The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome

The ribosomal elongation cycle describes a series of reactions prolonging the nascent polypeptide chain by one amino acid and driven by two universal elongation factors termed EF-Tu and EF-G in bacteria. Here we demonstrate that the extremely conserved LepA protein, present in all bacteria and mitochondria, is a third elongation factor required for accurate and efficient protein synthesis. LepA has the unique function of back-translocating posttranslocational ribosomes, and the results suggest that it recognizes ribosomes after a defective translocation reaction and induces a back-translocation, thus giving EF-G a second chance to translocate the tRNAs correctly. We suggest renaming LepA as elongation factor 4 (EF4).     

Energetics and surface properties of Pseudomonas putida DOT-T1E in a two-phase fermentation system with 1-decanol as second phase

The solvent-tolerant strain Pseudomonas putida DOT-T1E was grown in batch fermentations in a 5-liter bioreactor in the presence and absence of 10% (vol/vol) of the organic solvent 1-decanol. The growth behavior and cellular energetics, such as the cellular ATP content and the energy charge, as well as the cell surface hydrophobicity and charge, were measured in cells growing in the presence and absence of 1-decanol. Although the cells growing in the presence of 1-decanol showed an about 10% reduced growth rate and a 48% reduced growth yield, no significant differences were measured either in the ATP and potassium contents or in the energy charge, indicating that the cells adapted completely at the levels of membrane permeability and energetics. Although the bacteria needed additional energy for adaptation to the presence of the solvent, they were able to maintain or activate electron transport phosphorylation, allowing homeostasis of the ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities and more negative cell surface charges were observed in cells grown in the presence of 1-decanol. Both reactions occurred within about 10 min after the addition of the solvent and were significantly different after killing of the cells with toxic concentrations of HgCl2. This adaptation of the surface properties of the bacterium to the presence of solvents seems to be very similar to previously observed reactions on the level of lipopolysaccharides, with which bacteria adapt to environmental stresses, such as heat shock, antibiotics, or low oxygen content. The results give clear physiological indications that the process with P. putida DOT-T1E as the biocatalyst and 1-decanol as the solvent is a stable system for two-phase biotransformations that will allow the production of fine chemicals in economically sound amounts.     

Primers containing universal bases reduce multiple amoA gene specific DGGE band patterns when analysing the diversity of beta-ammonia oxidizers in the environment

The gene encoding the active site of the ammonia monooxygenase (amoA) has been exploited as molecular marker for studying ammonia-oxidizing bacteria (AOB) diversity in the environment. Primers amplifying functional genes are often degenerated and therefore produce multiple band patterns, when analysed with the Denaturing gradient gel electrophoresis (DGGE) approach. To improve the DGGE band patterns we have designed new primer sets which contain inosine residues and are specific for the amoA gene. Primers were evaluated analysing pure AOB cultures and two habitats (wastewater treatment plant, soda pools). We found that the application of inosine primers helped to reduce the apparent complexity of the DGGE band pattern. Comparison of sequences from environmental samples using either degenerated or inosine containing amoA primers retrieved both identical and additional sequences. Both primer sets seem to be limited in their ability to detect the presence of all AOB by DGGE analyses.     

Identification of gametes and treatment of linear dependencies in the gametic QTL-relationship matrix and its inverse

The estimation of gametic effects via marker-assisted BLUP requires the inverse of the conditional gametic relationship matrix G. Both gametes of each animal can either be identified (distinguished) by markers or by parental origin. By example, it was shown that the conditional gametic relationship matrix is not unique but depends on the mode of gamete identification. The sum of both gametic effects of each animal – and therefore its estimated breeding value – remains however unaffected. A previously known algorithm for setting up the inverse of G was generalized in order to eliminate the dependencies between columns and rows of G. In the presence of dependencies the rank of G also depends on the mode of gamete identification. A unique transformation of estimates of QTL genotypic effects into QTL gametic effects was proven to be impossible. The properties of both modes of gamete identification in the fields of application are discussed.     

The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins

Bacteria and archaea use distinct pathways for salvaging exogenous cobinamide (Cbi), a precursor of adenosylcobalamin (coenzyme B(12)). The bacterial pathway depends on a bifunctional enzyme with kinase and guanylyltransferase activities (CobP in aerobic adenosylcobalamin synthesizers) to convert adenosylcobinamide (AdoCbi) to AdoCbi-guanosine diphosphate (AdoCbi-GDP) via an AdoCbi-phosphate intermediate. Archaea lack CobP, and use a different strategy for the synthesis of AdoCbi-GDP. Archaea cleave off the aminopropanol group of AdoCbi using the CbiZ AdoCbi amidohydrolase to generate adenosylcobyric acid, which is converted to AdoCbi-phosphate by the CbiB synthetase, and to AdoCbi-GDP by the CobY guanylyltransferase. We report phylogenetic, in vivo and in vitro evidence that the genome of Rhodobacter sphaeroides encodes functional enzymes for Cbi salvaging systems of both bacterial and archaeal origins. Products of the reactions were identified by high-performance liquid chromatography, UV-visible spectroscopy and bioassay. The cbiZ genes of several bacteria and archaea restored Cbi salvaging in a strain of Salmonella enterica unable to salvage Cbi. Phylogenetic data led us to conclude that CbiZ is an enzyme of archaeal origin that was horizontally transferred to bacteria. Reasons why some bacteria may contain both types of Cbi salvaging systems are discussed.     

