Mechanisms of iron-sulfur protein maturation in mitochondria, cytosol and nucleus of eukaryotes

Iron-sulfur (Fe/S) clusters are important cofactors of numerous proteins involved in electron transfer, metabolic and regulatory processes. In eukaryotic cells, known Fe/S proteins are located within mitochondria, the nucleus and the cytosol. Over the past years the molecular basis of Fe/S cluster synthesis and incorporation into apoproteins in a living cell has started to become elucidated. Biogenesis of these simple inorganic cofactors is surprisingly complex and, in eukaryotes such as Saccharomyces cerevisiae, is accomplished by three distinct proteinaceous machineries. The "iron-sulfur cluster (ISC) assembly machinery" of mitochondria was inherited from the bacterial ancestor of mitochondria. ISC components are conserved in eukaryotes from yeast to man. The key principle of biosynthesis is the assembly of the Fe/S cluster on a scaffold protein before it is transferred to target apoproteins. Cytosolic and nuclear Fe/S protein maturation also requires the function of the mitochondrial ISC assembly system. It is believed that mitochondria contribute a still unknown compound to biogenesis outside the organelle. This compound is exported by the mitochondrial "ISC export machinery" and utilised by the "cytosolic iron-sulfur protein assembly (CIA) machinery". Components of these two latter systems are also highly conserved in eukaryotes. Defects in the mitochondrial ISC assembly and export systems, but not in the CIA machinery have a strong impact on cellular iron uptake and intracellular iron distribution showing that mitochondria are crucial for both cellular Fe/S protein assembly and iron homeostasis.     

Prediction of plant species distribution in lowland river valleys in Belgium: modelling species response to site conditions

In ecological modelling, limitations in data and their applicability for predictive modelling are more rule than exception. Often modelling has to be performed on sub-optimal data, as explicit and controlled collection of (more) appropriate data would not be feasible. An example of predictive ecological modelling is given with application of generalized additive and generalized linear models fitted to presence–absence records of plant species and site condition data from four nutrient-poor Flemish lowland valleys. Standard regression procedures are used for modelling, although explanatory and response data do not meet all the assumptions implicit in these procedures. Data were non-randomly collected and are spatially autocorrelated; model residuals retain part of that correlation. The scale of most site-condition records does not match the scale of the response variable (species distribution). Hence, interpolated and up-scaled explanatory variables are used. Data are aggregated from distinct phytogeographical regions to allow for generalized models, applicable to a wider population of river valleys in the same region. Nevertheless, ecologically sound models are obtained, which predict well the distribution of most plant species for the Flemish river valleys considered.     

The development of standard samples with a defined number of antigen-specific T cells to harmonize T cell assays: a proof-of-principle study

The validation of assays that quantify antigen-specific T cell responses is critically dependent on cell samples that contain clearly defined measurable numbers of antigen-specific T cells. An important requirement is that such cell samples are handled and analyzed in a comparable fashion to peripheral blood mononuclear cells (PBMC). We performed a proof-of-principle study to show that retrovirally TCR-transduced T cells spiked at defined numbers in autologous PBMC can be used as standard samples for HLA/peptide multimer staining. NY-ESO-1_157–165-specific, TCR-transduced CD8+ T cell batches were successfully generated from PBMC of several HLA-A*0201 healthy donors, purified by magnetic cell sorting on the basis of HLA tetramer (TM) staining and expanded with specific antigen in vitro. When subsequently spiked into autologous PBMC, the detection of these CD3+CD8+TM+ T cells was highly accurate with a mean accuracy of 91.6 %. The standard cells can be preserved for a substantial period of time in liquid nitrogen. Furthermore, TM staining of fresh and cryopreserved standard samples diluted at decreasing concentrations into autologous cryopreserved unspiked PBMC revealed that the spiked CD3+CD8+TM+ T cells could be accurately detected at all dilutions in a linear fashion with a goodness-of-fit of over 0.99 at a frequency of at least 0.02 % among the CD3+CD8+ T cell population. Notably, the CD3+CD8+TM+ cells of the standard samples were located exactly within the gates used to analyze patient samples and displayed a similar scatter pattern. The performance of the cryopreserved standard samples in the hands of 5 external investigators was good with an inter-laboratory variation of 32.9 % and the doubtless identification of one outlier.     

A novel tetrameric lectin from Lycoris aurea with four mannose binding sites per monomer

The mannose-binding agglutinin from bulbs of Lycoris aurea (LAA) agglutinates rabbit but not human erythrocytes. The molecular mass of the monomer in SDS/PAGE is 12 kDa while the apparent molecular mass in gel filtration is 48 kDa, indicating that LAA is a homotetramer. The full-length cDNA of LAA contains 683 bp with an open reading frame encoding a protomer of 162 amino-acid residues. Hydrophobic Cluster Analysis and molecular modeling of the 109-residue mature polypeptide suggested a similar secondary and tertiary structure to those of Narcissus pseudonarcissus agglutinin (NPA). Molecular docking revealed that, besides the three mannose-binding sites common among Amaryllidaceae lectins, LAA also contains a fourth unique mannose-binding site formed by a tryptophan cluster. The existence of four mannose-binding sites in each monomer of LAA is very unusual and has only been reported for NPA earlier.     

