Papers of the month

2012

• March 2012
  • Buescher et al. and Nicolas et al. from the BaSysBio consortium diected by Philippe Noirot studied the dynamic metabolic and transcriptional responses of B. subtilis to changes of the growth conditions. One of the major issues is the adaptation of the cells upon a nutrient switch from glucose to malate and vice versa. Importantly, the study by Nicholas et al. provides an analysis of gene expression at 104 different conditions as revealed by tiling arrays.
  • Relevant SubtiWiki pages: Philippe Noirot, Michael Hecker, Uwe Völker, Philippe Bessières, Uwe Sauer, Stephane Aymerich, Tony Wilkinson, metabolism, transcription, CcpA, Sigma factors, sRNAs, Rho

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

Joerg Martin Buescher, Wolfram Liebermeister, Matthieu Jules, Markus Uhr, Jan Muntel, Eric Botella, Bernd Hessling, Roelco Jacobus Kleijn, Ludovic Le Chat, François Lecointe, Ulrike Mäder, Pierre Nicolas, Sjouke Piersma, Frank Rügheimer, Dörte Becher, Philippe Bessieres, Elena Bidnenko, Emma L Denham, Etienne Dervyn, Kevin M Devine, Geoff Doherty, Samuel Drulhe, Liza Felicori, Mark J Fogg, Anne Goelzer, Annette Hansen, Colin R Harwood, Michael Hecker, Sebastian Hubner, Claus Hultschig, Hanne Jarmer, Edda Klipp, Aurélie Leduc, Peter Lewis, Frank Molina, Philippe Noirot, Sabine Peres, Nathalie Pigeonneau, Susanne Pohl, Simon Rasmussen, Bernd Rinn, Marc Schaffer, Julian Schnidder, Benno Schwikowski, Jan Maarten Van Dijl, Patrick Veiga, Sean Walsh, Anthony J Wilkinson, Jörg Stelling, Stéphane Aymerich, Uwe Sauer
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
Science: 2012, 335(6072);1099-103
[PubMed:22383848] [WorldCat.org] [DOI] (I p)

• A comment on these papers:

Guilhem Chalancon, Kai Kruse, M Madan Babu
Cell biology. Reconfiguring regulation.
Science: 2012, 335(6072);1050-1
[PubMed:22383834] [WorldCat.org] [DOI] (I p)

• February 2012
  • Levine et al. from the lab of Michael Elowitz show how B. subtilis cells can defer sporulation for multiple cell cycles in response to sudden environmental stress. This deferral is controlled by a pulsed positive feedback loop in which phosphorelay kinase expression is activated by pulses of Spo0A phosphorylation.
  • Relevant SubtiWiki pages: Michael Elowitz, Jonathan Dworkin, phosphorelay, sporulation, Spo0A

Joe H Levine, Michelle E Fontes, Jonathan Dworkin, Michael B Elowitz
Pulsed feedback defers cellular differentiation.
PLoS Biol: 2012, 10(1);e1001252
[PubMed:22303282] [WorldCat.org] [DOI] (I p)

• A comment on this paper:

• January 2012
  • Segev et al. from the lab of Sigal Ben-Yehuda demonstrate that ribosomal RNAs are degraded in aging spores by RNase Y. Moreover, the authors show that individual mRNAs experience degradation or accumulation in spores. The study suggests that the kinetics of spore germination depends on the conditions that a spore had experienced before.
  • Relevant SubtiWiki pages: Sigal Ben-Yehuda, RNase Y, germination, RNases

Einat Segev, Yoav Smith, Sigal Ben-Yehuda
RNA dynamics in aging bacterial spores.
Cell: 2012, 148(1-2);139-49
[PubMed:22209493] [WorldCat.org] [DOI] (I p)

2011

• December 2011
  • Bange et al. from the lab of Irmgard Sinning show how the YlxH protein activates the SRP-GTPase FlhF. The study sheds light on the evolutionary transition from RNA- to protein-driven activation in SRP-GTPases.
  • Relevant SubtiWiki pages: Irmgard Sinning, FlhF, YlxH, signal recognition particle, motility and chemotaxis

Gert Bange, Nico Kümmerer, Przemyslaw Grudnik, Robert Lindner, Georg Petzold, Dieter Kressler, Ed Hurt, Klemens Wild, Irmgard Sinning
Structural basis for the molecular evolution of SRP-GTPase activation by protein.
Nat Struct Mol Biol: 2011, 18(12);1376-80
[PubMed:22056770] [WorldCat.org] [DOI] (I e)

