Cascading predation effects of Daphnia and copepods on microbial food web components

1. We performed a mesocosm experiment to investigate the structuring and cascading effects of two predominant crustacean mesozooplankton groups on microbial food web components. The natural summer plankton community of a mesotrophic lake was exposed to density gradients of Daphnia and copepods. Regression analysis was used to reveal top–down impacts of mesozooplankton on protists and bacteria after days 9 and 15. 2. Selective grazing by copepods caused a clear trophic cascade via ciliates to nanoplankton. Medium‐sized (20–40 μm) ciliates (mainly Oligotrichida) were particularly negatively affected by copepods whereas nanociliates (mainly Prostomatida) became more abundant. Phototrophic and heterotrophic nanoflagellates increased significantly with increasing copepod biomass, which we interpret as an indirect response to reduced grazing pressure from the medium‐sized ciliates. 3. In Daphnia‐treatments, ciliates of all size classes as well as nanoflagellates were reduced directly but the overall predation effect became most strongly visible after 15 days at higher Daphnia biomass. 4. The response of bacterioplankton involved only modest changes in bacterial biomass and cell‐size distribution along the zooplankton gradients. Increasing zooplankton biomass resulted either in a reduction (with Daphnia) or in an increase (with copepods) of bacterial biovolume, activity and production. Patterns of bacterial diversity, as measured by polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE), showed no distinct grouping after 9 days, whereas a clear treatment‐coupled similarity clustering occurred after 15 days. 5. The experiment demonstrated that zooplankton‐mediated predatory interactions cascade down to the bacterial level, but also revealed that changes occurred rather slowly in this summer plankton community and were most pronounced with respect to bacterial activity and composition.     

Alternative splicing and protein function

Background  

Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data.     

Multiubiquitylation by E4 enzymes: 'one size' doesn't fit all

Selective protein degradation by the 26S proteasome requires the covalent attachment of several ubiquitin molecules in the form of a multiubiquitin chain. Ubiquitylation usually involves three classes of enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2) and a ubiquitin ligase (E3). However, in some cases, multiubiquitylation requires the additional activity of certain ubiquitin-chain elongation factors. Yeast UFD2 (ubiquitin fusion degradation), for example, binds to oligoubiquitylated substrates (proteins modified by only a few ubiquitin molecules) and catalyses multiubiquitin-chain assembly in collaboration with E1, E2 and E3. Enzymes possessing this specific activity have been proposed to be termed 'E4 enzymes'. Recent studies have provided accumulating evidence that has led some researchers in the field to conclude that E4, indeed, represents a distinct and novel class of enzymes.     

AP-1 in Toxoplasma gondii mediates biogenesis of the rhoptry secretory organelle from a post-Golgi compartment

We have previously demonstrated that Toxoplasma gondii has a tyrosine-based sorting system, which mediates protein targeting to the lysosome-like rhoptry secretory organelle. We now show that rhoptry protein targeting is also dependent on a dileucine motif and occurs from a post-Golgi endocytic organelle to mature rhoptries in an adaptin-dependent fashion. The T. gondii AP-1 adaptin complex is implicated in this transport because the micro1 chain of T. gondii AP-1 (a) was localized to multivesicular endosomes and the limiting and luminal membranes of the rhoptries; (b) bound to endocytic tyrosine motifs in rhoptry proteins, but not in proteins from dense granule secretory organelles; (c) when mutated in predicted tyrosine-binding motifs, led to accumulation of the rhoptry protein ROP2 in a post-Golgi multivesicular compartment; and (d) when depleted via antisense mRNA, resulted in accumulation of multivesicular endosomes and immature rhoptries. These are the first results to implicate AP-1 in transport from a post-Golgi compartment to a mature secretory organelle and substantially expand the role for AP-1 in anterograde protein transport.     

Formation of caspase-3 complexes and fragmentation of caspase-12 during anisomycin-induced apoptosis in AKR-2B cells without aggregation of Apaf-1

