Energetic problems faced by micro-organisms growing or surviving on parsimonious energy sources and at acidic pH: I. Acidithiobacillus ferrooxidans as a paradigm

AbstractThe mitochondrial paradigm for a chemiosmotic energy transduction mechanism requires frequently misunderstood modifications for application to microbes growing and surviving at acidic pH values and/or with relatively weak reductants as energy sources. Here the bioenergetics of the iron oxidiser Acidithiobacillus ferrooxidans are reviewed and analysed so as to develop the general bioenergetic principles for understanding organisms that grow under these conditions. Extension of the principles outlined herein to organisms that survive (as opposed to grow) under these conditions is to be presented in a subsequent article

Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

Archaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA.Publisher PDFPeer reviewe