Papers of the month

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Contents

2016

Jason M Peters, Alexandre Colavin, Handuo Shi, Tomasz L Czarny, Matthew H Larson, Spencer Wong, John S Hawkins, Candy H S Lu, Byoung-Mo Koo, Elizabeth Marta, Anthony L Shiver, Evan H Whitehead, Jonathan S Weissman, Eric D Brown, Lei S Qi, Kerwyn Casey Huang, Carol A Gross
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.
Cell: 2016, 165(6);1493-506
[PubMed:27238023] [WorldCat.org] [DOI] (I p)


  • February 2016
    • Recently, cell-cell communication by so-called nanotubes has been reported. Now, two papers from the lab of Sigal Ben-Yehuda implicate the phosphodiesterase YmdB in nanotube formation, intercellular molecular trade, and in the development of B. subtilis colonies.
    • Relevant SubtiWiki pages: Sigal Ben-Yehuda, YmdB

Gyanendra P Dubey, Ganesh Babu Malli Mohan, Anna Dubrovsky, Triana Amen, Shai Tsipshtein, Alex Rouvinski, Alex Rosenberg, Daniel Kaganovich, Eilon Sherman, Ohad Medalia, Sigal Ben-Yehuda
Architecture and Characteristics of Bacterial Nanotubes.
Dev. Cell: 2016, 36(4);453-61
[PubMed:26906740] [WorldCat.org] [DOI] (I p)

Gideon Mamou, Ganesh Babu Malli Mohan, Alex Rouvinski, Alex Rosenberg, Sigal Ben-Yehuda
Early Developmental Program Shapes Colony Morphology in Bacteria.
Cell Rep: 2016, 14(8);1850-7
[PubMed:26904951] [WorldCat.org] [DOI] (I p)


2015

  • November 2015
    • Bacteria contain many classes of ion channels, but their functions have largely remained elusive. Now, Prindle et al. from the lab of Gürol M. Süel have shown that the YugO potassium ion channel is used to propagate electrical signals throughout Bacillus subtilis biofilms in a long-range process that coordinates the metabolic responses of the community.
    • Relevant SubtiWiki pages: Gürol M. Süel, YugO, biofilm formation

Arthur Prindle, Jintao Liu, Munehiro Asally, San Ly, Jordi Garcia-Ojalvo, Gürol M Süel
Ion channels enable electrical communication in bacterial communities.
Nature: 2015, 527(7576);59-63
[PubMed:26503040] [WorldCat.org] [DOI] (I p)

  • See comments on this issue:

Cláudio Nunes-Alves
Biofilms: Electrifying long-range signalling.
Nat. Rev. Microbiol.: 2015, 13(12);737
[PubMed:26548916] [WorldCat.org] [DOI] (I p)

Sarah D Beagle, Steve W Lockless
Microbiology: Electrical signalling goes bacterial.
Nature: 2015, 527(7576);44-5
[PubMed:26503058] [WorldCat.org] [DOI] (I p)


Jintao Liu, Arthur Prindle, Jacqueline Humphries, Marçal Gabalda-Sagarra, Munehiro Asally, Dong-yeon D Lee, San Ly, Jordi Garcia-Ojalvo, Gürol M Süel
Metabolic co-dependence gives rise to collective oscillations within biofilms.
Nature: 2015, 523(7562);550-4
[PubMed:26200335] [WorldCat.org] [DOI] (I p)


Elizabeth A Libby, Lindsie A Goss, Jonathan Dworkin
The Eukaryotic-Like Ser/Thr Kinase PrkC Regulates the Essential WalRK Two-Component System in Bacillus subtilis.
PLoS Genet.: 2015, 11(6);e1005275
[PubMed:26102633] [WorldCat.org] [DOI] (I e)

Sandro F F Pereira, Ruben L Gonzalez, Jonathan Dworkin
Protein synthesis during cellular quiescence is inhibited by phosphorylation of a translational elongation factor.
Proc. Natl. Acad. Sci. U.S.A.: 2015, 112(25);E3274-81
[PubMed:26056311] [WorldCat.org] [DOI] (I p)