Treatment of AKR-2B fibroblasts with anisomycin (10 microM) led to a rapid disintegration of the cells (t1/2 = 5 h) which was complete after 24 h. Cell death was associated with typical hallmarks of apoptosis like membrane blebbing, exposure of phophatidylserine on the cell surface, nuclear condensation and specific cleavage of rRNA. However, there was no dissipation of the mitochondrial potential and no intranucleosomal fragmentation. By affinity labeling with YVK(-bio)D.aomk in combination with immunostaining against activated caspase-3 analyzed by 2-D gel electrophoresis it was shown that caspase-3 is the dominant executioner caspase. Gel filtration experiments of cytosolic extract analyzed by Western blotting revealed the formation of high-molecular-weight complexes of caspase-3 (600 kDa and 250 kDa, respectively), but there was no complex formation of Apaf-1. Anisomycin treatment led to a strong activation of the stress kinases p38 kinases and the jun kinases, that was not sufficient for the activation of caspase-3 which required much higher concentrations. By using the selective inhibitors SB 203580 for p38 kinases and SP 600125 for c-jun kinases, respectively, it is shown that activation of these kinases is not necessary for cell death induced by anisomycin in AKR-2B cells. Furthermore, we disclose the activation of caspase-12 in AKR-2B cells following the addition of anisomycin. Caspase-12 zymogen present as a cytosolic complex (> 600 kDa) is activated by anisomycin leading to an uncomplexed cleaved enzyme. Since anisomycin treatment did neither lead to stress of the endoplasmic reticulum nor to a breakdown of intracellular Ca(2+)-stores, alternative pathways involved in the activation of caspases are discussed.     

Dent Disease with mutations in OCRL1

Dent disease is an X-linked renal proximal tubulopathy associated with mutations in the chloride channel gene CLCN5. Lowe syndrome, a multisystem disease characterized by renal tubulopathy, congenital cataracts, and mental retardation, is associated with mutations in the gene OCRL1, which encodes a phosphatidylinositol 4,5-bisphosphate (PIP(2)) 5-phosphatase. Genetic heterogeneity has been suspected in Dent disease, but no other gene for Dent disease has been reported. We studied male probands in 13 families, all of whom met strict criteria for Dent disease but lacked mutations in CLCN5. Linkage analysis in the one large family localized the gene to a candidate region at Xq25-Xq27.1. Sequencing of candidate genes revealed a mutation in the OCRL1 gene. Of the 13 families studied, OCRL1 mutations were found in 5. PIP(2) 5-phosphatase activity was markedly reduced in skin fibroblasts cultured from the probands of these five families, and protein expression, measured by western blotting, was reduced or absent. Slit-lamp examinations performed in childhood or adulthood for all five probands showed normal results. Unlike patients with typical Lowe syndrome, none of these patients had metabolic acidosis. Three of the five probands had mild mental retardation, whereas two had no developmental delay or behavioral disturbance. These findings demonstrate that mutations in OCRL1 can occur with the isolated renal phenotype of Dent disease in patients lacking the cataracts, renal tubular acidosis, and neurological abnormalities that are characteristic of Lowe syndrome. This observation confirms genetic heterogeneity in Dent disease and demonstrates more-extensive phenotypic heterogeneity in Lowe syndrome than was previously appreciated. It establishes that the diagnostic criteria for disorders resulting from mutations in the Lowe syndrome gene OCRL1 need to be revised.     

Neurochemically distinct myenteric neurone populations containing calbindin have specific distribution patterns around the circumference of the gastric corpus

We recently described calbindin immunoreactivity in the myenteric plexus of the guinea-pig stomach. To study the neurochemical coding of calbindin D28 k (CALB)-containing myenteric neurones, the presence of calretinin (CALRET), choline acetyltransferase (ChAT), enkephalin (ENK), neuropeptide Y, serotonin (5-HT), somatostatin (SOM) and substance P(SP) was investigated immunohistochemically in colchicine-treated preparations. Nitric oxide synthase-containing neurones were detected by NADPH-diaphorase histochemistry. In addition, we investigated the neurone distribution patterns around the gastric corpus. Most CALB neurones were ChAT positive. ChAT/CALB neurones were either CALRET (ca 75%) or 5-HT positive and most contained in addition SP and/or ENK. All 5-HT neurones contained CALB. CALB labelled on average 2.3, 4.8 and 7.5 neurones per ganglion at the lesser curvature, in the central region and the greater curvature, respectively, which indicated a preferential localisation at the greater curvature. Compared to the total number of myenteric neurones, the proportion of CALB neurones increased significantly from the lesser curvature (6%) towards the greater curvature (18%). This shift, although observed for most ChAT/CALB-positive populations, was most prominent for the ChAT/CALB/CALRET/SP/ENK-encoded neurones. SOM-positive and ChAT-only encoded neurones were preferentially located at the lesser curvature. The remaining ten neurochemically defined populations did not exhibit an uneven distribution. The colocalisation of CALB with CALRET or 5-HT is specific for myenteric neurones in the stomach and represents one significant difference to the neurochemical code of CALB neurones in the guinea-pig intestine. The functional significance of the unevenness of neurone distribution along the circumference of the gastric corpus remains to be studied.     

