Papers of the month

2024

• February 2024
  • This is the month of translation factors. The group of Heather Feaga has identified the ABCF ATPase YfmR as a protein that is essential to rescue ribosomes stalled at polyproline stretches in the absence of Efp. Similar results on the resolution of stalled ribosomes by YfmR and YkpA are also reported in a preprint from the group of Vasili Hauryliuk. Moreover, the so far unknown stress protein YocB is a novel hibernation factor that interacts with TufA to to inhibit protein synthesis and protect their ribosomes from damage.
  • Relevant SubtiWiki pages: Heather Feaga, Vasili Hauryliuk, translation factors, YfmR, YkpA, YocB

• January 2024
  • Temperate Bacillus phages often use the small-molecule arbitrium communication system to control lysis/lysogeny decisions, but the underlying mechanisms remain largely unknown. Now, two studies show that the arbitrium system of B. subtilis phage ϕ3T modulates the host-encoded MazE-MazF toxin-antitoxin system to regulate the phage life cycle. Upon infection, the MazF ribonuclease is activated by three phage genes. At low arbitrium signal concentrations, MazF is inactivated by two phage-encoded MazE homologues, the arbitrium-controlled AimX and the later-expressed YosL proteins. The results show how a bacterial toxin-antitoxin system has been co-opted by a phage to control lysis/lysogeny decisions without compromising host viability.
  • Relevant SubtiWiki pages: Avigdor Eldar, Wilfried Meijer, AimX, AimR, YosL, MazE, MazF

2023

• December 2023
  • DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded and single-stranded DNA to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Now, Pelliciari et al. show that B. subtilis DnaA assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. Their results provide a molecular basis clue how DnaA specifically engages the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS).
  • Relevant SubtiWiki pages: Heath Murray, DNA replication, DnaA

• October 2023
  • B. subtilis spores are metabolically dormant and resistant to microbicides, while germinated spores are easy to kill. Thus, understanding germination may facilitate the development of "germinate-to-eradicate" strategies. A recent high-profile paper [Science (2022) 378:43] (POTM October 2022) suggested that increasing spore electrochemical potential is how memory is "stored" based on measurements of accumulation of the dye thioflavin-T after germinant exposure. Now,Li et al. challenge this view and show that inferring spores' electrochemical potential from thioflavin-T accumulation is problematic. Thioflavin-T accumulation during the early stages of germination is due to its binding to the spore coat rather than to changes in spores' electrochemical potential. Thus, using thioflavin-T uptake by germinating spores to assess the involvement of electrochemical potential in memory of germinant exposure, as suggested recently, is questionable.
  • Relevant SubtiWiki pages: Peter Setlow, Germination

• September 2023
  • Cell wall synthesis requires an interplay of breaking old and making new bonds in peptidoglycan. Due to their redundancy, it has been difficult so far, to study the function of individual cell wall hydrolyses. Now, Wilson et al. from the labs of Ethan Garner and Simon Foster have deleted 40 potential hydrolyses, keeping only LytE and CwlO. Each of these hydrolases is still dispensable in the deletion strain. The study demonstrates that the only essential function of cell wall hydrolases in B. subtilis is to enable cell growth by expanding the wall and that LytE or CwlO alone are sufficient for this function.
  • Relevant SubtiWiki pages: Ethan Garner, Simon Foster, LytE, CwlO, Autolytic activity required for peptidoglycan synthesis

• May 2023
  • Two recent papers provide an excellent overview on new developments in the functional annotation of the B. subtilis genome and on the use of B. subtilis as a model organism in research and a workhorse in biotechnology.
  • Relevant SubtiWiki pages: Erhard Bremer, Antoine Danchin, Colin Harwood, John Helmann, Jörg Stülke, Marc Bramkamp

Erhard Bremer, Alexandra Calteau, Antoine Danchin, Colin Harwood, John D Helmann, Claudine Médigue, Bernhard O Palsson, Agnieszka Sekowska, David Vallenet, Abril Zuniga, Cristal Zuniga
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.
Microb Biotechnol: 2023, 16(6);1203-1231
[PubMed:37002859] [WorldCat.org] [DOI] (I p)

