Discovery of a photosynthesizing animal that can survive for months in a light-dependent manner

Recently M. E. Rumpho and coworkers (USA) established that the marine slug Elysia chlorotica, a gastropod mollusk that feeds on the eukaryotic filamentous yellow-green alga Vaucheria litorea, recruits chloroplasts from the alga and transports them from the digestive apparatus into a special organ of the slug that resembles a green leaf and is an approximately 100-fold increased parapodium—an outgrowth of the slug’s body. The chloroplasts survive inside the slug for up to 10 months and perform active photosynthesis accompanied by assimilation of CO₂. Under conditions of starvation, this photosynthesis becomes for the animal the only source of energy and fixed carbon. For functioning, chloroplasts have to constantly import some short-lived proteins that are encoded in the nucleus of the photosynthesizing organism. Therefore, the authors supposed that a transfer of the corresponding genes must have occurred between the algal and mollusk nuclei. This hypothesis was experimentally confirmed for two genes encoding proteins of the photosynthesizing apparatus. The questions arise of what mechanism was responsible for the transfer of these genes and how the slug created its photosynthesizing organ resembling the leaf of a higher plant rather than the primitive filamentous algal structure which was the source of the acquired chloroplasts and the photosynthesis genes.     

A genomic survey shows that the haloarchaeal type tyrosyl tRNA synthetase is not a synapomorphy of opisthokonts

The haloarchaeal-type tyrosyl tRNA synthetase (tyrRS) have previously been proposed to be a molecular synapomorphy of the opisthokonts. To re-evaluate this we have performed a taxon-wide genomic survey of tyrRS in eukaryotes and prokaryotes. Our phylogenetic trees group eukaryotes with archaea, with all opisthokonts sharing the haloarchaeal-type tyrRS. However, this type of tyrRS is not exclusive to opisthokonts, since it also encoded by two amoebozoans. Whether this is a consequence of lateral gene transfer or lineage sorting remains unsolved, but in any case haloarchaeal-type tyrRS is not a synapomorphy of opisthokonts. This demonstrates that molecular markers should be re-evaluated once a better taxon sampling becomes available.     

Exact continuum solution for a channel that can be occupied by two ions

The classical Nernst-Planck continuum equation is extended to the case where the channel can be occupied simultaneously by two ions. A two-dimensional partial differential equation is derived to describe the steady-state channel. This differential equation is of the form of the generalized Laplace equation, but it has the novel feature that the boundary conditions are periodic. The finite difference solution takes approximately 8 s on a large computer. The equations are solved for the special case of a cylindrical channel with a fixed charge in the center. It is assumed that the forces on the ions result entirely from the sum of the Born image potential, the fixed charge potential, the interaction potential between the two ions, and the applied voltage. Approximate simple analytical expressions are derived for these potential terms, based on the assumption that the electric field perpendicular to the channel wall is zero. The potentials include the contribution from a diffuse charge (Debye-Huckel) reaction field in the bulk solution for the monovalent cation flux was obtained for channels with a radius of 4 A and lengths of 16 and 32 A and a fixed charge valence of -1 and -1.5. For these channels, a significant fraction (up to 90%) of the total resistance is contributed by the bulk solution and results were obtained for the case where the "channel" included 8 A of bulk solution at each channel end. These results for the two-ion channel were compared with the analytical solution for a one-ion channel. The one-ion channel is a fair approximation to the two-ion channel for a fixed charge of -1, underestimating the flux at high concentrations by approximately 30%. However, for a fixed charge of -1.5, the one-ion model is a poor approximation, with the two-ion flux about seven times that of the one-ion model at high concentrations. The absolute conductance and concentration dependence of these channels (with a fixed charge of -1) mimic the behavior of the large conductance K+ channel and the acetylcholine receptor channel.     

Esterase A is a proteinase from rat urine that can activate plasminogen

A proteinase which can activate human, dog and rat plasminogen to plasmin has been isolated from the urine of female rats, using affinity chromatography on benzamidine-coupled Sepharose. Inhibition by diisopropylfluorophosphate, tosyl-L-lysine chloromethylketone and benzamidine classified the enzyme as trypsin-like. The proteinase has weak activity on alpha-casein and hemoglobin, but will not lyse fibrin clots. It readily cleaves arginyl amides, including synthetic substrates specific for human glandular kallikrein and other serine proteinases. A chromogenic substrate for human urokinase (pyro Glu-Gly-Arg-pNA) is a poor substrate for the rat proteinase. Characteristics of the enzyme, such as its molecular weight (25 900), kinetic parameters and inhibition by aprotinin, indicate that this proteinase is esterase A, described by several investigators. Esterase A is shown not to be a true urinary plasminogen activator but rather is a unique arginine-specific proteinase. Urokinase-like and kallikrein-like activity are part of a broader proteolytic activity displayed by this enzyme.     

