GDP-fucose uptake into the Golgi apparatus during xyloglucan biosynthesis requires the activity of a transporter-like protein other than the UDP-glucose transporter

The molecular mechanisms regulating hemicelluloses and pectin biosynthesis are poorly understood. An important question in this regard is how glycosyltransferases are oriented in the Golgi cisternae, and how nucleotide sugars are made available for the synthesis of the polymers. Here we show that the branching enzyme xyloglucan alpha,1-2 fucosyltransferase (XG-FucTase) from growing pea (Pisum sativum) epicotyls was latent and protected against proteolytic inactivation on intact, right-side-in pea stem Golgi vesicles. Moreover, much of the XG-FucTase activity was membrane associated. These data indicate that XG-FucTase is a membrane-bound luminal enzyme. GDP-Fuc uptake studies demonstrated that GDP-Fuc was taken up into Golgi vesicles in a protein-mediated process, and that this uptake was not competed by UDP-Glc, suggesting that a specific GDP-Fuc transporter is involved in xyloglucan biosynthesis. Once in the lumen, Fuc was transferred onto endogenous acceptors, including xyloglucan. GDPase activity was detected in the lumen of the vesicles, suggesting than the GDP produced upon transfer of Fuc was hydrolyzed to GMP and inorganic phosphate. We suggest than the GDP-Fuc transporter and GDPase may be regulators of xyloglucan fucosylation in the Golgi apparatus from pea epicotyls.     

Metabolism of Uridine 5′-Diphosphate-Glucose in Golgi Vesicles from Pea Stems

Uridine 5′-diphosphate-glucose (UDP-Glc) is transported into the lumen of the Golgi cisternae, where is used for polysaccharide biosynthesis. When Golgi vesicles were incubated with UDP-[³H]Glc, [³H]Glc was rapidly transferred to endogenous acceptors and UDP-Glc was undetectable in Golgi vesicles. This result indicated that a uridine-containing nucleotide was rapidly formed in the Golgi vesicles. Since little is known about the fate of the nucleotide derived from UDP-Glc, we analyzed the metabolism of the nucleotide moiety of UDP-Glc by incubating Golgi vesicles with [α-³²P]UDP-Glc, [β-³²P]UDP-Glc, and [³H]UDP-Glc and identifying the resulting products. After incubation of Golgi vesicles with these radiolabeled substrates we could detect only uridine 5′-monophosphate (UMP) and inorganic phosphate (Pi). UDP could not be detected, suggesting a rapid hydrolysis of UDP by the Golgi UDPase. The by-products of UDP hydrolysis, UMP and Pi, did not accumulate in the lumen, indicating that they were able to exit the Golgi lumen. The exit of UMP was stimulated by UDP-Glc, suggesting the presence of a putative UDP-Glc/UMP antiporter in the Golgi membrane. However, the exit of Pi was not stimulated by UDP-Glc, suggesting that the exit of Pi occurs via an independent membrane transporter.     

Comparative analysis of the meiotic effects of wheat ph1b and ph2b mutations in wheat×rye hybrids

 Wheat-wheat and wheat-rye homoeologous pairing at metaphase I and wheat-rye recombination at anaphase I were examined by genomic in situ hybridization (GISH) in wild-type (Ph1Ph2) and mutant ph1b and ph2b wheat×rye hybrids. The metaphase-I analysis revealed that the relative contribution of wheat-rye chromosome associations in ph2b wheat×rye was similar to that of the wild-type hybrid genotype but differed from the effect of the ph1b mutation. The greater pairing promotion effect of the ph1b mutation appears to be relatively more on distant homoeologous partner metaphase-I associations, whereas the lower promoting effect of ph2b is evenly distributed among all types of homoeologous associations. This finding reveals that distinct mechanisms are involved in the control of wheat homoeologous pairing by the two Ph genes. The frequency of wheat-rye recombination calculated from anaphase-I analysis was lower than expected from the metaphase-I data. A greater discrepancy was found in ph2b than in ph1b wheat×rye hybrids, which may suggest a more distal chiasma localization in the former hybrid genotype. Received: 20 June 1997 / Accepted: 9 December 1997     

