Enhancing yield of <Emphasis Type="Italic">S</Emphasis>-adenosylmethionine in <Emphasis Type="Italic">Pichia pastoris</Emphasis> by controlling NH<Subscript>4</Subscript><Superscript>+</Superscript> concentration

Yield of S-adenosylmethionine was improved significantly in recombinant Pichia pastoris by controlling NH₄ ⁺ concentration. The highest production rate was 0.248 g/L h when NH₄ ⁺ concentration was 450 mmol/L and no repression of cell growth was observed. Within very short induction time (47 h), 11.63 g/L SAM was obtained in a 3.7 L bioreactor.     

SNP marker diversity in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Single nucleotide polymorphism (SNP) markers have become a genetic technology of choice because of their automation and high precision of allele calls. In this study, our goal was to develop 94 SNPs and test them across well-chosen common bean (Phaseolus vulgaris L.) germplasm. We validated and accessed SNP diversity at 84 gene-based and 10 non-genic loci using KASPar technology in a panel of 70 genotypes that have been used as parents of mapping populations and have been previously evaluated for SSRs. SNPs exhibited high levels of genetic diversity, an excess of middle frequency polymorphism, and a within-genepool mismatch distribution as expected for populations affected by sudden demographic expansions after domestication bottlenecks. This set of markers was useful for distinguishing Andean and Mesoamerican genotypes but less useful for distinguishing within each gene pool. In summary, slightly greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool but polymorphism rate between genotypes was consistent with genepool and race identity. Our survey results represent a baseline for the choice of SNP markers for future applications because gene-associated SNPs could themselves be causative SNPs for traits. Finally, we discuss that the ideal genetic marker combination with which to carry out diversity, mapping and association studies in common bean should consider a mix of both SNP and SSR markers.     

Characterization of AT-rich microsatellites in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Polymorphism of microsatellite markers is often associated with the simple sequence repeat motif targeted. AT-rich microsatellites tend to be highly variable and this appears to be notable, especially in legume genomes. To analyze the value of AT-rich microsatellites for common bean (Phaseolus vulgaris L.), we developed a total of 85 new microsatellite markers, 74 of which targeted ATA or other AT-rich motif loci and 11 of which were made for GA, CA or CAC motif loci. We evaluated the loci for the level of allelic diversity in comparison to previously characterized microsatellites using a panel of 18 standard genotypes and genetically mapped any loci polymorphic in the DOR364 × G19833 population. The majority of the microsatellites produced single bands and detected single loci, however, 15 of the AT-rich microsatellites produced multiple or double banding patterns; while only one of the GA or CA-rich microsatellites did. The polymorphism information content (PIC) values averaged 0.892 and 0.600 for the AT and ATA motif microsatellites, respectively, but only 0.140 for the CA-rich microsatellites. GA microsatellites, which had a large average number of repeats, had high to intermediate PIC, averaging 0.706. A total of 45 loci could be genetically mapped and distribution of the loci across the genome was skewed towards non-distal locations with a greater prevalence of loci on linkage groups b02, b09 and b11. AT-rich microsatellites were found to be a useful source of polymorphic markers for mapping and diversity assessment in common bean that appears to uncover higher diversity than other types of simple sequence repeat markers.     

Exploring the quantitative resistance to <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> pv. <Emphasis Type="Italic">phaseolicola</Emphasis> in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Pseudomonas syringae pv. phaseolicola is an important disease that causes halo blight in common bean. The genetic mechanisms underlying quantitative halo blight resistance are poorly understood in this species, as most disease studies have focused on qualitative resistance. The present work examines the genetic basis of quantitative resistance to the nine halo blight races in different organs (primary and trifoliate leaf, stem and pod) of an Andean recombinant inbred line (RIL) progeny. Using a multi-environment quantitative trait locus (QTL) mapping approach, 76 and 101 main-effect and epistatic QTLs were identified, respectively. Most of the epistatic interactions detected were due to loci without detectable QTL additive main effects. Main and epistatic QTLs detected were mainly consistent across the environment conditions. The homologous genomic regions corresponding to 26 of the 76 main-effect detected QTLs were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins and known defence genes. Main-effect QTLs for resistance to races 3, 4 and 5 in leaf, stem and pod were located on chromosome 2 within a 3.01-Mb region, where a cluster of nine NL genes was detected. The NL gene Phvul.002G323300 is located in this region, which can be considered an important putative candidate gene for the non-organ-specific QTL identified here. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for halo blight resistance in common bean.     

Seasonal changes in plasma membrane H<Superscript>+</Superscript>-ATPase activity of <Emphasis Type="Italic">Vaccinium myrtillus</Emphasis> (L.) and <Emphasis Type="Italic">Pinus sylvestris</Emphasis> (L.)

