Papers of the month

2012

• November 2012
  • Watson and Fedor identify the first ATP-responsive riboswitch. This riboswitch controls the expression of the ydaO gene and the ktrA-ktrB operon. Gene expression is decreased upon binding of ATP to the riboswitch. In consequence, the target genes are induced if the energy charge of the cell is low.
  • Relevant SubtiWiki pages: ydaO, ydaO riboswitch, riboswitch, ktrA-ktrB

• October 2012
  • Plata et al. from the labs of Dennis Vitkup and Uwe Sauer use a probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlations to functionally annotate so far unknown enzymes.
  • Relevant SubtiWiki pages: ykgB, spsI, spsJ, Uwe Sauer, Dennis Vitkup, metabolism

• September 2012
  • Chiba and Ito studied how the translation of YidC2, a membrane protein biogenesis factor, is controlled by SpoIIIJ availability via ribosome stalling of the mifM mRNA.
  • Relevant SubtiWiki pages: Koreaki Ito, translation, YidC2, SpoIIIJ, mifM

• August 2012
  • Houry et al. from the lab of Romain Briandet showed how motile Bacillus thuringiensis bacteria can penetrate a Staphylococcus aureus biofilm and eventually kill the biofilm bacteria with their antibacterial compounds.
  • Relevant SubtiWiki pages: Romain Briandet, Stephane Aymerich, biofilm formation, biosynthesis of antibacterial compounds

• July 2012
  • Dago et al. from the lab of Hendrik Szurmant studied the interactions between histidine kinase domains of two-component systems that result in autophosphorylation.
  • Relevant SubtiWiki pages: Hendrik Szurmant, Jim Hoch, two-component systems, KinA, KinD, protein-protein interactions

• June 2012
  • Kolodkin-Gal et al. from the labs of Roberto Kolter and Richard Losick demonstrate that D-amino acids produced by RacX and YlmE and norspermidine produced by GabT and YaaO act together in preventing biofilm formation and triggering biofilm disassembly.
  • Relevant SubtiWiki pages: Roberto Kolter, Richard Losick, biofilm formation, RacX, YlmE, GabT, YaaO

• May 2012
  • Elsholz et al. from the lab of Ulf Gerth demonstrate that protein phosphorylation on arginine residues is of great importance for B. subtilis. In addition to the previously identified target CtsR, 86 proteins are shown to be phosphorylated on arginine. The protein arginine kinase and phosphatase, McsB and YwlE, respectively, may thus have an important regulatory role in B. subtilis.
  • Relevant SubtiWiki pages: Ulf Gerth, Kürsad Turgay, Ulrike Mäder, Dörte Becher, Michael Hecker, phosphoproteins, protein kinases and phosphatases, McsB, YwlE

• April 2012
  • Meisner et al. and Levdikov et al. from the labs of Charles Moran and Tony Wilkinson, respectively, have reported the structure of the complex between SpoIIQ and SpoIIIAH. These two proteins interact through two membranes to connect the forespore and the mother cell during sporulation. The structure of the complex suggests that it is the extracellular component of a gap junction-like intercellular channel for the traffic of proteins between the two compartments.
  • Relevant SubtiWiki pages: Charles Moran, Tony Wilkinson, sporulation, SpoIIQ, SpoIIIAH

Levdikov VM, Blagova EV, McFeat A, Fogg MJ, Wilson KS, Wilkinson AJ  
Structure of components of an intercellular channel complex in sporulating Bacillus subtilis. 
Proc Natl Acad Sci U S A. 2012 Mar 19. [Epub ahead of print] 
PubMed:22431604

Jeffrey Meisner, Tatsuya Maehigashi, Ingemar André, Christine M Dunham, Charles P Moran
Structure of the basal components of a bacterial transporter.
Proc Natl Acad Sci U S A: 2012, 109(14);5446-51
[PubMed:22431613] [WorldCat.org] [DOI] (I p)

• 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

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• 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

Jamie Richards, Quansheng Liu, Olivier Pellegrini, Helena Celesnik, Shiyi Yao, David H Bechhofer, Ciarán Condon, Joel G Belasco
An RNA pyrophosphohydrolase triggers 5'-exonucleolytic degradation of mRNA in Bacillus subtilis.
Mol Cell: 2011, 43(6);940-9
[PubMed:21925382] [WorldCat.org] [DOI] (I p)

• 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

• 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

• 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:

• 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

Yaara Oppenheimer-Shaanan, Ezequiel Wexselblatt, Jehoshua Katzhendler, Eylon Yavin, Sigal Ben-Yehuda
c-di-AMP reports DNA integrity during sporulation in Bacillus subtilis.
EMBO Rep: 2011, 12(6);594-601
[PubMed:21566650] [WorldCat.org] [DOI] (I p)

• 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