• April 2023
  • B. subtilis spores are able to resist a variety of hostile conditions and can remain metabolically inactive for centuries. In the presence of nutrients, the spores can initiate germination in minutes. How the inactive spores detect the nutrients and start outgrowth, has remained a matter of debate. Now, Gao et al. from the lab of David Rudner discovered that germinant receptors embedded in the spore membrane oligomerize into nutrient-gated ion channels and then ion release triggers exit from dormancy.
  • Relevant SubtiWiki pages: David Rudner, GerAA, GerAB, GerAC, germination, SpoVA

• March 2023
  • Special note: This is the first BioRxiv paper of the month since the preprint server has at least partially been included in PubMed!

The biofilms of B. subtilis are embedded in a self-made polysaccharide matrix. Little is known about the steps of matrix synthesis. Now, Arbour et al. have identified the enzymes that use the add the starting material UDP-N,N’-diacetylbacillosamine to undecaprenypyrophosphate and then add the second sugar residue, N-acetyl-glucosamine, EpsL and EpsD, respectively.

• • Relevant SubtiWiki pages: Nicola Stanley-Wall, EpsD, EpsL, Matrix polysaccharide synthesis

• February 2023
  • Many proteins act only in complex with other proteins. However, it is difficult to get an overview about protein-protein interactions at the global proteome level. Now, O'Reilly et al. from the group of Juri Rappsilber have identified the global interactome of B. subtilis by combining in vivo protein cross-linking and complex cofractionation with mass-spectrometry. They also predicted complex structures using AlphaFold multimer. Importantly, several uncharacterized proteins interact with known proteins. Based on such an interaction, the former YneR protein was identified as PdhI, an inhibitor of pyruvate dehydrogenase.
  • Relevant SubtiWiki pages: Juri Rappsilber, PdhI, PdhA-PdhB-PdhC-PdhD, YabR, YugI, see the list of protein complexes with novel structural predictions

A comment on the paper:

2022

• November 2022
  • Cell wall synthesis involves the flipping of sugar-loaded undecaprenyl pyrophosphate molecules to the surface of the cell. So far, it has remained enigmatic, how the released undecaprenyl phosphate can then be recycled. Now, Roney & Rudner have identified the last missing piece of the part list of cell envelope biogenesis and surface modification pathways in B. subtilis and other bacteria. Using a transposon screen, they identified the uptake gene product as responsible for undecaprenyl phosphate flipping to the cytoplasmic side of the membrane.
  • Relevant SubtiWiki pages: David Rudner, cell wall biosynthesis, UptA

• October 2022
  • B. subtilis spores can spend years in a dormant, biochemically inactive state, yet they retain the ability to process information from cues that can release them from dormancy and trigger germination. Now, Kikuchi et al. show that despite continued dormancy, the spores can integrate environmental signals over time through a preexisting electrochemical potential. The works reveals a decision-making mechanism that operates in physiologically inactive cells.
  • Relevant SubtiWiki pages: Gürol M. Süel, germination, Potassium uptake/export

• September 2022
  • More than 25 years ago, PrkA has been described as a protein kinase. However, the function of the protein has always remained enigmatic. Now, using an elegant combination of bioinformatic and experimental approaches Zhang et al. from the lab of Anne Galinier demonstrate that PrkA is not a protein kinase, but an AAA+ type ATP-dependent protease. This protease activity is important for sporulation of B. subtilis. Moreover, the activity of PrkA is controlled by PrkC-dependent phosphorylation of Thr-217.
  • Relevant SubtiWiki pages: Anne Galinier, PrkA, PrkC, sporulation

• August 2022
  • The conserved nucleotide diadenosine tetraphosphate (Ap4A) is induced under various stresses, including heat. In a non-biased screen, Giammarinaro et al. have identified a critical role of Ap4A in binding the IMP dehydrogenase GuaB, thus inhibiting a central step in purine metabolism and heat resistance. The authors clarify the molecular mechanism of Ap4A action on the inosine-5′-monophosphate dehydrogenase (IMPDH) enzyme and demonstrate the Ap4A is a bona fide nucleotide second messenger.
  • Relevant SubtiWiki pages: Gert Bange, Jade Wang, GuaB

