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Escherichia coli Insertion Sequence IS150: Transposition via Circular and Linear Intermediates. Markus Haas, 2002.IS150, a member of the widespread IS3 family, contains two consecutive out-of-phase open reading frames, orfA and orfB, that partially overlap . These open reading frames encode three proteins, InsA, InsB, and the InsAB protein, which is jointly encoded by both open reading frames by means of programmed translational frameshifting . We demonstrate that the InsAB protein represents the IS150 element's transposase . In vivo, the wild-type IS150 element generates circular excision products and linear IS150 molecules . Circular and linear species have previously been detected with mutant derivatives of other members of the IS3 family . Our finding supports the assumption that these products represent true transposition intermediates of members of this family . Analysis of the molecular nature of these two species suggested that the circular forms are precursors of the linear molecules . Elimination of InsA synthesis within the otherwise intact element led to accumulation of large amounts of the linear species, indicating that the primary role of InsA may be to prevent abortive production of the linear species and to couple generation of these species to productive insertion events . Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. Christine Eymann, 2002.The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches . Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences . According to their altered synthesis patterns in response to DL-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes) . Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes . However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis . The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp . The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.) . Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG) . On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins . A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp .
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