  • June 2015
    • The precise quantification of the dynamic changes in metabolite concentrations is a major challenge in metabolomics. Two new studies make use of the combination of metablite-sensitive riboswitches with an in vitro selected Spinach aptamer, which binds a pro-fluorescent, cell-permeable small molecule mimic of the GFP chromophore. Fluorescence can then be determined as a measure of the concentration of the metabolite that binds the riboswitch. The present studies use this approach for the essential second messenger c-di-AMP as well as for S-adenosyl-methionine and guanine.
    • Relevant SubtiWiki pages: riboswitch, metabolism, methods

Colleen A Kellenberger, Chen Chen, Aaron T Whiteley, Daniel A Portnoy, Ming C Hammond
RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messenger Cyclic di-AMP.
J. Am. Chem. Soc.: 2015, 137(20);6432-5
[PubMed:25965978] [WorldCat.org] [DOI] (I p)

Mingxu You, Jacob L Litke, Samie R Jaffrey
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch.
Proc. Natl. Acad. Sci. U.S.A.: 2015, 112(21);E2756-65
[PubMed:25964329] [WorldCat.org] [DOI] (I p)


  • Mai 2015
    • In B. subtilis, ribosomal stalling is used to regulate the expression of the membrane protein biogenesis factor YidC2. This is achieved by stalling during translation of the MifM leader peptide. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Sohmen et al. have determined the structure of the MifM-stalled 70S ribosome and have unraveled a network of interactions between MifM and the ribosomal tunnel, which induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event.
    • Relevant SubtiWiki pages: translation, ribosome, yidC2, MifM, L22

Daniel Sohmen, Shinobu Chiba, Naomi Shimokawa-Chiba, C Axel Innis, Otto Berninghausen, Roland Beckmann, Koreaki Ito, Daniel N Wilson
Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Nat Commun: 2015, 6;6941
[PubMed:25903689] [WorldCat.org] [DOI] (I e)


Ian R Price, Ahmed Gaballa, Fang Ding, John D Helmann, Ailong Ke
Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.
Mol. Cell: 2015, 57(6);1110-23
[PubMed:25794619] [WorldCat.org] [DOI] (I p)

Michael Dambach, Melissa Sandoval, Taylor B Updegrove, Vivek Anantharaman, L Aravind, Lauren S Waters, Gisela Storz
The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element.
Mol. Cell: 2015, 57(6);1099-109
[PubMed:25794618] [WorldCat.org] [DOI] (I p)


Maria A Schumacher, Naga Babu Chinnam, Bonnie Cuthbert, Nam K Tonthat, Travis Whitfill
Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Genes Dev.: 2015, 29(4);451-64
[PubMed:25691471] [WorldCat.org] [DOI] (I p)


  • February 2015
    • To proliferate efficiently, cells must co-ordinate cell division with chromosome segregation. In B. subtilis, the nucleoid occlusion protein Noc binds to specific DNA sequences scattered around the chromosome and helps to protect genomic integrity by coupling the initiation of division to the progression of chromosome replication and segregation. However, how it inhibits division has remained unclear. Now, Adams et al. from the lab of Jeff Errington demonstrate that Noc associates with the cell membrane via an N-terminal amphipathic helix. Importantly, the membrane-binding affinity of this helix is weak and requires the assembly of nucleoprotein complexes, thus establishing a mechanism for DNA-dependent activation of Noc. Furthermore, division inhibition by Noc requires recruitment of Noc binding site DNA to the cell membrane and is dependent on its ability to bind DNA and membrane simultaneously. The results suggest a simple model in which the formation of large membrane-associated nucleoprotein complexes physically occludes assembly of the division machinery.
    • Relevant SubtiWiki pages: Noc, Jeff Errington, cell division, chromosome segregation

David William Adams, Ling Juan Wu, Jeff Errington
Nucleoid occlusion protein Noc recruits DNA to the bacterial cell membrane.
EMBO J.: 2015, 34(4);491-501
[PubMed:25568309] [WorldCat.org] [DOI] (I p)