• March 2022
  • DNA helicases of the RecD2 family are ubiquitous. Bacillus subtilis RecD2 in association with the single-stranded binding protein SsbA may contribute to replication fork progression, but its detailed action remains unknown. Now, Ramos et al. have investigated the role of RecD2 during DNA replication and its interaction with the RecA recombinase. RecD2 inhibits replication restart. RecA inhibits leading and lagging strand synthesis, and RecD2, which physically interacts with RecA, counteracts this negative effect. The inactivation of recD2 promotes RecA–ssDNA accumulation at low mitomycin C levels, and RecA threads persist for a longer time after induction of DNA damage. In vitro, RecD2 modulates RecA-mediated DNA strand-exchange and catalyzes branch migration. These findings show how RecD2 may contribute to overcome a replicative stress, removing RecA from the ssDNA and, thus, it may act as a negative modulator of RecA filament growth.
  • Relevant SubtiWiki pages: Peter Graumann, Juan C. Alonso, RecD2, RecA, SsbA, DNA replication

• February 2022
  • Nucleoprotein complexes play an integral role in genome organization of both eukaryotes and prokaryotes as they may affect global chromosome organization by mediating long-range anchored chromosomal loop formation that results in spatial segregation of large sections of DNA. While such megabase-range interactions are ubiquitous in eukaryotes, they have so far not been demonstrated in prokaryotes. Now, Dugar et al. from the lab of Leendert Hamoen found that a transcription factor, Rok, forms large nucleoprotein complexes in B. subtilis. They demonstrate that these complexes robustly interact with each other over large distances. Importantly, these Rok-dependent long-range interactions lead to anchored chromosomal loop formation, thereby spatially isolating large sections of DNA, as previously observed for insulator proteins in eukaryotes.
  • Relevant SubtiWiki pages: Leendert Hamoen, Rok, DNA condensation/ segregation

Gaurav Dugar, Andreas Hofmann, Dieter W Heermann, Leendert W Hamoen
A chromosomal loop anchor mediates bacterial genome organization.
Nat Genet: 2022, 54(2);194-201
[PubMed:35075232] [WorldCat.org] [DOI] (I p)

• January 2022
  • ppGpp is a second messenger nucleotide synthesized in response to amino acid starvation. Now, Anderson et al. from the lab of Jade Wang demonstrate that (p)ppGpp also binds to the transcription regulator PurR that represses the expression of genes involved in purine biosynthesis. Specifically, (p)ppGpp acts as an anti-inducer by preventing binding of the inducer molecule PRPP to PurR. Thus, control of nucleotide biosynthesis seems to be a key function of (p)ppGpp.
  • Relevant SubtiWiki pages: Jade Wang, Vincent Lee, PurR, PurR regulon, Targets of (p)ppGpp, pycA, Biosynthesis/ acquisition of purine nucleotides

Brent W Anderson, Maria A Schumacher, Jin Yang, Asan Turdiev, Husan Turdiev, Jeremy W Schroeder, Qixiang He, Vincent T Lee, Richard G Brennan, Jue D Wang
The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus.
Nucleic Acids Res: 2022, 50(2);847-866
[PubMed:34967415] [WorldCat.org] [DOI] (I p)

2021

• July 2021
  • Each ribonucleotide has specific functions in addition to being a substrate in nucleic acid synthesis. ATP, GTP, and UTP play key role in energy metabolism, in translation, and in polysaccharide biosynthesis, respectively. This month, two papers describe important functions of CTP in processes related to cell division. Balaguer et al. from the lab of Fernando Moreno-Herrero demonstrate that CTP binds to the chromosome segregation protein ParB to facilitate the interaction with parS DNA sites. Moreover, Jalal et al. show that CTP triggers binding of the nucleoid occlusion protein Noc to specific binding sites and subsequent binding to the membrane. Thus, CTP is involved in central processes in cell division.
  • Relevant SubtiWiki pages: Fernando Moreno-Herrero, ParB, Noc, DNA condensation/ segregation, cell division

