Growth rate correlates negatively with protein turnover in Arabidopsis accessions

Previous studies with Arabidopsis accessions revealed that biomass correlates negatively to dusk starch content and total protein, and positively to the maximum activities of enzymes in photosynthesis. We hypothesized that large accessions have lower ribosome abundance and lower rates of protein synthesis, and that this is compensated by lower rates of protein degradation. This would increase growth efficiency and allow more investment in photosynthetic machinery. We analysed ribosome abundance and polysome loading in 19 accessions, modelled the rates of protein synthesis and compared them with the observed rate of growth. Large accessions contained less ribosomes than small accessions, due mainly to cytosolic ribosome abundance falling at night in large accessions. The modelled rates of protein synthesis resembled those required for growth in large accessions, but were up to 30% in excess in small accessions. We then employed ¹³CO₂ pulse‐chase labelling to measure the rates of protein synthesis and degradation in 13 accessions. Small accessions had a slightly higher rate of protein synthesis and much higher rates of protein degradation than large accessions. Protein turnover was negligible in large accessions but equivalent to up to 30% of synthesised protein day^?1 in small accessions. We discuss to what extent the decrease in growth in small accessions can be quantitatively explained by known costs of protein turnover and what factors may lead to the altered diurnal dynamics and increase of ribosome abundance in small accessions, and propose that there is a trade‐off between protein turnover and maximisation of growth rate.     

Refolding of Npro fusion proteins

The autoprotease N^pro significantly enhances expression of fused peptides and proteins and drives the formation of inclusion bodies during protein expression. Upon refolding, the autoprotease becomes active and cleaves itself specifically at its own C‐terminus releasing the target protein with its authentic N‐terminus. N^pro wild‐type and its mutant EDDIE, respectively, were fused N‐terminally to the model proteins green fluorescent protein, staphylococcus Protein A domain D, inhibitory peptide of senescence‐evasion‐factor, and the short 16 amino acid peptide pep6His. In comparison with the N^pro wild‐type, the tailored mutant EDDIE displayed an increased rate constant for refolding and cleavage from 1.3 × 10^?4 s^?1 to 3.5 × 10^?4 s^?1, and allowed a 15‐fold higher protein concentration of 1.1 mg/mL when studying pep6His as a fusion partner. For green fluorescent protein, the rate constant was increased from 2.4 × 10^?5 s^?1 to 1.1 × 10^?4 s^?1 when fused to EDDIE. When fused to small target peptides, refolding and cleavage yields were independent of initial protein concentration, even at high concentrations of 3.9 mg/mL, although cleavage rates were strongly influenced by the fusion partner. This behavior differed from conventional 1st order refolding kinetics, where yield strongly depends on initial protein concentration due to an aggregation reaction of higher order. Refolding and cleavage of EDDIE fusion proteins follow a monomolecular reaction for the autoproteolytic cleavage over a wide concentration range. At high protein concentrations, deviations from the model assumptions were observed and thus smaller rate constants were required to approximate the data. Biotechnol. Bioeng. 2009; 104: 774–784 © 2009 Wiley Periodicals, Inc.     

The immunomodulatory sphingosine 1-phosphate analog FTY720 reduces lesion size and improves neurological outcome in a mouse model of cerebral ischemia

Cerebral ischemia is accompanied by fulminant cellular and humoral inflammatory changes in the brain which contribute to lesion development after stroke. A tight interplay between the brain and the peripheral immune system leads to a biphasic immune response to stroke consisting of an early activation of peripheral immune cells with massive production of proinflammatory cytokines followed by a systemic immunosuppression within days of cerebral ischemia that is characterized by massive immune cell loss in spleen and thymus. Recent work has documented the importance of T lymphocytes in the early exacerbation of ischemic injury. The lipid signaling mediator sphingosine 1-phosphate-derived stable analog FTY720 (fingolimod) acts as an immunosuppressant and induces lymphopenia by preventing the egress of lymphocytes, especially T cells, from lymph nodes. We found that treatment with FTY720 (1 mg/kg) reduced lesion size and improved neurological function after experimental stroke in mice, decreased the numbers of infiltrating neutrophils, activated microglia/macrophages in the ischemic lesion and reduced immunohistochemical features of apoptotic cell death in the lesion.     