  • January 2015
    • Proteases are crucial for the maintenance of protein integrity, but also for controlling the cellular levels of specific proteins. For the LonA protease, it has so far been unknown how the protease can specifically target a selected protein as degradation target. Now, Mukherjee et al. from the lab of Daniel Kearns have studied the degradation of SwrA, a master regulator of flagellar biosynthesis by LonA. They found that the adaptor protein SmiA is required for the productive degradation of SwrA by LonA. This regulatory mechanism is important to prevent hyperflagellation in liquid media.
    • Relevant SubtiWiki pages: LonA, SwrA, SmiA, proteolysis, Daniel Kearns

Sampriti Mukherjee, Anna C Bree, Jing Liu, Joyce E Patrick, Peter Chien, Daniel B Kearns
Adaptor-mediated Lon proteolysis restricts Bacillus subtilis hyperflagellation.
Proc. Natl. Acad. Sci. U.S.A.: 2015, 112(1);250-5
[PubMed:25538299] [WorldCat.org] [DOI] (I p)


2014

  • December 2014
    • Cell division is facilitated by a molecular machine - the divisome - that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by FtsZ is regulated by several factors, including the divisome component EzrA. Cleverley et al. now describe the structure of the cytoplasmic domain of EzrA which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and EzrA is proposed to be the founding member of the bacterial spectrin family.
    • Relevant SubtiWiki pages: EzrA, FtsZ, divisome, cell division, Rick Lewis

Robert M Cleverley, Jeffrey R Barrett, Arnaud Baslé, Nhat Khai Bui, Lorraine Hewitt, Alexandra Solovyova, Zhi-Qiang Xu, Richard A Daniel, Nicholas E Dixon, Elizabeth J Harry, Aaron J Oakley, Waldemar Vollmer, Richard J Lewis
Structure and function of a spectrin-like regulator of bacterial cytokinesis.
Nat Commun: 2014, 5;5421
[PubMed:25403286] [WorldCat.org] [DOI] (I e)


  • November 2014
    • Integration of prophages into coding sequences of the host genome results in loss of function of the interrupted gene. In B. subtilis 168, the SP-beta prophage is inserted into a uncharacterized spore polysaccharide synthesis gene, spsM. In vegetative cells, the lytic cycle is induced in response to DNA damage. In the process, the SP-beta prophage is excised from the genome to form phage particles. Now, Abe et al. demonstrate that the excision of the SP-beta prophage also occurs systematically during sporulation to reconstitute a functional spsM gene from the incomplete yodU and ypqP pseudogenes. Because phage excision is limited to the mother cell genome, and does not occur in the forespore genome, the SP-beta prophage is an integral part of the spore genome. Thus, after germination, the SP-beta prophage is propagated vertically to the progeny. The authors suggest their results indicate that the two pathways of SP-beta prophage excision support both the phage life cycle and normal sporulation of the host cells.
    • Relevant SubtiWiki pages: SP-beta prophage, sporulation, yodU, ypqP, SprA, SprB

Kimihiro Abe, Yuta Kawano, Keito Iwamoto, Kenji Arai, Yuki Maruyama, Patrick Eichenberger, Tsutomu Sato
Developmentally-regulated excision of the SPβ prophage reconstitutes a gene required for spore envelope maturation in Bacillus subtilis.
PLoS Genet.: 2014, 10(10);e1004636
[PubMed:25299644] [WorldCat.org] [DOI] (I e)

    • See also:

Pilar Sanchez-Vizuete, Dominique Le Coq, Arnaud Bridier, Jean-Marie Herry, Stéphane Aymerich, Romain Briandet
Identification of ypqP as a New Bacillus subtilis biofilm determinant that mediates the protection of Staphylococcus aureus against antimicrobial agents in mixed-species communities.
Appl. Environ. Microbiol.: 2015, 81(1);109-18
[PubMed:25326298] [WorldCat.org] [DOI] (I p)


  • October 2014
    • Drug exporters help the bacterial cell to cope with potentially toxic compounds. The expression of the transporters is usually switched on in response to the transported drugs. Reilman et al. have studied the regulation of the BmrC/BmrD multidrug ABC transporter in B. subtilis. They report that the induction of bmrC-bmrD depends on the translation of a small leader peptide, BmrB. This is the first report on a ribosome-mediated transcriptional attenuation mechanism in the control of a multidrug ABC transporter.
    • Relevant SubtiWiki pages: BmrB, ABC transporter, bmrC-bmrD, AbrB

