Selective leakage of host-cell proteins during high-cell-density cultivation of recombinant and non-recombinant Escherichia coli

Significant leakage of host-cell proteins into the culture medium occurred during high-cell-density cultivation of E. coli. Identification of these medium proteins revealed almost exclusively a periplasmic origin. Release of periplasmic proteins into the culture medium was observed throughout the entire cultivation of recombinant or non-recombinant cells. Leakage was intensified, however, in the final part of high-cell-density cultures (>100 g L(-)(1) dry cell mass) or when a temperature upshift was used for induction of recombinant protein synthesis. After temperature upshift, formation rates and residual cellular concentrations of periplasmic proteins declined with individual rates; e.g., the cellular content of the large periplasmic dipeptide binding protein DppA (57.4 kDa) started to decline about 4 h after the temperature upshift, whereas the smaller periplasmic d-galactose/d-glucose binding protein MglB (33.4 kDa) was already lost during the first hour after the upshift. In addition to periplasmic proteins, the osmotic-shock-sensitive heat-shock protein DnaK was found in significantly higher proportion in the cell-free medium of the temperature-challenged culture than other cytoplasmic proteins. Cell lysis was not observed even after prolonged cultivation. Thus, loss of a subset of cellular proteins of mainly periplasmic origin ordinarily occurs during cultivation and is intensified through stressful conditions in high-cell-density cultures. The selective release of cellular proteins of periplasmic origin offers the opportunity to simplify the downstream processing of recombinant proteins directed to the periplasm of E. coli.     

Electrostatic recognition in substrate binding to serine proteases

Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes. Thus, we are able to directly link protease structures to their electrostatic substrate preferences. Additionally, we present a new metric that measures similarities in substrate preferences focusing only on electrostatics. It efficiently compares these electrostatic substrate preferences between different proteases. This new metric can be interpreted as the electrostatic part of our previously developed substrate similarity metric. Consequently, we suggest, that substrate recognition in terms of electrostatics and shape complementarity are rather orthogonal aspects of substrate recognition. This is in line with a 2‐step mechanism of protein‐protein recognition suggested in the literature.     

An RNAi-Based Approach to Down-Regulate a Gene Family In Vivo

Genetic redundancy poses a major problem to the analysis of gene function. RNA interference allows the down-regulation of several genes simultaneously, offering the possibility to overcome genetic redundancy, something not easily achieved with traditional genetic approaches. Previously we have used a polycistronic miR155-based framework to knockdown expression of three genes of the early B cell factor family in cultured cells. Here we develop the system further by generating transgenic mice expressing the RNAi construct in vivo in an inducible manner. Expression of the transgene from the strong CAG promoter is compatible with a normal function of the basal miRNA/RNAi machinery, and the miR155 framework readily allows inducible expression from the Rosa26 locus as shown by Gfp. However, expression of the transgene in hematopoietic cells does not lead to changes in B cell development and neuronal expression does not affect cerebellar architecture as predicted from genetic deletion studies. Protein as well as mRNA levels generated from Ebf genes in hetero- and homozygous animals are comparable to wild-type levels. A likely explanation for the discrepancy in the effectiveness of the RNAi construct between cultured cells and transgenic animals lies in the efficiency of the sequences used, possibly together with the complexity of the transgene. Since new approaches allow to overcome efficiency problems of RNAi sequences, the data lay the foundation for future work on the simultaneous knockdown of several genes in vivo.     

Exposure of Petunia Seedlings to Ethylene Decreased Apical Dominance by Reducing the Ratio of Auxin to Cytokinin

Seedlings of Petunia x hybrida ‘Orchid’ treated with the ethylene-releasing compound ethephon at 0.9, 1.7, and 3.5 mM evolved ethylene at a higher rate as the concentration of ethephon increased. Regardless of the concentration of ethephon applied, ethylene evolution peaked 6 to 8 h following application. Evidence that ethephon application decreased apical dominance included an increase in the number of new nodes on the main stem and a sustained increase in the length of new and existing lateral shoots compared to the control (no ethephon). Plants treated with 3.5 mM ethephon developed mild chlorosis, whereas a concentration of 1.7 mM ethephon decreased apical dominance without phytotoxic effects. The auxin/cytokinin ratio decreased in the apical shoot section as early as 1 h after ethephon treatment. In contrast, a decrease in the ratio in the subapical shoot section was not detected until 24 h after ethephon application. Reduction in auxin/cytokinin ratio was a result of a decrease in indole-3-acetic acid (IAA) and an increase of zeatin riboside (ZR), but not isopentenyladenosine (iPA). These results suggest that exposing ‘Orchid’ petunia seedlings to ethylene via ethephon lowers the auxin/cytokinin ratio, thereby promoting the outgrowth of lateral shoots.     