Evidence for a physiological role of intracellularly occurring photolabile nitrogen oxides in human skin fibroblasts

Nitric oxide (NO) plays a pivotal role in human skin biology. Cutaneous NO can be produced enzymatically by NO synthases (NOS) as well as enzyme independently via photodecomposition of photolabile nitrogen oxides (PNOs) such as nitrite or nitroso compounds, both found in human skin tissue in comparably high concentrations. Although the physiological role of NOS-produced NO in human skin is well defined, nothing is known about the biological relevance or the chemical origin of intracellularly occurring PNOs. We here, for the first time, give evidence that in human skin fibroblasts (FB) PNOs represent the oxidation products of NOS-produced NO and that in human skin fibroblasts intracellularly occurring PNOs effectively protect against the injurious effects of UVA radiation by a NO-dependent mechanism. In contrast, in PNO-depleted FB cultures an increased susceptibility to UVA-induced lipid peroxidation and cell death is observed, whereas supplementation of PNO-depleted FB cultures with physiological nitrite concentrations (10 microM) or with exogenously applied NO completely restores UVA-increased injuries. Thus, intracellular PNOs are biologically relevant and represent an important initial shield functioning in human skin physiology against UVA radiation. Consequently, nonphysiological low PNO concentrations might promote known UVA-related skin injuries such as premature aging and carcinogenesis.     

Spike-frequency adaptation generates intensity invariance in a primary auditory interneuron

Adaptation of the spike-frequency response to constant stimulation, as observed on various timescales in many neurons, reflects high-pass filter properties of a neuron's transfer function. Adaptation in general, however, is not sufficient to make a neuron's response independent of the mean intensity of a sensory stimulus, since low frequency components of the stimulus are still transmitted, although with reduced gain. We here show, based on an analytically tractable model, that the response of a neuron is intensity invariant, if the fully adapted steady-state spike-frequency response to constant stimuli is independent of stimulus intensity. Electrophysiological recordings from the AN1, a primary auditory interneuron of crickets, show that for intensities above 60 dB SPL (sound pressure level) the AN1 adapted with a time-constant of approximately 40 ms to a steady-state firing rate of approximately 100 Hz. Using identical random amplitude-modulation stimuli we verified that the AN1's spike-frequency response is indeed invariant to the stimulus' mean intensity above 60 dB SPL. The transfer function of the AN1 is a band pass, resulting from a high-pass filter (cutoff frequency at 4 Hz) due to adaptation and a low-pass filter (100 Hz) determined by the steady-state spike frequency. Thus, fast spike-frequency adaptation can generate intensity invariance already at the first level of neural processing.     

Arachidonic-acid-derived eicosanoids: roles in biology and immunopathology

Arachidonic acid (AA)-derived eicosanoids belong to a complex family of lipid mediators that regulate a wide variety of physiological responses and pathological processes. They are produced by various cell types through distinct enzymatic pathways and act on target cells via specific G-protein-coupled receptors. Although originally recognized for their capacity to elicit biological responses such as vascular homeostasis, protection of the gastric mucosa and platelet aggregation, eicosanoids are now understood to regulate immunopathological processes ranging from inflammatory responses to chronic tissue remodelling, cancer, asthma, rheumatoid arthritis and autoimmune disorders. Here, we review the major properties of eicosanoids and their expanding roles in biology and medicine.     

Plasmodium falciparum glycosylphosphatidylinositol toxin interacts with the membrane of non-parasitized red blood cells: a putative mechanism contributing to malaria anemia

Following exposure to synthetic Plasmodium falciparum glycosylphosphatidylinositol (P.f.-GPI), red blood cells (RBCs) reacted with antibodies in the serum of a patient with severe acute P. falciparum malaria. Carbohydrate microarray analysis of the patient's serum confirmed the presence of both, IgM and IgG antibodies against P.f.-GPI. The antibodies failed to bind to RBCs when P.f.-GPI lacking the lipid portion was applied. Addition of the detergent Triton X-100 during preincubation with P.f.-GPI resulted in increased recognition. Recognition of P.f.-GPI was dependent on the concentrations of synthetic P.f.-GPI, the serum and the numbers of RBCs. IgM antibodies dominated P.f.-GPI-sensitized RBCs recognition. Recognition by IgM antibodies proved highest during the 1stweek of acute malaria and decreased during the following 2weeks as assessed by flow cytometry and carbohydrate microarray analysis. These results strongly support the notion that released P.f.-GPI can insert into non-parasitized RBC membranes and results in recognition by circulating anti-GPI antibodies and possibly subsequent elimination. This process may contribute to malaria-associated anemia.