Ewoud Reilman, Ruben A T Mars, Jan Maarten van Dijl, Emma L Denham
The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism.
Nucleic Acids Res.: 2014, 42(18);11393-407
[PubMed:25217586] [WorldCat.org] [DOI] (I p)


Aiming Ren, Dinshaw J Patel
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Nat. Chem. Biol.: 2014, 10(9);780-6
[PubMed:25086509] [WorldCat.org] [DOI] (I p)

Ang Gao, Alexander Serganov
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Nat. Chem. Biol.: 2014, 10(9);787-92
[PubMed:25086507] [WorldCat.org] [DOI] (I p)


  • August 2014
    • Calcium is important for the activity of many many enzymes, and its cellular homeostasis is therefore important. Now, the previously unknown YetJ protein has been identified as a pH-sensitive calcium leak that allows reducing the inracellular calcium concentration. Chang et al. report the structure of YetJ and explain how two conserved Asp residues sense changes in the pH.
    • Relevant SubtiWiki pages: Metal ion homeostasis (K, Na, Ca, Mg), YetJ

Yanqi Chang, Renato Bruni, Brian Kloss, Zahra Assur, Edda Kloppmann, Burkhard Rost, Wayne A Hendrickson, Qun Liu
Structural basis for a pH-sensitive calcium leak across membranes.
Science: 2014, 344(6188);1131-5
[PubMed:24904158] [WorldCat.org] [DOI] (I p)


  • July 2014
    • T-boxes are regulatory mRNA elements which sense amino acid availability and control the expression of genes encoding aminoacyl-tRNA synthetases and biosynthetic enzymes. Sensing is thought to occur by the interaction of the uncharged tRNA with the T-box thus preventing the formation of a transcription terminator. It has however, not been known whether this regulation involves proteins. Now, Zhang and Ferre-D'Amare show that the B. subtilis glyQ-glyS T-box functions independently of any tRNA-binding protein. They demonstrate that the T-box detects the molecular volume of tRNA 3'-substituents.
    • Relevant SubtiWiki pages: T-box, glyQ

Jinwei Zhang, Adrian R Ferré-D'Amaré
Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout.
Mol. Cell: 2014, 55(1);148-55
[PubMed:24954903] [WorldCat.org] [DOI] (I p)


  • June 2014
    • Transcription by RNA polymerase is interrupted by pauses that play diverse regulatory roles. However, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. Using nascent transcript sequencing, Larson et al. identified a 16-nucleotide consensus pause sequence. The pauses result from RNA polymerase-nucleic acid interactions that inhibit next-nucleotide addition. The consensus sequence is enriched at translation start sites in Bacillus subtilis.
    • Relevant SubtiWiki pages: RNA polymerase, transcription, translation

Matthew H Larson, Rachel A Mooney, Jason M Peters, Tricia Windgassen, Dhananjaya Nayak, Carol A Gross, Steven M Block, William J Greenleaf, Robert Landick, Jonathan S Weissman
A pause sequence enriched at translation start sites drives transcription dynamics in vivo.
Science: 2014, 344(6187);1042-7
[PubMed:24789973] [WorldCat.org] [DOI] (I p)

  • See a comment on this issue:

Jeffrey W Roberts
Molecular biology. Molecular basis of transcription pausing.
Science: 2014, 344(6189);1226-7
[PubMed:24926002] [WorldCat.org] [DOI] (I p)


Jan Muntel, Vincent Fromion, Anne Goelzer, Sandra Maaβ, Ulrike Mäder, Knut Büttner, Michael Hecker, Dörte Becher
Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)).
Mol. Cell Proteomics: 2014, 13(4);1008-19
[PubMed:24696501] [WorldCat.org] [DOI] (I p)


Neville S Gilhooly, Mark S Dillingham
Recombination hotspots attenuate the coupled ATPase and translocase activities of an AddAB-type helicase-nuclease.
Nucleic Acids Res.: 2014, 42(9);5633-43
[PubMed:24682829] [WorldCat.org] [DOI] (I p)

