Complete genome sequence of Streptomyces lividans TK24.

Streptomyces lividans TK24 is the standard host for the heterologous expression of a number of different proteins and antibiotic-synthesizing enzymes. As such, it is often used as an experimental microbial cell factory for the production of secreted heterologous proteins including human cytokines and industrial enzymes, and of several antibiotics. It accepts methylated DNA and is an ideal Streptomyces cloning system.

Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb).

Cell compartmentalization serves both the isolation and the specialization of cell functions. After synthesis in the cytoplasm, over a third of all proteins are targeted to other subcellular compartments. Knowing how proteins are distributed within the cell and how they interact is a prerequisite for understanding it as a whole.

The gut microbiota in mouse models of inflammatory bowel disease.

The intestine and the intestinal immune system have evolved through a symbiotic homeostasis under which a highly diverse microbial flora is maintained in the gastrointestinal tract while pathogenic bacteria are recognized and eliminated. Disruption of the balance between the immune system and the gut microbiota results in the development of multiple pathologies in humans. Inflammatory bowel diseases (IBD) have been associated with alterations in the composition of intestinal flora but whether these changes are causal or result of inflammation is still under dispute.

Quaternary dynamics of the SecA motor drive translocase catalysis.

Most secretory preproteins exit bacterial cells through the protein translocase, comprising the SecYEG channel and the dimeric peripheral ATPase motor SecA. Energetic coupling to work remains elusive. We now demonstrate that translocation is driven by unusually dynamic quaternary changes in SecA.

1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans.

Searching for Darwinian selection in natural populations has been the focus of a multitude of studies over the last decades. Here we present the 1000 Genomes Selection Browser 1.0 (http://hsb.

The Escherichia coli peripheral inner membrane proteome.

Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes.

A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2.

Computational methods for miRNA target prediction vary in the algorithm used; and while one can state opinions about the strengths or weaknesses of each particular algorithm, the fact of the matter is that they fall substantially short of capturing the full detail of physical, temporal and spatial requirements of miRNA::target-mRNA interactions. Here, we introduce a novel miRNA target prediction tool called Targetprofiler that utilizes a probabilistic learning algorithm in the form of a hidden Markov model trained on experimentally verified miRNA targets. Using a large scale protein downregulation data set we validate our method and compare its performance to existing tools.

Quality of nutritional information on the Internet in health and disease.

Background: Quality assessment of nutritional information on the internet may prove vital prior to providing public guidance on searching relative information.

Methods: The most popular web sites on four different topics ("Mediterranean diet", "sports nutrition", "nutrition, dysphagia and children" and "herbs and common cold") were assessed with the use of two validated questionnaires (EQIP and DISCERN).

Results: Medical categories produced significantly lower total quality scores when compared to "Mediterranean diet" and "sports nutrition" categories.

Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach.

The majority of existing computational tools rely on sequence homology and/or structural similarity to identify novel microRNA (miRNA) genes. Recently supervised algorithms are utilized to address this problem, taking into account sequence, structure and comparative genomics information. In most of these studies miRNA gene predictions are rarely supported by experimental evidence and prediction accuracy remains uncertain.

Assembly of the translocase motor onto the preprotein-conducting channel.

Bacterial protein secretion is catalysed by the SecYEG protein-conducting channel complexed with the SecA ATPase motor. To gain insight into the SecA-SecYEG interaction we used peptide arrays, thermodynamic quantification, mutagenesis and functional assays. Our data reveal that: (i) SecA binds with low affinity on several, peripheral, exposed SecYEG sites.

Crystallization and preliminary X-ray diffraction studies of an alcohol dehydrogenase from the Antarctic psychrophile Moraxella sp. TAE123.

An NAD(+)-dependent psychrophilic alcohol dehydrogenase (ADH) from the Antarctic psychrophile Moraxella sp. TAE123 has been purified to homogeneity. The enzyme consists of four identical subunits, each containing two Zn ions.

Proteomic Analysis of Liver from Transgenic Mice Overexpressing Small Heterodimer Partner.