Eco1 is a novel acetyltransferase that can acetylate proteins involved in cohesion

Cohesion between sister chromatids is established during S phase and maintained through G2 phase until it is resolved in anaphase (for review, see [1-3]). In Saccharomyces cerevisiae, a complex consisting of Scc1, Smc1, Smc3, and Scc3 proteins, called "cohesin," mediates the connection between sister chromatids. The evolutionary conserved yeast protein Eco1 is required for establishment of sister chromatid cohesion during S phase but not for its further maintenance during G2 or M phases or for loading the cohesin complex onto DNA. We address the molecular functions of Eco1 with sensitive sequence analytic techniques, including hidden Markov model domain fragment searches. We found a two-domain architecture with an N-terminal C2H2 Zn finger-like domain and an approximately 150 residue C-terminal domain with an apparent acetyl coenzyme A binding motif (http://mendel.imp.univie.ac.at/SEQUENCES/ECO1/). Biochemical tests confirm that Eco1 has the acetyltransferase activity in vitro. In vitro Eco1 acetylates itself and components of the cohesin complex but not histones. Thus, the establishment of cohesion between sister chromatids appears to be regulated, directly or indirectly, by a specific acetyltransferase.     

A privileged intraphagocyte niche is responsible for disseminated infection of Staphylococcus aureus in a zebrafish model

The innate immune system is the primary defence against the versatile pathogen, Staphylococcus aureus. How this organism is able to avoid immune killing and cause infections is poorly understood. Using an established larval zebrafish infection model, we have shown that overwhelming infection is due to subversion of phagocytes by staphylococci, allowing bacteria to evade killing and found foci of disease. Larval zebrafish coinfected with two S. aureus strains carrying different fluorescent reporter gene fusions (but otherwise isogenic) had bacterial lesions, at the time of host death, containing predominantly one strain. Quantitative data using two marked strains revealed that the strain ratios, during overwhelming infection, were often skewed towards the extremes, with one strain predominating. Infection with passaged bacterial clones revealed the phenomenon not to bedue to adventitious mutations acquired by the pathogen. After infection of the host, all bacteria are internalized by phagocytes and the skewing of population ratios is absolutely dependent on the presence of phagocytes. Mathematical modelling of pathogen population dynamics revealed the data patterns are consistent with the hypothesis that a small number of infected phagocytes serve as an intracellular reservoir for S. aureus, which upon release leads to disseminated infection. Strategies to specifically alter neutrophil/macrophage numbers were used to map the potential subpopulation of phagocytes acting as a pathogen reservoir, revealing neutrophils as the likely ‘niche’. Subsequently in a murine sepsis model, S. aureus abscesses in kidneys were also found to be predominantly clonal, therefore likely founded by an individual cell, suggesting a potential mechanism analogous to the zebrafish model with few protected niches. These findings add credence to the argument that S. aureus control regimes should recognize both the intracellular as well as extracellular facets of the S. aureus life cycle.     

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.     

Mouse glutamine synthetase is encoded by a single gene that can be expressed in a localized fashion

Two mouse glutamine synthetase (GSase) cDNAs were cloned that correspond to the 2.8 kb and 1.4 kb mRNA species found in many mouse tissues (1 kb = 10(3) base-pairs). There is a sequence homology of about 90% to other mammalian GSase cDNAs in the coding region. A 2.1 kb mRNA can be discerned in fat tissue, the most abundant source of GSase mRNA. Three genomic clones G4, G21 and G2 contain GSase sequences. By several criteria G21 and G2 are pseudogenes, while G4 is a functional gene composed of seven exons and six introns. Primer extension, RNase protection and Northern analysis provide evidence that all tissues use the same major RNA start site and the different-sized mRNAs are due to the usage of two different poly(A) sites, neither of which has the consensus AAUAAA sequence. When tested by transfection into Hep G2 human hepatoma cells the G4 promoter can produce correctly initiated mRNA with only 350 base-pairs of 5' regulatory sequences. A major interest in GSase expression is its restriction to pericentral hepatocytes in adult liver. In this paper we show by in situ hybridization that GSase mRNA is only found in glial cells in the adult brain and in proximal tubular epithelium of the kidney. Coupled with the earlier demonstration of expression of GSase only in pericentral hepatocytes, it is clear that this gene is regulated by position-specific signals in many cell types.     

