Identification and in vitro Analysis of the GatD/MurT Enzyme-Complex Catalyzing Lipid II Amidation in Staphylococcus aureus

The peptidoglycan of Staphylococcus aureus is characterized by a high degree of crosslinking and almost completely lacks free carboxyl groups, due to amidation of the D-glutamic acid in the stem peptide. Amidation of peptidoglycan has been proposed to play a decisive role in polymerization of cell wall building blocks, correlating with the crosslinking of neighboring peptidoglycan stem peptides. Mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin. We identified the enzymes catalyzing the formation of D-glutamine in position 2 of the stem peptide. We provide biochemical evidence that the reaction is catalyzed by a glutamine amidotransferase-like protein and a Mur ligase homologue, encoded by SA1707 and SA1708, respectively. Both proteins, for which we propose the designation GatD and MurT, are required for amidation and appear to form a physically stable bi-enzyme complex. To investigate the reaction in vitro we purified recombinant GatD and MurT His-tag fusion proteins and their potential substrates, i.e. UDP-MurNAc-pentapeptide, as well as the membrane-bound cell wall precursors lipid I, lipid II and lipid II-Gly5. In vitro amidation occurred with all bactoprenol-bound intermediates, suggesting that in vivo lipid II and/or lipid II-Gly5 may be substrates for GatD/MurT. Inactivation of the GatD active site abolished lipid II amidation. Both, murT and gatD are organized in an operon and are essential genes of S. aureus. BLAST analysis revealed the presence of homologous transcriptional units in a number of gram-positive pathogens, e.g. Mycobacterium tuberculosis, Streptococcus pneumonia and Clostridium perfringens, all known to have a D-iso-glutamine containing PG. A less negatively charged PG reduces susceptibility towards defensins and may play a general role in innate immune signaling

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Cell cycle related signalling in neuro2A cells proceeds via the receptor for advanced glycation end products

Re-expression of cell cycle related genes such as cyclin-dependent kinases (cdk), cyclins, or cdk inhibitors in differentiated neurons in Alzheimer’s disease (AD) is rooted in aberrant mitogenic signaling. Since microglia and astroglia proliferate in the vicinity of amyloid plaques, it is likely that plaque components or factors secreted from plaque-activated glia induce mitogenic signaling in neurons. Mitogenic compounds might be S100B, overexpressed by activated astrocytes, or advanced glycation end products (AGEs), a component of plaques. Both S100B and AGEs may interact with the multiligand receptor for AGEs (RAGE) and trigger for the activation of the p42/44 mitogen-activated protein kinase (p42/44 MAPK), whether they also count for cell cycle related signaling in neurons remains unresolved. By immunohistochemical staining, we confirmed that cyclin D1 positive neurons are surrounded by AGE deposits, demonstrating the potential relevance in vivo. For exploring the mitogenic signal cascade, we used Neuro2a cells overexpressing human full-length RAGE (FL-RAGE) or the cytosolic deletion mutant (Δ-RAGE). In both cell lines, S100B and AGEs induced the production of reactive oxygen species but not in a RAGE-dependent manner. By contrast, in FL-RAGE cells but not in Δ-RAGE cells S100B and AGEs activate p42/44 MAPK, augment cyclin D1/cdk4 protein and RNA levels and the transition into the S-phase. Moreover, in FL-RAGE cells, decreased protein levels of the cdk inhibitor p16 were observed, and the p42/44 MAPK inhibitor UO126 prevented AGE and S100B stimulated cyclin D1 expression and hindered cells to enter the S-phase. Our results demonstrate that S100B and AGE may serve as mitogenic sources for the stimulation of neurons to progress through the cell cycle whereby signaling proceeds via RAGE → p42/44 MAPK → cyclin D1/cdk4

The Academic Dispositif: Towards a Context-Centred Discourse Analysis

This contribution outlines the dispositif approach, which combines a linguistic discourse analysis of texts with a sociological study of the social context (i.e. the dispositif understood as an institutional arrangement of practices and structures). The authors use the discourse of academic researchers to exemplify this approach. By articulating correspondence analysis of self-representations on researchers’ homepages with institutional data of sociology professors in the United Kingdom, they outline a research design that consists of three components: a linguistic analysis of texts, a sociological analysis of institutional contexts, and a theoretical account of how the two are related in the academic dispositif. The dispositif perspective on discourse aims to respond to a demand for systematic discourse research on the social and institutional contexts of discursive practices