The small heterodimer partner (SHP) is a key regulator of genes involved in cholesterol-bile acid homeostasis and functions as a specific transcription repressor. Differential protein expression in the liver of transgenic mice expressing the human SHP gene was compared with wild-type animals. Liver protein extracts were analyzed by two-dimensional electrophoresis and the proteins were identified by MALDI-TOF-MS.

Functional large-scale production of a novel Jonesia sp. xyloglucanase by heterologous secretion from Streptomyces lividans.

The gene encoding a novel xyloglucanase (Xeg) belonging to family 74 glycoside hydrolases was isolated from a Jonesia sp. strain through functional screening in Escherichia coli. The encoded xyloglucanase is a protein of 972 aminoacyl residues with a 23 residue aminoterminal signal peptide.

The role of the platelet glycoprotein IIb/IIIa in thrombosis and haemostasis.

Haemostasis is a finely balanced and complex process ideally initiated only in response to disruption of the vascular endothelium as a means of preventing loss of blood from an injured vessel. Deviations from the ideal can lead to serious disease. Firstly, thrombosis, which arises as a consequence of inappropriate platelet-platelet interactions at a region of vessel damaged by atherosclerosis, can lead to occlusion of the affected vessel as in myocardial infarction or stroke.

Nhp6 facilitates Aft1 binding and Ssn6 recruitment, both essential for FRE2 transcriptional activation.

We found Nhp6a/b yeast HMG-box chromatin-associated architectural factors and Ssn6 (Cyc8) corepressor to be crucial transcriptional coactivators of FRE2 gene. FRE2 encoding a plasma membrane ferric reductase is induced by the iron-responsive, DNA-binding, transcriptional activator Aft1. We have shown that Nhp6 interacts directly with the Aft1 N-half, including the DNA-binding region, to facilitate Aft1 binding at FRE2 UAS.

Protein secretion biotechnology using Streptomyces lividans: large-scale production of functional trimeric tumor necrosis factor alpha.

We evaluated the feasibility of large-scale production of biopharmaceuticals expressed as heterologous polypeptides from the Gram-positive bacterium Streptomyces lividans. As a model protein we used murine tumor necrosis factor alpha (mTNFalpha). mTNFalpha fused C-terminally to the secretory signal peptide of the subtilisin-inhibitor protein from Streptomyces venezuelae.

Specification of left-right asymmetry in the embryonic gut of Drosophila.

Most animals exhibit stable left-right asymmetries in their body. Although significant progress has been made in elucidating the mechanisms that set up these asymmetries in vertebrates, nothing is known about them in Drosophila. This is usually attributed to the fact that no reversals of stable left-right asymmetries have been observed in Drosophila, although relevant surveys have been carried out.

Bacterial protein translocase: a unique molecular machine with an army of substrates.

Secretion of most polypeptides across the bacterial plasma membrane is catalyzed by the Sec protein translocase. This complex molecular machine comprises a flexible transmembrane conduit coupled to a motor-like component and displays four activities: (a) it is a specific receptor at its cytoplasmic side for all secretory polypeptides, (b) it converts metabolic energy from ATP and proton gradients into mechanical motion, (c) it prevents substrates from folding in statu translocanti and (d) it binds and releases short segments of the polymeric substrate sequentially. Combination of these activities allows translocase to move processively along the length of the substrate.

Following the leader: bacterial protein export through the Sec pathway.

Significant strides have been made during the past 20 years in our understanding of protein secretion across the bacterial inner membrane. Specialized chaperones select secretory polypeptide chains and usher them to a membrane-embedded preprotein translocase. This unique molecular machine envelops the polymeric substrate and migrates along its length in defined, energy-dependent steps.

Bacterial preprotein translocase: mechanism and conformational dynamics of a processive enzyme.

Preprotein translocase, the membrane transporter for secretory proteins, is a processive enzyme. It comprises the membrane proteins SecYEG(DFYajC) and the peripheral ATPase SecA, which acts as a motor subunit. Translocase subunits form dynamic complexes in the lipid bilayer and build an aqueous conduit through which preprotein substrates are transported at the expense of energy.