Smooth muscle caldesmon is an extended flexible monomeric protein in solution that can readily undergo reversible intra- and intermolecular sulfhydryl cross-linking. A mechanism for caldesmon's F-actin bundling activity

Caldesmon is a major F-actin binding protein of smooth muscle that has been implicated as a component of a thin filament regulatory system. Chicken gizzard caldesmon consists of polypeptides of Mr-135,000 and 140,000 which are closely related as determined by analysis of cyanogen bromide cleavage fragments. It is a highly extended flexible protein having a contour length of about 146 nm and a secondary structure composed primarily of random coil. Physical and chemical cross-linking data suggest that caldesmon exists as a monomer in solution. The cysteine content of caldesmon was determined to be 2 residues/polypeptide. Remarkably, in solution it readily undergoes sulfhydryl oxidation to form either an internal disulfide bridge in the protein or cross-links between individual polypeptides to form dimers, trimers, tetramers, etc. The internally cross-linked species have a smaller Stokes radius than the reduced molecules, indicating that the cross-link "trapped" the molecule in a compact conformation. Oxidized protein containing caldesmon oligomers is a potent F-actin bundling protein. Complete reduction of caldesmon abolishes the F-actin bundling activity. Since a vast excess of reducing agent is required to convert caldesmon from an oxidized to reduced state, it may exist in either state in vivo. Thus, the ability of caldesmon to undergo reversible sulfhydryl cross-linking, and thereby reversible F-actin cross-linking, may be of physiological significance.     

YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes

In bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger RNA (tmRNA). In the absence of tmRNA, however, there is evidence that stalled ribosomes are released from non-stop mRNAs. Here, we show a novel ribosome rescue system mediated by a small basic protein, YaeJ, from Escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (RF). In vitro translation experiments using the E. coli-based reconstituted cell-free protein synthesis system revealed that YaeJ can hydrolyze peptidyl–tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs containing rare codon clusters that extend downstream from the P-site and prevent Ala-tmRNA•SmpB from entering the empty A-site. In addition, YaeJ had no effect on translation of a normal mRNA with a stop codon. These results suggested a novel tmRNA-independent rescue system for stalled ribosomes in E. coli. YaeJ was almost exclusively found in the 70S ribosome and polysome fractions after sucrose density gradient sedimentation, but was virtually undetectable in soluble fractions. The C-terminal basic residue-rich extension was also found to be required for ribosome binding. These findings suggest that YaeJ functions as a ribosome-attached rescue device for stalled ribosomes.     

Characterization of Human gamma-glutamyl hydrolase in solution demonstrates that the enzyme is a non-dissociating homodimer

Human gamma-glutamyl hydrolase (hGH) is a key enzyme in the metabolism of folic acid and in the pharmacology of many antifolate drugs. hGH catalyzes removal of the poly-gamma-glutamate chains of intracellular folic acid and antifolates. hGH crystallized as a homodimer with two putative active sites. However, the quaternary structure and the number of species of the enzyme in solution have not been determined. hGH has now been characterized using analytical ultracentrifugation and dynamic light scattering. HisTag fusion proteins of wild-type hGH, rat GH, and hGH expressed as a glycosylated protein were studied. Analyses of HisTag wild-type hGH were conducted over a range of protein concentrations (1.4-200 microM), ionic strengths (0-1 M NaCl), and pH (4.5-8.5). A single species with a molecular mass consistent with a homodimer was observed. Glycosylated hGH and HisTag rat gamma-glutamyl hydrolase also formed very stable homodimers. The lack of dissociation of the dimer, the large monomer-monomer interface, and the presence of catalytically essential Tyr-36 in the homodimer interface sequences suggest that homodimer formation is required for the hGH monomer to fold into an active conformation. The conservation of hGH monomer-monomer interface sequences in other mammalian and plant gamma-glutamyl hydrolase molecules suggests that they also exist as stable homodimers.     

Idaten is a new cold-inducible transposon of Volvox carteri that can be used for tagging developmentally important genes

A cold-inducible transposon called Jordan has previously been used to tag and recover genes controlling key aspects of Volvox development, including the process called inversion. In a search for additional genes, we isolated 17 new inversionless mutants from cultures grown at 24 degrees (the temperature that activates Jordan transposition). These mutants were stable at 32 degrees, but generated revertants at 24 degrees . DNA blots revealed that one mutant had a transposon unrelated to Jordan inserted in invA ("inversionless A"). This new transposon, which we named Idaten, has terminal inverted repeats (TIRs) beginning with CCCTA, and upon insertion it creates a 3-bp target-site duplication. It appears to belong to the CACTA superfamily of class II DNA transposons, which includes En/Spm. No significant open reading frames were in the Idaten sequence, but we retrieved another element with Idaten-type TIRs encoding a protein similar to the En/Spm transposase as a candidate for an Idaten-specific transposase. We found that in five of the new inversionless strains we could not find any Jordan insertions causing the phenotype to possess insertions of an Idaten family member in a single locus (invC). This clearly indicates that Idaten is a potentially powerful alternative to Jordan for tagging developmentally important genes in Volvox.     

