Nothing Lasts Forever: Environmental Discourses on the Collapse of Past Societies

The study of the collapse of past societies raises many questions for the theory and practice of archaeology. Interest in collapse extends as well into the natural sciences and environmental and sustainability policy. Despite a range of approaches to collapse, the predominant paradigm is environmental collapse, which I argue obscures recognition of the dynamic role of social processes that lie at the heart of human communities. These environmental discourses, together with confusion over terminology and the concepts of collapse, have created widespread aporia about collapse and resulted in the creation of mixed messages about complex historical and social processes

A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing

Messenger- RNA- directed protein synthesis is accomplished by the ribosome(1-3). In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine ( tRNA(fMet))(4-6). The amino- terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side- reactions and to enhance the efficiency of translation initiation(7,8). The first enzymatic factor that processes nascent chains is peptide deformylase ( PDF)(5,9-11); it removes this formyl group as polypeptides emerge from the ribosomal tunnel(12,13) and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase(14). Bacterial PDFs are metalloproteases sharing a conserved N- terminal catalytic domain. All Gram- negative bacteria, including Escherichia coli, possess class- 1 PDFs characterized by a carboxy- terminal alpha- helical extension(15). Studies focusing on PDF as a target for antibacterial drugs(14,16) have not revealed the mechanism of its co- translational mode of action despite indications in early work that it co- purifies with ribosomes(17). Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C- terminal extension. Crystallographic analysis of the complex between the ribosome- interacting helix of PDF and the ribosome at 3.7 angstrom resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co- translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome- associated chaperone trigger factor