Investigation of the abundance and subunit composition of GABAA receptor subtypes in the cerebellum of alpha1-subunit-deficient mice

In cerebellum, 75% of all GABAA receptors contain alpha1 subunits. Here, we investigated compensatory changes in GABAA receptor subunit expression and composition in alpha1 subunit-knockout mice. In these mice the total number of cerebellar GABAA receptors was reduced by 46%. Whereas the number of receptors containing alpha6 subunits was unchanged, the total amount of alpha6 subunits was significantly elevated. RT-PCR showed no increase of alpha6 mRNA levels, arguing against increased biosynthesis of these subunits. Elevated levels of alpha6 subunits in alpha1 -/- mice might thus have been caused by an increased incorporation of unassembled alpha6 subunits, replacing alpha1 subunits in alpha1alpha6betagamma2 or alpha1alpha6betadelta receptors, thus rescuing alpha6 subunits from degradation. Elevated levels of alpha3 and alpha4 subunits in the cerebellum of alpha1 -/- mice possibly can be explained similarly. Finally, a small amount of receptors containing no gamma or delta subunits was identified in these mice. Results suggest a total loss of GABAA receptors in cell types where alpha1 was the only alpha subunit expressed and a partial compensation for receptor loss in cell types containing other alpha subunits. Our results do not support a significant compensatory synthesis of other GABAA receptor subunits in the cerebellum of alpha1 -/- mice.     

The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification

Background

Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.

Results

The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.

Conclusions

The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-548) contains supplementary material, which is available to authorized users.     

Isospora suis in an Epithelial Cell Culture System – An In Vitro Model for Sexual Development in Coccidia

Coccidian parasites are of major importance in animal production, public health and food safety. The most frequently used representative in basic research on this group is Toxoplasma gondii. Although this parasite is well investigated there is no adequate in vitro model for its sexual development available and knowledge on this important life cycle phase is therefore scarce. The use of Isospora suis , a sister taxon to T. gondii and the causative agent of piglet coccidiosis, could provide a solution for this. In the present study an in vitro model for neonatal porcine coccidiosis in cells representative for the in vivo situation in the piglet gut was developed and evaluated. The parasite development was investigated by light and transmission electron microscopy and optimum culture conditions were evaluated. Intestinal porcine epithelial cells (IPEC-J2) adequately representing the natural host cells supported the development of all endogenous life cycle stages of I . suis , including gametocytes and oocysts. A concentration of 5% fetal calf serum in the culture medium led to highest gametocyte densities on day 12 post infection. Low infection doses (≤1 sporozoite for 100 host cells) were best for oocyst and gametocyte development. The presented system can also be used for immunostaining with established antibodies developed against T. gondii (in our case, anti-TgIMC3 antibodies directed against the inner membrane complex 3). The complete life cycle of I . suis in a cell line representing the natural host cell type and species provides a unique model among coccidian parasites and can be used to address a wide range of topics, especially with regard to the sexual development of coccidia.     

Two models for screening chelating agents for cadmium removal

The effectiveness of some chelating agents to mobilize cadmium from Chinese hamster ovary cells after chronic exposure (20 hr), as well as from cytosolic metallothionein, was studied. In the first protocol, the most effective substance was 2,3-dimercaptopropanol, followed by 2,3-dimercaptopropane-1-sulfonate and 2,3-dimercaptosuccinic acid, whereas CaNa₃3-diethylenetriamine pentaacetic acid × 5H₂O showed less effect. Simultaneous incubation of cells with cadmium and the chelating agent resulted in a different order of effectiveness: CaNa₃ DTPA prevented cadmium uptake almost totally, 2,3-mercaptopropanol by 75% and 2,3-dimercaptopropane-1-sulfonate by 35%. Neither CaNa₃-diethylenetriamine pentaacetic acid × 5H₂O nor 2,3-dimercaptosuccinic acid had altered the distribution of cadmium between the cytosolic protein fractions after a 2 hr incubation of cells, whereas after this period, 2,3-dimercaptopropanol had removed all cadmium from metallothionein, and 2,3-dimercaptopropane-1-sulfonate about 50%. None of the chelating agents had reduced the amount of Cd bound to high molecular weight proteins. In the cell free system, 2,3-dimercaptopropanol and 2,3-dimercaptopropane-1-sulfonate were equally effective and removed all cadmium from metallothionein within ten minutes. CaNa₃-diethylenetriamine pentaacetic acid × 5H₂O, however, even after 60 min, had removed only 50% of the cadmium. The remaining cadmium was found distributed to the high molecular weight and lower molecular weight protein fractions.Abbreviations BAL 2,3-dimercaptopropanol - CHO Chinese hamster ovary cells - DMPS 2,3-dimercaptopropane-1-sulfonate - DMSA 2,3-dimercaptosuccinic acid - DTPA CaNa₃-diethylenetriaminepentaacetic acid × 5 H₂O - HMW proteins high molecular weight proteins - MT metallothionein     

Isoelectric patterns of peroxidase isoenzymes from tobacco tissue cultures

Summary Peroxidases from tobacco tissue cultures have been separated by thin-layer isoelectric focusing into 12–14 isoenzymes, which have been divided into three groups according to differences in isoelectric points. The isoelectric patterns of callus tissues with and without buds have been compared with those of leaves and stems developed in vitro. Qualitatively, there was a basic similarity of the isoelectric patterns, the same isoenzymes being present in all samples. Distinct quantitative differences in the content and substrate specificity were noted for some of the isoenzymes.