Wojciech W Krajewski, Xin Fu, Martin Wilkinson, Nora B Cronin, Mark S Dillingham, Dale B Wigley
Structural basis for translocation by AddAB helicase-nuclease and its arrest at χ sites.
Nature: 2014, 508(7496);416-9
[PubMed:24670664] [WorldCat.org] [DOI] (I p)


Laura Hobley, Sok Ho Kim, Yukari Maezato, Susan Wyllie, Alan H Fairlamb, Nicola R Stanley-Wall, Anthony J Michael
Norspermidine is not a self-produced trigger for biofilm disassembly.
Cell: 2014, 156(4);844-54
[PubMed:24529384] [WorldCat.org] [DOI] (I p)


Anna Oslizlo, Polonca Stefanic, Iztok Dogsa, Ines Mandic-Mulec
Private link between signal and response in Bacillus subtilis quorum sensing.
Proc. Natl. Acad. Sci. U.S.A.: 2014, 111(4);1586-91
[PubMed:24425772] [WorldCat.org] [DOI] (I p)


Yang Fu, Kaila Deiorio-Haggar, Mark W Soo, Michelle M Meyer
Bacterial RNA motif in the 5' UTR of rpsF interacts with an S6:S18 complex.
RNA: 2014, 20(2);168-76
[PubMed:24310371] [WorldCat.org] [DOI] (I p)


2013

Markus Mastny, Alexander Heuck, Robert Kurzbauer, Anja Heiduk, Prisca Boisguerin, Rudolf Volkmer, Michael Ehrmann, Christopher D A Rodrigues, David Z Rudner, Tim Clausen
CtpB assembles a gated protease tunnel regulating cell-cell signaling during spore formation in Bacillus subtilis.
Cell: 2013, 155(3);647-58
[PubMed:24243021] [WorldCat.org] [DOI] (I p)


  • November 2013
    • Cyclic di-AMP is an essential second messenger in B. subtilis and other Gram-positive bacteria. This molecule has been discovered only in 2008, and a lot of work has recently been devoted to the investigation of its function. This month, Nelson et al. from the lab of Ronald Breaker discovered that c-di-AMP binds to the ydaO riboswitch. This is extremely interesting since the molecule does also bind the KtrA potassium transporter. The ktrA-ktrB operon is also controlled by a ydaO riboswitch. Thus c-di-AMP is the first signalling nucleotide that controls a biological process by binding both a protein and the encoding mRNA.
    • Relevant SubtiWiki pages: Ronald Breaker, ydaO riboswitch, KtrA, ydaO, metabolism of signalling nucleotides

James W Nelson, Narasimhan Sudarsan, Kazuhiro Furukawa, Zasha Weinberg, Joy X Wang, Ronald R Breaker
Riboswitches in eubacteria sense the second messenger c-di-AMP.
Nat. Chem. Biol.: 2013, 9(12);834-9
[PubMed:24141192] [WorldCat.org] [DOI] (I p)

    • Additional papers on c-di-AMP from 2013

Rebecca M Corrigan, Ivan Campeotto, Tharshika Jeganathan, Kevin G Roelofs, Vincent T Lee, Angelika Gründling
Systematic identification of conserved bacterial c-di-AMP receptor proteins.
Proc. Natl. Acad. Sci. U.S.A.: 2013, 110(22);9084-9
[PubMed:23671116] [WorldCat.org] [DOI] (I p)

Felix M P Mehne, Katrin Gunka, Hinnerk Eilers, Christina Herzberg, Volkhard Kaever, Jörg Stülke
Cyclic di-AMP homeostasis in bacillus subtilis: both lack and high level accumulation of the nucleotide are detrimental for cell growth.
J. Biol. Chem.: 2013, 288(3);2004-17
[PubMed:23192352] [WorldCat.org] [DOI] (I p)


Bin Liu, William K Eliason, Thomas A Steitz
Structure of a helicase-helicase loader complex reveals insights into the mechanism of bacterial primosome assembly.
Nat Commun: 2013, 4;2495
[PubMed:24048025] [WorldCat.org] [DOI] (I p)