Seasonal changes in vanadate sensitive plasma membrane H⁺-ATPase activity of bilberry (Vaccinium myrtillus L.) and Scots pine (Pinus sylvestris L.) were studied in a period from February to August in northern Finland. The plasma membrane isolation was performed by sucrose gradient centrifugation, and the H⁺-ATPase activity was assayed by spectrophotometrical determination of released inorganic phosphate. The studied species showed seasonal changes from high winter to low spring activity, indicating probable physiological changes between hardened and dehardened tissue. ATPase activity of bilberry peaked up at the beginning of the growth period, obviously due to active phloem loading of photosynthates.     

Concentration-Dependent Effects on Intracellular and Surface pH of Exposing <Emphasis Type="Italic">Xenopus</Emphasis> oocytes to Solutions Containing NH<Subscript>3</Subscript>/NH<Subscript>4</Subscript><Superscript>+</Superscript>

Others have shown that exposing oocytes to high levels of (10–20 mM) causes a paradoxical fall in intracellular pH (pH_i), whereas low levels (e.g., 0.5 mM) cause little pH_i change. Here we monitored pH_i and extracellular surface pH (pH_S) while exposing oocytes to 5 or 0.5 mM NH₃/NH₄ ⁺. We confirm that 5 mM causes a paradoxical pH_i fall (−ΔpH_i ≅ 0.2), but also observe an abrupt pH_S fall (−ΔpH_S ≅ 0.2)—indicative of NH₃ influx—followed by a slow decay. Reducing [NH₃/NH₄ ⁺] to 0.5 mM minimizes pH_i changes but maintains pH_S changes at a reduced magnitude. Expressing AmtB (bacterial Rh homologue) exaggerates −ΔpH_S at both levels. During removal of 0.5 or 5 mM NH₃/NH₄ ⁺, failure of pH_S to markedly overshoot bulk extracellular pH implies little NH₃ efflux and, thus, little free cytosolic NH₃/NH₄ ⁺. A new analysis of the effects of NH₃ vs. NH₄ ⁺ fluxes on pH_S and pH_i indicates that (a) NH₃ rather than NH₄ ⁺ fluxes dominate pH_i and pH_S changes and (b) oocytes dispose of most incoming NH₃. NMR studies of oocytes exposed to ¹⁵N-labeled show no significant formation of glutamine but substantial accumulation in what is likely an acid intracellular compartment. In conclusion, parallel measurements of pH_i and pH_S demonstrate that NH₃ flows across the plasma membrane and provide new insights into how a protein molecule in the plasma membrane—AmtB—enhances the flux of a gas across a biological membrane.

Symbiotic response of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) to iron deficiency

In order to assess symbiotic activity (the nodules integrity and the iron use efficiency) in common bean (Phaseolus vulgaris L.) under low iron availability, the growth of plants and nodules, the concentration of leghaemoglobin and malondialdehyde, and activity of nitrogenase, catalase, peroxidase and superoxide dismutase were analysed in two (contrasting) common bean varieties subjected to iron deficiency. Results show that nitrogen fixation and leghaemoglobin accumulation decreased at limiting iron availability while malondialdehyde concentration increased under these conditions. The tolerant variety to iron deficiency, ARA14, was clearly less affected than the sensitive one, Coco blanc. A significant stimulation of peroxidase (POD) activity was observed in ARA14 under iron deficiency. At the same conditions, SOD and CAT activities in ARA14 plants were maintained at high level. It was also found that the iron use efficiency for leghaemoglobin accumulation, SOD, CAT and POD activities were critical for the protection of symbiotic system against oxidative burst and for the maintaining of an optimal functioning of N₂ fixing system.     

Integration of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) linkage and chromosomal maps

Fluorescent in situ hybridisation of pooled, closely linked RFLP markers was used to integrate the genetic linkage map and the mitotic chromosome map of the common bean. Pooled RFLP probes showed clear and reproducible signals and allowed the assignment of all linkage groups to the chromosomes of two Phaseolus vulgaris cultivars, Saxa and Calima. Low extension values for signals originating from clustered RFLPs suggest that these clones are physically close to each other and that clusters in the genetic map are not a result of suppression of recombination due to the occurrence of chromosome rearrangements. For linkage group K, clustering of markers could be associated with proximity to centromeres. High variation in the number of 45S rDNA loci was observed among cultivars, suggesting that these terminal sites are highly recombinogenic in common bean.     