Vegetation change in a man‐made salt marsh affected by a reduction in both grazing and drainage

Abstract. In order to restore natural salt marsh in a 460‐ha nature reserve established in man‐made salt marsh in the Dollard estuary, The Netherlands, the artificial drainage system was neglected and cattle grazing reduced. Vegetation changes were traced through two vegetation surveys and monitoring of permanent plots over 15 yr after the management had been changed. Exclosure experiments were started to distinguish grazing effects from effects of increased soil waterlogging caused by the neglect of the drainage system. Both vegetation surveys and permanent plots demonstrated a dichotomy in vegetation succession. The incidence of secondary pioneer vegetation dominated by Salicornia spp. and Suaeda maritima increased from 0 to 20%, whereas the late‐successional (Phragmites australis) vegetation from 10 to 15%. Grazing intensity decreased towards the sea. The grazed area contracted landward, which allowed vegetation dominated by tall species to increase seaward. Grazing and increased waterlogging interacted in several ways. The impact of trampling increased, and in the intensively grazed parts soil salinity increased. This can probably be explained by low vegetation cover in spring. Framework Ordination, an indirect‐gradient‐analysis technique, was used to infer the importance of environmental factors in influencing changes in species composition. Many changes were positively or negatively correlated with soil aeration and soil salinity, whereas elevation was of minor importance. Grazing accounted for only a few changes in species frequency. Changes in permanent plots were greater during the first than during the second half of the study period. In exclosures that were installed halfway through the study period, there was a relatively rapid recovery of previously dominant species that had decreased during the first half of the study period. Species richness per unit area in the reserve increased. At the seaward side of the marsh, the altered management allowed succession to proceed leading to establishment of stands of Phragmites australis, whereas on the landward side, the combination of moderate grazing with neglect of the drainage system appeared an effective measure in maintaining habitats for a wider range of halophytic species.     

Straight Line Foraging in Yellow-Eyed Penguins: New Insights into Cascading Fisheries Effects and Orientation Capabilities of Marine Predators

Free-ranging marine predators rarely search for prey along straight lines because dynamic ocean processes usually require complex search strategies. If linear movement patterns occur they are usually associated with travelling events or migratory behaviour. However, recent fine scale tracking of flying seabirds has revealed straight-line movements while birds followed fishing vessels. Unlike flying seabirds, penguins are not known to target and follow fishing vessels. Yet yellow-eyed penguins from New Zealand often exhibit directed movement patterns while searching for prey at the seafloor, a behaviour that seems to contradict common movement ecology theories. While deploying GPS dive loggers on yellow-eyed penguins from the Otago Peninsula we found that the birds frequently followed straight lines for several kilometres with little horizontal deviation. In several cases individuals swam up and down the same line, while some of the lines were followed by more than one individual. Using a remote operated vehicle (ROV) we found a highly visible furrow on the seafloor most likely caused by an otter board of a demersal fish trawl, which ran in a straight line exactly matching the trajectory of a recent line identified from penguin tracks. We noted high abundances of benthic scavengers associated with fisheries-related bottom disturbance. While our data demonstrate the acute way-finding capabilities of benthic foraging yellow-eyed penguins, they also highlight how hidden cascading effects of coastal fisheries may alter behaviour and potentially even population dynamics of marine predators, an often overlooked fact in the examination of fisheries’ impacts.     

Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps

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Highlights? A resource of genetic modules and networks induced by distinct types of DNA damage ? Networks distinguish DNA damage response pathways with high statistical power ? Rtt109, a histone acetyltransferase, affects the mutagenic bypass of DNA lesions ? The neddylation machinery and Irc21 affect cell-cycle control and genome stability     

The Binding Properties of the Particulate and Solubilized Sulfonylurea Receptor from Cerebral Cortex Are Modulated by the Mg2+ Complex of ATP

Glibenclamide closes an ATP-sensitive K+ channel (K-ATP channel) by interaction with the sulfonylurea receptor in the plasma membrane of pancreatic B cells and thereby initiates insulin release. Previous studies demonstrated that the Mg2+ complex of ATP decreases glibenclamide binding to the sulfonylurea receptor from pancreatic islets. The aim of the present study was to examine the effect of adenine and guanine nucleotides on binding of sulfonyl-ureas to the cerebral sulfonylurea receptor. For this purpose, binding properties of the particulate and solubilized site from rat or pig cerebral cortex were analyzed. Maximum recovery of receptors in detergent extracts amounted to 40-50%. Specific binding of [3H]glibenclamide to the solubilized receptors corresponded well to specific binding to microsomes. In microsomes and detergent extracts, the Mg2+ complexes of ATP, ADP, GTP, and GDP inhibited binding of [3H]glibenclamide. These effects were not observed in the absence of Mg2+. In detergent extracts, Mg-ATP (300 microM) reduced the number of high-affinity sites for [3H]-glibenclamide by 52% and increased the dissociation constant for [3H]glibenclamide by eightfold; Mg-ATP was half-maximally effective at 41 microM. Alkaline phosphatase accelerated the reversal of Mg-ATP-induced inhibition of [3H]glibenclamide binding. The data suggest similar control of the sulfonylurea receptor from brain and pancreatic islets by protein phosphorylation.     

MODBASE, a database of annotated comparative protein structure models

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10^–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server.