Arabidopsis S6 kinase mutants display chromosome instability and altered RBR1�CE2F pathway activity

The 40S ribosomal protein S6 kinase (S6K) is a conserved component of signalling pathways controlling growth in eukaryotes. To study S6K function in plants, we isolated single‐ and double‐knockout mutations and RNA‐interference (RNAi)‐silencing lines in the linked Arabidopsis S6K1 and S6K2 genes. Hemizygous s6k1s6k2/++ mutant and S6K1 RNAi lines show high phenotypic instability with variation in size, increased trichome branching, produce non‐viable pollen and high levels of aborted seeds. Analysis of their DNA content by flow cytometry, as well as chromosome counting using DAPI staining and fluorescence in situ hybridization, revealed an increase in ploidy and aneuploidy. In agreement with this data, we found that S6K1 associates with the Retinoblastoma‐related 1 (RBR1)–E2FB complex and this is partly mediated by its N‐terminal LVxCxE motif. Moreover, the S6K1–RBR1 association regulates RBR1 nuclear localization, as well as E2F‐dependent expression of cell cycle genes. Arabidopsis cells grown under nutrient‐limiting conditions require S6K for repression of cell proliferation. The data suggest a new function for plant S6K as a repressor of cell proliferation and required for maintenance of chromosome stability and ploidy levels.     

The nucleotide sugar transporters AtUTr1 and AtUTr3 are required for the incorporation of UDP‐glucose into the endoplasmic reticulum,are essential for pollen development and are needed for embryo sac progress in Arabidopsis thaliana

Uridine 5′‐diphosphate (UDP)‐glucose is transported into the lumen of the endoplasmic reticulum (ER), and the Arabidopsis nucleotide sugar transporter AtUTr1 has been proposed to play a role in this process; however, different lines of evidence suggest that another transporter(s) may also be involved. Here we show that AtUTr3 is involved in the transport of UDP‐glucose and is located at the ER but also at the Golgi. Insertional mutants in AtUTr3 showed no obvious phenotype. Biochemical analysis in both AtUTr1 and AtUTr3 mutants indicates that uptake of UDP‐glucose into the ER is mostly driven by these two transporters. Interestingly, the expression of AtUTr3 is induced by stimuli that trigger the unfolded protein response (UPR), a phenomenon also observed for AtUTr1, suggesting that both AtUTr1 and AtUTr3 are involved in supplying UDP‐glucose into the ER lumen when misfolded proteins are accumulated. Disruption of both AtUTr1 and AtUTr3 causes lethality. Genetic analysis showed that the atutr1 atutr3 combination was not transmitted by pollen and was poorly transmitted by the ovules. Cell biology analysis indicates that knocking out both genes leads to abnormalities in both male and female germ line development. These results show that the nucleotide sugar transporters AtUTr1 and AtUTr3 are required for the incorporation of UDP‐glucose into the ER, are essential for pollen development and are needed for embryo sac progress in Arabidopsis thaliana.     

An ecosystem approach to restoration and sustainable management of dry forest in southern Peru

The dry forest of the Peruvian south coast has undergone an almost total process of deforestation. Populations here have increased exponentially through immigration supplying labour to urban coastal development, and demonstrably unsustainable agro-industrial expansion for export markets. Society has become dislocated from local traditions of environmental and resource management whilst still retaining a wealth of Andean agricultural expertise. Indigenous communities still hold on to vestiges of traditional knowledge. Relicts of natural vegetation, traditional agriculture and agrobiodiversity continue to sustain ecosystem services. Moreover, offer livelihood options and resources for restoration. These aspects reflect a long cultural trajectory, including famous extinct cultures such as Nasca, that evolved within an ever-changing riparian and agricultural landscape influenced by external forces and which incorporated important processes of plant domestication and adaptation to climatic oscillation.     

Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies

Background

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required.

Results

We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms.

Conclusions

The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.     

Frugivory on Persea lingue in temperate Chilean forests: interactions between fruit availability and habitat fragmentation across multiple spatial scales

Habitat degradation and fragmentation are expected to reduce seed dispersal rates by reducing fruit availability as well as the movement and abundance of frugivores. These deleterious impacts may also interact with each other at different spatial scales, leading to nonlinear effects of fruit abundance on seed dispersal. In this study we assessed whether the degradation and fragmentation of southern Chilean forests had the potential to restrict seed dispersal the lingue (Persea lingue) tree, a fleshy-fruited tree species. Of five frugivore bird species, the austral thrush (Turdus falcklandii) and the fire-eyed diucon (Xolmis pyrope) were the only legitimate seed dispersers as well as being the most abundant species visiting lingue trees. The results showed little or no direct effect of habitat fragmentation on seed dispersal estimates, possibly because the assemblage of frugivore birds was comprised habitat-generalist species. Instead, the number of fruits removed per focal tree exhibited an enhanced response to crop size, but only in the more connected fragments. In the fruit-richer fragment networks, there was an increased fragment-size effect on the proportion of fruits removed in comparison to fruit-poor networks in which the fragment size effect was spurious. We suggest that such nonlinear effects are widespread in fragmented forest regions, resulting from the link between the spatial scales over which frugivores sample resources and the spatial heterogeneity in fruiting resources caused by habitat fragmentation and degradation.     

Relationships between heterozygosity and fitness in the Iberian threatened larkspur Delphinium bolosii (Ranunculaceae)

The relationship between individual heretozygosity and fitness was explored in the perennial larkspur Delphinium bolosii (Ranunculaceae), an endangered species endemic to Catalonia (North-Eastern Spain), as a part of several studies prior to designing a programme for the reintroduction of this species in a locality where it has been extinct for approximately one century. Allozyme electrophoresis was used to quantify the levels of heterozygosity at nearly to one hundred surveyed individuals in two extant populations. At the same time, eight parameters of vegetative and reproductive fitness were measured. A principal component analysis reduced the original fitness variables to three uncorrelated principal components, two associated with the maternal plant and the other one with the offspring. However, none of the components were significantly correlated with heterozygosity. The low number of variable allozyme markers and the likely influence of ecological factors could be responsible for the lack of correlation between individual heterozygosity and fitness.     

Arbuscular mycorrhizal propagules in soils from a tropical forest and an abandoned cornfield in Quintana Roo, Mexico: visual comparison of most-probable-number estimates

The present study was aimed at comparing the number of arbuscular mycorrhizal fungi (AMF) propagules found in soil from a mature tropical forest and that found in an abandoned cornfield in Noh-Bec Quintana Roo, Mexico, during three seasons. Agricultural practices can dramatically reduce the availability and viability of AMF propagules, and in this way delay the regeneration of tropical forests in abandoned agricultural areas. In addition, rainfall seasonality, which characterizes deciduous tropical forests, may strongly influence AMF propagules density. To compare AMF propagule numbers between sites and seasons (summer rainy, winter rainy and dry season), a “most probable number” (MPN) bioassay was conducted under greenhouse conditions employing Sorgum vulgare L. as host plant. Results showed an average value of 3.5 ± 0.41 propagules in 50 ml of soil for the mature forest while the abandoned cornfield had 15.4 ± 5.03 propagules in 50 ml of soil. Likelihood analysis showed no statistical differences in MPN of propagules between seasons within each site, or between sites, except for the summer rainy season for which soil from the abandoned cornfield had eight times as many propagules compared to soil from the mature forest site for this season. Propagules of arbuscular mycorrhizal fungi remained viable throughout the sampling seasons at both sites. Abandoned areas resulting from traditional slash and burn agriculture practices involving maize did not show a lower number of AMF propagules, which should allow the establishment of mycotrophic plants thus maintaining the AMF inoculum potential in these soils.