  • September 2013
    • Biofilms of B. subtilis consist of cells in a matrix made up of extracellular polysaccharides, the amyloid-like TasA protein, and the hydrophobic protein BslA. Now, Hobley et al. from the lab of Nicola Stanley-Wall determined the structure of BslA and found that the protein has an extremely hydrophobic cap domain that acts like a raincoat for the biofilm. The authors suggest that BslA is a bacterial hydrophobin.
    • Relevant SubtiWiki pages: Nicola Stanley-Wall, biofilm formation, BslA

Laura Hobley, Adam Ostrowski, Francesco V Rao, Keith M Bromley, Michael Porter, Alan R Prescott, Cait E MacPhee, Daan M F van Aalten, Nicola R Stanley-Wall
BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm.
Proc. Natl. Acad. Sci. U.S.A.: 2013, 110(33);13600-5
[PubMed:23904481] [WorldCat.org] [DOI] (I p)

    • A comment on this paper:

Ursula Hofer
Bacterial physiology: a raincoat for Bacillus subtilis.
Nat. Rev. Microbiol.: 2013, 11(10);660-1
[PubMed:23979433] [WorldCat.org] [DOI] (I p)


  • August 2013
    • In cells, the concentration of ribonucleotides by far exceeds that of deoxyribonucleotides. This poses problems since the DNA polymerase incorporates one rNTP every 2.3 kb during chromosome replication. Now, Yao et al. investigated how these misincorporations are repaired. They demonstrate that this repair is initiated by RNase HII that nicks DNA at single rNMP residues to initiate replacement with dNMPs.
    • Relevant SubtiWiki pages: DNA replication, DNA repair, rnhB, rnhC, mutS, mutL

Nina Y Yao, Jeremy W Schroeder, Olga Yurieva, Lyle A Simmons, Mike E O'Donnell
Cost of rNTP/dNTP pool imbalance at the replication fork.
Proc. Natl. Acad. Sci. U.S.A.: 2013, 110(32);12942-7
[PubMed:23882084] [WorldCat.org] [DOI] (I p)


  • July 2013
    • Ca2+ efflux by Ca2+ cation antiporter (CaCA) proteins is important for maintenance of Ca2+ homeostasis across the cell membrane. Now, Wu et al. determined the structure of the B. subtilis Ca2+/H+ antiporter protein ChaA. By structural and mutational analyses, they establish structural bases for mechanisms of Ca2+/H+ exchange and its pH regulation. Moreover, this work also sheds light on the evolutionary adaptation to different energy modes in the CaCA protein family.
    • Relevant SubtiWiki pages: ChaA, membrane proteins, metal ion homeostasis (K, Na, Ca, Mg)

Mousheng Wu, Shuilong Tong, Sandro Waltersperger, Kay Diederichs, Meitian Wang, Lei Zheng
Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation.
Proc. Natl. Acad. Sci. U.S.A.: 2013, 110(28);11367-72
[PubMed:23798403] [WorldCat.org] [DOI] (I p)


  • June 2013
    • DNA transfer across membranes is important in many fundamental processes. However, the molecular mechanisms behind this transport are only poorly understood. Now, Fiche et al. analysed the assembly and molecular architecture of the SpoIIIE DNA translocation complex. This study reveals that in contrast to a previous model, DNA transfer occurs through an aqueous DNA-conducting pore that could be structurally maintained by the divisional machinery, with SpoIIIE acting as a checkpoint preventing membrane fusion until completion of chromosome segregation.
    • Relevant SubtiWiki pages: sporulation, SpoIIIE, DNA condensation/ segregation

Jean-Bernard Fiche, Diego I Cattoni, Nele Diekmann, Julio Mateos Langerak, Caroline Clerte, Catherine A Royer, Emmanuel Margeat, Thierry Doan, Marcelo Nöllmann
Recruitment, assembly, and molecular architecture of the SpoIIIE DNA pump revealed by superresolution microscopy.
PLoS Biol.: 2013, 11(5);e1001557
[PubMed:23667326] [WorldCat.org] [DOI] (I p)