Selective degradation of the PKC-epsilon isoform during cell death in AKR-2B fibroblasts

The protein kinase C (PKC) family of serine/threonine protein kinases is involved in intracellular signals that regulate growth, differentiation, and apoptosis. AKR-2B cells express the PKC isoforms alpha, gamma, epsilon, lambda, mu, und zeta (J. Hoppe, R. Sch?fer, V. Hoppe, and A. Sachinidis, Cell Death Differ. 6, 546-556). Here we show that during serum starvation only PKC-epsilon was cleaved. An N-terminal fragment of 42 kDa remained associated with subcellular components, presumably the Golgi apparatus. The C-terminal part (catalytic domain) was further degraded and was no longer detectable in vivo. As published before, the activation of the DEVDase in AKR-2B cells is prevented by numerous agents like PDGF, TPA, and DEVD.cmk (R. Sch?fer, D. Karbach, and J. Hoppe, Exp. Cell Res. 240, 28--39). All these agents completely prevented PKC-epsilon cleavage, indicating a tight correlation between DEVDase activity and PKC-epsilon cleavage. By using recombinant caspase-3 or highly purified DEVDase from cytosolic extracts we localized by Edman degradation the cleavage site in recombinant PKC-epsilon to asp383 in the hinge region between regulatory and catalytic domains. The corresponding tetrapeptide sequences SSPD and SATD for human and mouse PKC-epsilon, respectively, are unusual for caspase-3. Expression of the catalytic domain or of the cleavage-resistant mutant D383A had no effect on cell death in AKR-2B cells.     

Endocytosis in different lifestyles of protozoan parasitism: role in nutrient uptake with special reference to Toxoplasma gondii

A fundamental property of any eukaryotic cell is endocytosis, that is the ability to take up external fluid, solutes and particulate matter into membrane-bound intracellular vesicles by various mechanisms. Toxoplasma gondii is an intracellular protozoan parasite of the phylum Apicomplexa with a wide geographical and host range distribution. Significant progress in studying the cell biology of this parasite has been accomplished over the last few years. Only recently endocytic compartments and endocytic trafficking have come to a closer dissection in T. gondii. In this review, we discuss the evidence for an endocytic compartment and present a model for an endocytic pathway in Toxoplasma against a background of endocytosis in kinetoplastida and the extensive insights gained from mammalian and yeast cells.     

Toxoplasma gondii ADP-ribosylation factor 1 mediates enhanced release of constitutively secreted dense granule proteins

Toxoplasma gondii dense granules are morphologically similar to dense matrix granules in specialized secretory cells, yet are secreted in a constitutive, calcium-independent fashion. We previously demonstrated that secretion of dense granule proteins in permeabilized parasites was augmented by the non-hydrolyzable GTP analogue guanosine 5'-3-O-(thio)triphosphate (GTPgammaS) (Chaturvedi, S., Qi, H., Coleman, D. L., Hanson, P., Rodriguez, A., and Joiner, K. A. (1998) J. Biol. Chem. 274, 2424-2431). As now demonstrated by pharmacological and electron microscopic approaches, GTPgammaS enhanced release of dense granule proteins in the permeabilized cell system. To investigate the role of ADP-ribosylation factor 1 (ARF1) in this process, a cDNA encoding T. gondii ARF1 (TgARF1) was isolated. Endogenous and transgenic TgARF1 localized to the Golgi of T. gondii, but not to dense granules. An epitope-tagged mutant of TgARF1 predicted to be impaired in GTP hydrolysis (Q71L) partially dispersed the Golgi signal, with localization to scattered vesicles, whereas a mutant impaired in nucleotide binding (T31N) was cytosolic in location. Both mutants caused partial dispersion of a Golgi/trans-Golgi network marker. TgARF1 mutants inhibited delivery of the secretory reporter, Escherichia coli alkaline phosphatase, to dense granules, precluding an in vivo assessment of the role of TgARF1 in release of intact dense granules. To circumvent this limitation, recombinant TgARF1 was purified using two separate approaches, and used in the permeabilized cell assay. TgARF1 protein purified on a Cibacron G3 column and able to bind GTP stimulated dense granule secretion in the permeabilized cell secretion assay. These results are the first to show that ARF1 can augment release of constitutively secreted vesicles at the target membrane.