• November 2011
  • Locke et al. show how the SigB-dependent general stress response is controlled by signals using stochastic pulse frequency modulation through a compact regulatory architecture.
  • Relevant SubtiWiki pages: Michael Elowitz, SigB, General stress response

Locke JC, Young JW, Fontes M, Hernández Jiménez MJ, Elowitz MB  
Stochastic pulse regulation in bacterial stress response. 
Science. 2011 334:366-369. 
PubMed:21979936

• October 2011
  • Richards et al. identify the nudix hydrolase RppH as the pyrophosphohydrolase that triggers 5'-exonucleolytic degradation of mRNA by RNase J1 in B. subtilis.
  • Relevant SubtiWiki pages: David Bechhofer, Ciaran Condon, RNA processing and degradation, nudix hydrolase, RppH, RNase J1

• September 2011
  • A series of papers deals with RNA processing and degradation in B. subtilis. Three papers establish that RNase Y is the functional equivalent of RNase E from E. coli. Moreover, the role of RNase J1 in endonucleolytic cleavage of the trp leader mRNA is demonstrated.
  • Relevant SubtiWiki pages: David Bechhofer, Rick Lewis, Ulrike Mäder, Harald Putzer, Jörg Stülke, RNases, RNA degradosome, RNase Y, RNase Y targets, RNase J1

Gintaras Deikus, David H Bechhofer
5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA.
J Biol Chem: 2011, 286(40);34932-40
[PubMed:21862575] [WorldCat.org] [DOI] (I p)

Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J  
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. 
Mol Microbiol. 2011 81(6): 1459-73. 
PubMed:21815947

Patrice Bruscella, Karen Shahbabian, Soumaya Laalami, Harald Putzer
RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis.
Mol Microbiol: 2011, 81(6);1526-41
[PubMed:21843271] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Joseph Newman, Fabian M Rothe, Alexandra S Solovyova, Cecilia Rodrigues, Christina Herzberg, Fabian M Commichau, Richard J Lewis, Jörg Stülke
RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli.
J Bacteriol: 2011, 193(19);5431-41
[PubMed:21803996] [WorldCat.org] [DOI] (I p)

• August 2011
  • Chi et al. demonstrate that S-bacillithiolation of the repressor OhrR and of four enzymes of the methionine biosynthesis pathway protects the B. subtilis cell against hypochlorite stress.
  • Relevant SubtiWiki pages: Haike Antelmann, Dörte Becher, Ulrike Mäder, resistance against oxidative and electrophile stress, Spx regulon, CtsR regulon, PerR regulon, OhrR, MetE, YxjG, PpaC, SerA, YphP

Bui Khanh Chi, Katrin Gronau, Ulrike Mäder, Bernd Hessling, Dörte Becher, Haike Antelmann
S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics.
Mol Cell Proteomics: 2011, 10(11);M111.009506
[PubMed:21749987] [WorldCat.org] [DOI] (I p)

• July 2011
  • Domínguez-Escobar et al. from Rut Carballido-Lopez' lab and Garner et al. report that movement of actin-like filaments is driven by the peptidoglycan elongation machinery. Both papers suggest that the MreB-like filaments serve to restrict the mobility of the peptidoglycan synthesizing machinery
    
  • Relevant SubtiWiki pages: Rut Carballido-Lopez, David Rudner, MreB, MreBH, Mbl, MreC, MreD, PbpA, RodA, RodZ, penicillin-binding proteins, cell shape, cell wall synthesis, cell wall biosynthetic complex

• A comment on these papers:

Andrew Jermy
Bacterial physiology: MreB takes a back seat.
Nat Rev Microbiol: 2011, 9(8);560-1
[PubMed:21725336] [WorldCat.org] [DOI] (I e)

• June 2011
  • Oppenheimer-Shaanan et al. from Sigal Ben-Yehuda's lab report that cyclic di-AMP acts as a secondary messenger that couples DNA integrity with progression of sporulation
    
  • Relevant SubtiWiki pages: Sigal Ben-Yehuda, DisA, GdpP, metabolism of signalling nucleotides, cell division

• May 2011
  • Miles et al. identified the enzyme for the key final step in the biosynthesis of queuosine, a hypermodified base found in the wobble positions of tRNA Asp, Asn, His, and Tyr from bacteria to man
    
  • Relevant SubtiWiki pages: QueG, translation

Zachary D Miles, Reid M McCarty, Gabriella Molnar, Vahe Bandarian
Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification.
Proc Natl Acad Sci U S A: 2011, 108(18);7368-72
[PubMed:21502530] [WorldCat.org] [DOI] (I p)