  • May 2013
    • Paul et al. demonstrate that the orientation of the genes on the chromosome has a significant impact on their evolution: Gene encoded on the lagging strand evolve faster than those on the leading strand. This faster evolution is caused by collisions between the DNA replication and transcription machineries that result in DNA damage and subsequent fixation of errors as mutations. Importantly, essential genes are strongly underrepresented on the lagging strand thus providing a "built-in" protection of the encoded important proteins against possible deleterious mutations.
    • Relevant SubtiWiki pages: transcription, DNA replication, essential genes

Sandip Paul, Samuel Million-Weaver, Sujay Chattopadhyay, Evgeni Sokurenko, Houra Merrikh
Accelerated gene evolution through replication-transcription conflicts.
Nature: 2013, 495(7442);512-5
[PubMed:23538833] [WorldCat.org] [DOI] (I p)


Romain Mercier, Yoshikazu Kawai, Jeff Errington
Excess membrane synthesis drives a primitive mode of cell proliferation.
Cell: 2013, 152(5);997-1007
[PubMed:23452849] [WorldCat.org] [DOI] (I p)


  • March 2013
    • The mechanism of membrane fission in bacteria has been a long-standing enigma. Now, Doan et al. from the lab of David Rudner demonstrate how the FisB protein (previously YunB) mediates membrane fission during sporulation This activity of FisB is based on its ability to bind to lipids, specifically to cardiolipin.
    • Relevant SubtiWiki pages: David Rudner, FisB, sporulation

Thierry Doan, Jeff Coleman, Kathleen A Marquis, Alex J Meeske, Briana M Burton, Erdem Karatekin, David Z Rudner
FisB mediates membrane fission during sporulation in Bacillus subtilis.
Genes Dev.: 2013, 27(3);322-34
[PubMed:23388828] [WorldCat.org] [DOI] (I p)

  • See also:

Irene S Tan, Kumaran S Ramamurthi
Membrane remodeling: FisB will do in a pinch.
Curr. Biol.: 2013, 23(6);R251-3
[PubMed:23518060] [WorldCat.org] [DOI] (I p)


Sylvain Durand, Laetitia Gilet, Ciarán Condon
The essential function of B. subtilis RNase III is to silence foreign toxin genes.
PLoS Genet.: 2012, 8(12);e1003181
[PubMed:23300471] [WorldCat.org] [DOI] (I p)

  • A comment on this paper:

Fabian M Commichau, Jörg Stülke
A mystery unraveled: essentiality of RNase III in Bacillus subtilis is caused by resident prophages.
PLoS Genet.: 2012, 8(12);e1003199
[PubMed:23300472] [WorldCat.org] [DOI] (I p)

  • See also:

Sylvain Durand, Natalie Jahn, Ciarán Condon, Sabine Brantl
Type I toxin-antitoxin systems in Bacillus subtilis.
RNA Biol: 2012, 9(12);1491-7
[PubMed:23059907] [WorldCat.org] [DOI] (I p)


Jean-Philippe Castaing, Attila Nagy, Vivek Anantharaman, L Aravind, Kumaran S Ramamurthi
ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein.
Proc. Natl. Acad. Sci. U.S.A.: 2013, 110(2);E151-60
[PubMed:23267091] [WorldCat.org] [DOI] (I p)


2012

  • December 2012
    • Kim et al. show how the ATP hydrolysis controls the global conformation of the SecA translocase and drives protein secretion. The intricate network of structural interactions, which couple local electrostatic changes during ATP hydrolysis to global conformational and dynamic changes in SecA, form the foundation of the allosteric mechanochemistry that efficiently harnesses the chemical energy stored in ATP to drive complex mechanical processes.
    • Relevant SubtiWiki pages: SecA, protein secretion

Dorothy M Kim, Haiyan Zheng, Yuanpeng J Huang, Gaetano T Montelione, John F Hunt
ATPase active-site electrostatic interactions control the global conformation of the 100 kDa SecA translocase.
J. Am. Chem. Soc.: 2013, 135(8);2999-3010
[PubMed:23167435] [WorldCat.org] [DOI] (I p)


Peter Y Watson, Martha J Fedor
The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis.
Nat. Chem. Biol.: 2012, 8(12);963-5
[PubMed:23086297] [WorldCat.org] [DOI] (I p)


