applicability of PCR-based assays to discriminate between fumonisin B₁-producing and nonproducing isolates.
Methods and Results:  Fumonisin B₁ levels in 20 Fusarium isolates obtained from Welsh onion plants and seeds of seven commercial cultivars were determined by HPLC. Thirteen of the 20 isolates produced fumonisin B₁. PCR assay with FUM1 gene-specific primers amplified a DNA fragment (700 bp) only from fumonisin-producing isolates.
Conclusions:  Fusarium proliferatum isolates that can produce fumonisin B₁ were often associated with wilted Welsh onion plants and seeds of some commercial cultivars. The PCR assay with FUM1 gene-specific primers has the potential to discriminate between fumonisin B₁-producing and nonproducing isolates.
Significance and Impact of the Study:  This study revealed that F. proliferatum producing fumonisin B₁ is associated with Welsh onion plants and that commercial cultivar seeds may be contaminated with the fungus. PCR amplification of FUM1 gene can be a useful tool for the rapid identification of fumonisin B₁-producing F. proliferatum isolates.