Microsatellite characterization of Andean races of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

The Andean gene pool of common bean (Phaseolus vulgaris L.) has high levels of morphological diversity in terms of seed color and size, growth habit and agro-ecological adaptation, but previously was characterized by low levels of molecular marker diversity. Three races have been described within the Andean gene pool: Chile, Nueva Granada and Peru. The objective of this study was to characterize a collection of 123 genotypes representing Andean bean diversity with 33 microsatellite markers that have been useful for characterizing race structure in common beans. The genotypes were from both the primary center of origin as well as secondary centers of diversity to which Andean beans spread and represented all three races of the gene pool. In addition we evaluated a collection of landraces from Colombia to determine if the Nueva Granada and Peru races could be distinguished in genotypes from the northern range of the primary center. Multiple correspondence analyses of the Andean race representatives identified two predominant groups corresponding to the Nueva Granada and Peru races. Some of the Chile race representatives formed a separate group but several that had been defined previously as from this race grouped with the other races. Gene flow was more notable between Nueva Granada and Peru races than between these races and the Chile race. Among the Colombian genotypes, the Nueva Granada and Peru races were identified and introgression between these two races was especially notable. The genetic diversity within the Colombian genotypes was high, reaffirming the importance of this region as an important source of germplasm. Results of this study suggest that the morphological classification of all climbing beans as Peru race genotypes and all bush beans as Nueva Granada race genotypes is erroneous and that growth habit traits have been mixed in both races, requiring a re-adjustment in the concept of morphological races in Andean beans.     

Plasmid content of salt stress-tolerant <Emphasis Type="Italic">Rhizobium</Emphasis> strains from Egyptian soils nodulating common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Plasmid profile analysis is useful to characterize Rhizobium strains within the same species. Among the 16 Rhizobium strains examined, 14 had distinct plasmid profiles. The size of plasmids ranged from 40 to 650 kb, and three plasmids of 650, 510 and 390 kb were common to several strains. Plasmid analysis revealed that Rhizobium etli contained a mega-plasmid, similar in size to Rhizobium tropici. All the salt-tolerant strains examined had a plasmid of 250 kb, except for strain EBRI 29. This suggests that this plasmid may play an important adaptive role under salt stress conditions.     

Movement of Abscisic Acid in <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> Plants

THE movement of abscisic acid (ABA) in plants seems to have been studied only in isolated segments of tissue^1–4. We have used ¹⁴C-labelled ABA of relatively high specific activity to investigate its movement in a number of plant species, in both isolated tissue segments and whole plants. The movement of 2-¹⁴C-ABA in intact seedlings of Phaseolus vulgaris is described here.     

Phosphoproteomic Analysis in <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> Roots Treated with <Emphasis Type="Italic">Rhizobium etli</Emphasis> Nodulation Factors

Legumes are unique in their ability to establish symbiotic interactions with rhizobacteria, providing a source of assimilable nitrogen; this symbiosis is regulated by complex signaling process between the plant and the bacteria. The participation of specific protein kinases during the initial steps of the nodulation process has been established. However, their substrates or the signaling networks implicated are not fully understood. Herein, a phosphoproteomic analysis of Phaseolus vulgaris roots treated for 24 h with specific Nod factors was performed using an immobilized metal ion affinity chromatography enrichment and two-dimensional gel electrophoresis approach with mass spectrometry identification. A total of 33 protein spots showing more than 1.5-fold shift were identified (17 protein spots in which the relative abundance increased and 16 that decreased). The majority of the identified root phosphoproteins displaying an increased relative abundance are presumed to have functions related to the biosynthesis and folding of proteins, energy metabolism, or cytoskeleton rearrangements, which reflect the metabolic status of the roots as being part of the developmental processes leading to nodule initiation and the importance of cytoskeleton rearrangement in the P. vulgaris–rhizobia symbiosis. The proteins in which relative abundance decreased are associated with defense and oxido-reduction processes, which could indicate a suppression of plant defense responses during the establishment of the rhizobia–legume interaction and an increase of reactive oxygen species production.     

Nucleotide diversity of a genomic sequence similar to <Emphasis Type="Italic">SHATTERPROOF</Emphasis> (<Emphasis Type="Italic">PvSHP1</Emphasis>) in domesticated and wild common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Evolutionary studies in plant and animal breeding are aimed at understanding the structure and organization of genetic variations of species. We have identified and characterized a genomic sequence in Phaseolus vulgaris of 1,200 bp (PvSHP1) that is homologous to SHATTERPROOF-1 (SHP1), a gene involved in control of fruit shattering in Arabidopsis thaliana. The PvSHP1 fragment was mapped to chromosome Pv06 in P. vulgaris and is linked to the flower and seed color gene V. Amplification of the PvSHP1 sequence from the most agronomically important legume species showed a high degree of interspecies diversity in the introns within the Phaseoleae, while the coding region was conserved across distant taxa. Sequencing of the PvSHP1 sequence in a sample of 91 wild and domesticated genotypes that span the geographic distribution of this species in the centers of origin showed that PvSHP1 is highly polymorphic and, therefore, particularly useful to further investigate the origin and domestication history of P. vulgaris. Our data confirm the gene pool structure seen in P. vulgaris along with independent domestication processes in the Andes and Mesoamerica; they provide additional evidence for a single domestication event in Mesoamerica. Moreover, our results support the Mesoamerican origin of this species. Finally, we have developed three indel-spanning markers that will be very useful for bean germplasm characterization, and particularly to trace the distribution of the domesticated Andean and Mesoamerican gene pools.     

