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  • 1
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    Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-03
    Description: Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nicolas, Pierre -- Mader, Ulrike -- Dervyn, Etienne -- Rochat, Tatiana -- Leduc, Aurelie -- Pigeonneau, Nathalie -- Bidnenko, Elena -- Marchadier, Elodie -- Hoebeke, Mark -- Aymerich, Stephane -- Becher, Dorte -- Bisicchia, Paola -- Botella, Eric -- Delumeau, Olivier -- Doherty, Geoff -- Denham, Emma L -- Fogg, Mark J -- Fromion, Vincent -- Goelzer, Anne -- Hansen, Annette -- Hartig, Elisabeth -- Harwood, Colin R -- Homuth, Georg -- Jarmer, Hanne -- Jules, Matthieu -- Klipp, Edda -- Le Chat, Ludovic -- Lecointe, Francois -- Lewis, Peter -- Liebermeister, Wolfram -- March, Anika -- Mars, Ruben A T -- Nannapaneni, Priyanka -- Noone, David -- Pohl, Susanne -- Rinn, Bernd -- Rugheimer, Frank -- Sappa, Praveen K -- Samson, Franck -- Schaffer, Marc -- Schwikowski, Benno -- Steil, Leif -- Stulke, Jorg -- Wiegert, Thomas -- Devine, Kevin M -- Wilkinson, Anthony J -- van Dijl, Jan Maarten -- Hecker, Michael -- Volker, Uwe -- Bessieres, Philippe -- Noirot, Philippe -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA, UR1077, Mathematique Informatique et Genome, Jouy-en-Josas, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383849" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Algorithms ; Bacillus subtilis/*genetics/*physiology ; Binding Sites ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Oligonucleotide Array Sequence Analysis ; *Promoter Regions, Genetic ; RNA, Antisense/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Regulon ; Sigma Factor/metabolism ; Terminator Regions, Genetic ; *Transcription, Genetic ; *Transcriptome
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-04-16
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Cell division in E. coli in diverse cell shapes [Biophysics and Computational Biology] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-05-02
    Description: Cell division in typical rod-shaped bacteria such as Escherichia coli shows a remarkable plasticity in being able to adapt to a variety of irregular cell shapes. Here, we investigate the roles of the Min system and the nucleoid-occlusion factor SlmA in supporting this adaptation. We study “squeezed” E. coli in narrow nanofabricated channels where these bacteria exhibit highly irregular shapes and large volumes. Despite the severely anomalous morphologies we find that most of these bacteria maintain their ability to divide into two equally sized daughters with an accuracy comparable to that of normal rod-shaped cells (about 4%). Deletion of either slmA or minC shows that the molecular systems associated with these genes are largely dispensable for accurate cell division in these irregular cell shapes. Using fluorescence time-lapse microscopy, we determine that the functionality of the Min system is affected by the cell shape, whereas the localization of a nucleoid relative to the cell division proteins (the divisome) remains unperturbed in a broad spectrum of morphologies, consistent with nucleoid occlusion. The observed positioning of the nucleoid relative to the divisome appears not to be affected by the nucleoid-occlusion factor SlmA. The current study underscores the importance of nucleoid occlusion in positioning the divisome and shows that it is robust against shape irregularities.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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