Germán Plata, Tobias Fuhrer, Tzu-Lin Hsiao, Uwe Sauer, Dennis Vitkup
Global probabilistic annotation of metabolic networks enables enzyme discovery.
Nat. Chem. Biol.: 2012, 8(10);848-54
[PubMed:22960854] [WorldCat.org] [DOI] (I p)


Shinobu Chiba, Koreaki Ito
Multisite ribosomal stalling: a unique mode of regulatory nascent chain action revealed for MifM.
Mol. Cell: 2012, 47(6);863-72
[PubMed:22864117] [WorldCat.org] [DOI] (I p)


Ali Houry, Michel Gohar, Julien Deschamps, Ekaterina Tischenko, Stéphane Aymerich, Alexandra Gruss, Romain Briandet
Bacterial swimmers that infiltrate and take over the biofilm matrix.
Proc. Natl. Acad. Sci. U.S.A.: 2012, 109(32);13088-93
[PubMed:22773813] [WorldCat.org] [DOI] (I p)


Angel E Dago, Alexander Schug, Andrea Procaccini, James A Hoch, Martin Weigt, Hendrik Szurmant
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis.
Proc. Natl. Acad. Sci. U.S.A.: 2012, 109(26);E1733-42
[PubMed:22670053] [WorldCat.org] [DOI] (I p)


Laura Hobley, Sok Ho Kim, Yukari Maezato, Susan Wyllie, Alan H Fairlamb, Nicola R Stanley-Wall, Anthony J Michael
Norspermidine is not a self-produced trigger for biofilm disassembly.
Cell: 2014, 156(4);844-54
[PubMed:24529384] [WorldCat.org] [DOI] (I p)

Ilana Kolodkin-Gal, Shugeng Cao, Liraz Chai, Thomas Böttcher, Roberto Kolter, Jon Clardy, Richard Losick
A self-produced trigger for biofilm disassembly that targets exopolysaccharide.
Cell: 2012, 149(3);684-92
[PubMed:22541437] [WorldCat.org] [DOI] (I p)


Alexander K W Elsholz, Kürsad Turgay, Stephan Michalik, Bernd Hessling, Katrin Gronau, Dan Oertel, Ulrike Mäder, Jörg Bernhardt, Dörte Becher, Michael Hecker, Ulf Gerth
Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis.
Proc. Natl. Acad. Sci. U.S.A.: 2012, 109(19);7451-6
[PubMed:22517742] [WorldCat.org] [DOI] (I p)


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)

Vladimir M Levdikov, Elena V Blagova, Amanda McFeat, Mark J Fogg, Keith S Wilson, Anthony J Wilkinson
Structure of components of an intercellular channel complex in sporulating Bacillus subtilis.
Proc. Natl. Acad. Sci. U.S.A.: 2012, 109(14);5441-5
[PubMed:22431604] [WorldCat.org] [DOI] (I p)


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)


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:

Liza Gross
Built-in timer delays differentiation.
PLoS Biol.: 2012, 10(1);e1001254
[PubMed:22303284] [WorldCat.org] [DOI] (I p)


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

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)


James C W Locke, Jonathan W Young, Michelle Fontes, María Jesús Hernández Jiménez, Michael B Elowitz
Stochastic pulse regulation in bacterial stress response.
Science: 2011, 334(6054);366-9
[PubMed:21979936] [WorldCat.org] [DOI] (I p)


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)


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)

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, Marc Schaffer, Ulrike Mäder, Christine Diethmaier, Christina Herzberg, Jörg Stülke
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y.
Mol. Microbiol.: 2011, 81(6);1459-73
[PubMed:21815947] [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)


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)


Ethan C Garner, Remi Bernard, Wenqin Wang, Xiaowei Zhuang, David Z Rudner, Tim Mitchison
Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis.
Science: 2011, 333(6039);222-5
[PubMed:21636745] [WorldCat.org] [DOI] (I p)

Julia Domínguez-Escobar, Arnaud Chastanet, Alvaro H Crevenna, Vincent Fromion, Roland Wedlich-Söldner, Rut Carballido-López
Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria.
Science: 2011, 333(6039);225-8
[PubMed:21636744] [WorldCat.org] [DOI] (I p)

  • 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)


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

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)

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