even skipped is required to produce a trans-acting signal for larval neuroblast proliferation that can be mimicked by ecdysone

Development of a multicellular organism requires precise coordination of cell division and cell type determination. The selector homeoprotein Even skipped (Eve) plays a very specific role in determining cell identity in the Drosophila embryo, both during segmentation and in neuronal development. However, studies of gene expression in eve mutant embryos suggest that eve regulates the embryonic expression of the vast majority of genes. We present here genetic interaction and phenotypic analysis showing that eve functions in the trol pathway to regulate the onset of neuroblast division in the larval CNS. Surprisingly, Eve is not detected in the regulated neuroblasts, and culture experiments reveal that Eve is required in the body, not the CNS. Furthermore, the effect of an eve mutation can be rescued both in vivo and in culture by the hormone ecdysone. These results suggest that eve is required to produce a trans-acting factor that stimulates cell division in the larval brain.     

Small angle X-ray studies reveal that Aspergillus niger glucoamylase has a defined extended conformation and can form dimers in solution

The industrially important glucoamylase 1 is an exo-acting glycosidase with substrate preference for alpha-1,4 and alpha-1,6 linkages at non-reducing ends of starch. It consists of a starch binding and a catalytic domain interspersed by a highly glycosylated polypeptide linker. The linker function is poorly understood and structurally undescribed, and data regarding domain organization and intramolecular functional cooperativity are conflicting or non-comprehensive. Here, we report a combined small angle x-ray scattering and calorimetry study of Aspergillus niger glucoamylase 1, glucoamylase 2, which lacks a starch binding domain, and an engineered low-glycosylated variant of glucoamylase 1 with a short linker. Low resolution solution structures show that the linker adopts a compact structure rendering a well defined extended overall conformation to glucoamylase. We demonstrate that binding of a short heterobidentate inhibitor simultaneously directed toward the catalytic and starch binding domains causes dimerization of glucoamylase and not, as suggested previously, an intramolecular conformational rearrangement mediated by linker flexibility. Our results suggest that glucoamylase functions via transient dimer formation during hydrolysis of insoluble substrates and address the question of the cooperative effect of starch binding and hydrolysis.     

A method for collecting soil percolate and soil solution in the field

Summary A soil-water extractor is described which uses an absorbent sponge material for sampling soil percolate and solution. Good agreement existed between soil extracts (1:5 soil:water) and extracts obtained from the extractor sponge after equilibration at low water tensions (pF 0–2.5) in the range, 0–100 g/g soil (0–1400 g/ml solution) for solute anions (Cl^-, NO₂ ^- and NO₃ ^–, R² > 0.98), and for ammonium ions (NH₄ ⁺, R²=0.93).Percolate was recovered in a field soil in volumes sufficient to permit analysis of constituents. Concentrations of solute Cl^- ions in these percolates were similar to those in the added water and in percolate from a zero-tension lysimeter. Poor relationships were obtained in the field between soil solution extracts from the sponge and 1:10 soil water extracts. For the present, the soil extractor may be used for sampling and monitoring movement of percolate and solute fronts, in the wetter range of soil water content.     

Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance

The SOS3 (for SALT OVERLY SENSITIVE3) calcium binding protein and SOS2 protein kinase are required for sodium and potassium ion homeostasis and salt tolerance in Arabidopsis. We have shown previously that SOS3 interacts with and activates the SOS2 protein kinase. We report here the identification of a SOS3 binding motif in SOS2 that also serves as the kinase autoinhibitory domain. Yeast two-hybrid assays as well as in vitro binding assays revealed a 21-amino acid motif in the regulatory domain of SOS2 that is necessary and sufficient for interaction with SOS3. Database searches revealed a large family of SOS2-like protein kinases containing such a SOS3 binding motif. Using a yeast two-hybrid system, we show that these SOS2-like kinases interact with members of the SOS3 family of calcium binding proteins. Two-hybrid assays also revealed interaction between the N-terminal kinase domain and the C-terminal regulatory domain within SOS2, suggesting that the regulatory domain may inhibit kinase activity by blocking substrate access to the catalytic site. Removal of the regulatory domain of SOS2, including the SOS3 binding motif, resulted in constitutive activation of the protein kinase, indicating that the SOS3 binding motif can serve as a kinase autoinhibitory domain. Constitutively active SOS2 that is SOS3 independent also was produced by changing Thr(168) to Asp in the activation loop of the SOS2 kinase domain. Combining the Thr(168)-to-Asp mutation with the autoinhibitory domain deletion created a superactive SOS2 kinase. These results provide insights into regulation of the kinase activities of SOS2 and the SOS2 family of protein kinases.