Arbuscular mycorrhiza confers Pb tolerance in <Emphasis Type="Italic">Calopogonium mucunoides</Emphasis>

Heavy metals (HMs) are environmental pollutants of great concern to humans because of their high potential toxicity. Lead is a HM that is present in the soil in very small amounts, but anthropogenic activities have increased its content in some locations, which can make these areas unproductive or inappropriate for crop production. However, there are some plants that can grow in contaminated soils and, thus, can be useful for the removal or stabilisation of such contaminants. In addition, plants that are not able to tolerate high concentrations of HMs in the soil can become tolerant or increase their performance when associated with arbuscular mycorrhizal (AM) fungi. Accordingly, this study was carried out to verify whether the inoculation of Glomus etunicatum, an AM fungus species, in Calopogonium mucunoides would influence plant tolerance to increasing concentrations of Pb in the soil. The experimental design was completely randomised, in a 2 × 4 factorial design, and the treatments consisted of inoculation (or not) with the AM fungus, G. etunicatum, and the addition of four Pb concentrations (0, 250, 500 or 1,000 mg kg⁻¹) to the soil. The results showed that the association of C. mucunoides with G. etunicatum promoted biomass production, and nutrient uptake (P, S and Fe) was also positively influenced by mycorrhization. The malondialdehyde content was higher in non-mycorrhizal leaves, suggesting a reduction in the damage to membranes by lipid peroxidation in plants associated with mycorrhizae. However, the Pb concentration in the shoots did not differ between the mycorrhizal and non-mycorrhizal plants. The results of our study suggest that the AM symbiosis can be considered very effective in contributing to the tolerance of C. mucunoides to Pb.     

Methane Yield and Feed Quality Parameters of Mixed Silages from Maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) and Common Bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

European agricultural policy increasingly focuses on environmental friendly cropping systems. Intercropping of maize (Zea mays L.) and common beans (Phaseolus vulgaris L.) has been suggested as an alternative cropping system with environmental benefits. The aim of this study was to assess methane yield potential of mixed silages. Based on material from two field experiments at three sites in Germany, mixed silages were produced with proportions of individual components varying from 0 to 100 % of fresh matter in increments of 12.5 %. Chemical parameters (neutral detergent fiber (NDF), acid detergent fiber (ADF), crude protein (XP), starch, sugar, and crude fat) were determined, and batch tests were performed to measure methane yield potential from silages. With increasing bean proportion, concentrations of XP increased while NDF, methane yield, and methane content decreased. While methane yield showed a negative relationship with XP content (R ² = 0.56***), a positive relation was found with NDF (R ² = 0.55***). The reduction of methane yield of circa 1 L of methane per each additional bean percentage in the silages could not be explained by the chemical parameters of the silages. It is hypothesized that other chemical compounds, such as lectins, which were not determined in the present study, may have influenced methane production.     

Embryo abortion and histological features in the interspecific cross between <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L. and <Emphasis Type="Italic">P. coccineus</Emphasis> L

In this paper, the causes of early embryo abortion in the reciprocal crosses between Phaseolus vulgaris L. (a cultivar) and Phaseolus coccineus L. (a wild form) were studied. Methacrylate resin sections, 3–5 μm thick, of 3 to 14 day-old seeds were used to examine the embryo developmental stages and the state of seed tissue. It was observed that, embryos aborted at different developmental stages (globular to early cotyledon) depending on the maternal parent. The use of P. coccineus cytoplasm resulted in a higher number of abortion than in reciprocal crosses. Many of them took place between 5 and 6 days after pollination (DAP). Histological analyses permitted to observe that the embryo development was slower in the cross between P. coccineus and P. vulgaris, compared to parental seeds. It would be related to a deficient endosperm development in reciprocal crosses and, in some extent, hypertrophy of the suspensor might be the main cause of early embryo abortion. Then, it would be practical to overcome this incompatibility by rescuing the embryo at the globular stage of development.