Arabidopsis thaliana plants acclimated to low dose rates of ultraviolet B radiation show specific changes in morphology and gene expression in the absence of stress symptoms

Ultraviolet B (UV-B) acclimation comprises complex and poorly understood changes in plant metabolism. The effects of chronic and ecologically relevant UV-B dose rates on Arabidopsis thaliana were determined. The UV-B acclimation process was studied by measuring radiation effects on morphology, physiology, biochemistry and gene expression. Chronic UV-B radiation did not affect photosynthesis or the expression of stress responsive genes, which indicated that the UV-acclimated plants were not stressed. UV-induced morphological changes in acclimated plants included decreased rosette diameter, decreased inflorescence height and increased numbers of flowering stems, indicating that chronic UV-B treatment caused a redistribution rather than a cessation of growth. Gene expression profiling indicated that UV-induced morphogenesis was associated with subtle changes in phytohormone (auxins, brassinosteroids and gibberellins) homeostasis and the cell wall. Based on the comparison of gene expression profiles, it is concluded that acclimation to low, chronic dose rates of UV-B is distinct from that to acute, stress-inducing UV-B dose rates. Hence, UV-B-induced morphogenesis is functionally uncoupled from stress responses.     

Analysis of Genome Sequences from Plant Pathogenic Rhodococcus Reveals Genetic Novelties in Virulence Loci

Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with the fas operon central to virulence. The Fas proteins synthesize, modify, and activate a mixture of growth regulating cytokinins, which cause a hormonal imbalance in plants, resulting in abnormal growth. We sequenced and compared the genomes of 20 isolates of Rhodococcus to gain insights into the mechanisms and evolution of virulence in these bacteria. Horizontal gene transfer was identified as critical but limited in the scale of virulence evolution, as few loci are conserved and exclusive to phytopathogenic isolates. Although the fas operon is present in most phytopathogenic isolates, it is absent from phytopathogenic isolate A21d2. Instead, this isolate has a horizontally acquired gene chimera that encodes a novel fusion protein with isopentyltransferase and phosphoribohydrolase domains, predicted to be capable of catalyzing and activating cytokinins, respectively. Cytokinin profiling of the archetypal D188 isolate revealed only one activate cytokinin type that was specifically synthesized in a fas-dependent manner. These results suggest that only the isopentenyladenine cytokinin type is synthesized and necessary for Rhodococcus phytopathogenicity, which is not consistent with the extant model stating that a mixture of cytokinins is necessary for Rhodococcus to cause leafy gall symptoms. In all, data indicate that only four horizontally acquired functions are sufficient to confer the trait of phytopathogenicity to members of the genetically diverse clade of Rhodococcus.     

The destruction of an endemic species flock: quantitative data on the decline of the haplochromine cichlids of Lake Victoria

Synopsis The Lake Victoria fish fauna included an endemic cichlid flock of more than 300 species. To boost fisheries, Nile perch (Lates sp.) was introduced into the lake in the 1950s. In the early 1980s an explosive increase of this predator was observed. Simultaneously, catches of haplochromines decreased. This paper describes the species composition of haplochromines in a research area in the Mwanza Gulf of Lake Victoria prior to the Nile perch upsurge. The decline of the haplochromines as a group and the decline of the number of species in various habitats in the Mwanza Gulf was monitored between 1979 and 1990. Of the 123+ species originally caught at a series of sampling stations ca. 80 had disappeared from the catches after 1986. In deepwater regions and in sub-littoral regions haplochromine catches decreased to virtually zero after the Nile perch boom. Haplochromines were still caught in the littoral regions where Nile perch densities were lower. However, a considerable decrease of species occurred in these regions too. It is expected that a remnant of the original haplochromine fauna will survive in the littoral region of the lake. Extrapolation of the data of the Mwanza Gulf to the entire lake would imply that approximately 200 of the 300+ endemic haplochromine species have already disappeared, or are threatened with extinction. Although fishing had an impact on the haplochromine stocks, the main cause of their decline was predation by Nile perch. The speed of decline differed between species and appeared to depend on their abundance and size, and on the degree of habitat overlap with Nile perch. Since the Nile perch upsurge, the food web of Lake Victoria has changed considerably and the total yield of the fishery has increased three to four times. Dramatic declines of native species have also been observed in other lakes as a result of the introduction of alien predators. However, such data concern less speciose communities and, in most cases, the actual process of extinction has not been monitored.     

GlycoPEGylation of recombinant therapeutic proteins produced in Escherichia coli

Covalent attachment of polyethylene glycol, PEGylation, has been shown to prolong the half-life and enhance the pharmacodynamics of therapeutic proteins. Current methods for PEGylation, which rely on chemical conjugation through reactive groups on amino acids, often generate isoforms in which PEG is attached at sites that interfere with bioactivity. Here, we present a novel strategy for site-directed PEGylation using glycosyltransferases to attach PEG to O-glycans. The process involves enzymatic GalNAc glycosylation at specific serine and threonine residues in proteins expressed without glycosylation in Escherichia coli, followed by enzymatic transfer of sialic acid conjugated with PEG to the introduced GalNAc residues. The strategy was applied to three therapeutic polypeptides, granulocyte colony stimulating factor (G-CSF), interferon-alpha2b (IFN-alpha2b), and granulocyte/macrophage colony stimulating factor (GM-CSF), which are currently in clinical use.