• June 2021
  • Genome replication is a fundamental requirement for life. To initiate replication, conserved initiation proteins assemble at replication origins and direct loading of replicative helicases. Despite decades of study on bacterial DNA replication, the diversity of bacterial chromosome origin architecture has confounded the search for molecular mechanisms directing the initiation process. Now, Pelliciari et al. from the lab of Heath Murray have elucidated the mechanism for B. subtilis. They report that a pair of dsDNA binding sites (DnaA-boxes) guide the replication initiator DnaA onto adjacent ssDNA binding motifs (DnaA-trios) where DnaA assembles into an oligomer that stretches DNA to promote origin unwinding. These core elements are present in the majority of bacterial chromosome origins and their principle activities of the origin unwinding system are conserved. This basal mechanism for oriC unwinding is thus broadly functionally conserved and therefore may represent an ancestral system to open bacterial chromosome origins.
  • Relevant SubtiWiki pages: Heath Murray, DNA replication, DnaA

• May 2021
  • This month, the paper of the month serves to pay tribute to the work of the late Dan Tawfik who passed away in a climbing accident. It has been known for a long time that many enzymes moonlight in controlling gene expression. Now, Jayaraman et al. from Dan's lab of report that a large multi-enzyme complex in B. subtilis that consists of two enzymes catalyzing opposite rather than sequential reactions (“counter-enzymes”): glutamate synthase (GltA-GltB) and glutamate dehydrogenase (GudB), that make and break glutamate, respectively. The primary role of complex formation is to inhibit GudB’s activity as this enzyme is constitutively expressed including in glutamate-limiting conditions. The data suggest that this complex has a regulatory role at fluctuating glutamate concentrations.
  • Relevant SubtiWiki pages: Dan Tawfik, glutamate metabolism, GltA, GltB, GudB

Paper

• April 2021
  • Sigma factors are important specificity factors of RNA polymerase that allow the recognition of specific promoters. Now, McCormick et al. from the lab of Gene-Wei Li report that the induction of stress genes by SigB also may strongly enhance translation of the controlled genes. These genes have multiple promoters, a more upstream promoter recognized by SigA and more downstream promoter recognized by SigB. Transcription from the upstream promoter results in long untranslated regions of the mRNA that may form secondary structures and thus prevent translation. Transcription from the SigB-dependent promoter results in shorter untranslated regions that may more efficiently be translated.
  • Relevant SubtiWiki pages: Gene-Wei Li, transcription, translation, SigA, SigB, ctc, yvrE

• March 2021
  • Although many components of the B. subtilis cell division machinery have been identified, the mechanisms by which they work together to divide the cell remain poorly understood. Key among these components is the tubulin FtsZ, which forms a Z ring at the midcell and recruits the other cell division proteins, collectively called the divisome. Now, Squyres et al. from the lab of Ethan Garner applied live-cell single-molecule imaging to describe the dynamics of the divisome in detail, and to evaluate the individual roles of FtsZ-binding proteins, specifically FtsA, EzrA, SepF and ZapA, in cytokinesis. They show that the divisome comprises two subcomplexes that move differently: stationary FtsZ-binding proteins that transiently bind to treadmilling FtsZ filaments, and a moving complex that includes cell wall synthases.
  • Relevant SubtiWiki pages: Ethan Garner, cell division, FtsZ, EzrA, SepF, ZapA

• February 2021
  • Higher organisms as well as photosynthetic bacteria possess circadian clocks that create a 24-hour temporal structure. So far, circadian clocks have not been identified in nonphotosynthetic bacteria. Now, Eelderink-Chen et al. identify circadian rhythms sharing the canonical properties of circadian clocks in B. subtilis: free-running period, entrainment, and temperature compensation. The study shows that gene expression in B. subtilis can be synchronized in 24-hour light or temperature cycles and exhibit phase-specific characteristics of entrainment. Upon release to constant dark and temperature conditions, bacterial biofilm populations have temperature-compensated free-running oscillations with a period close to 24 hours.
  • Relevant SubtiWiki pages: Akos T Kovacs, ytvA

Zheng Eelderink-Chen, Jasper Bosman, Francesca Sartor, Antony N Dodd, Ákos T Kovács, Martha Merrow
A circadian clock in a nonphotosynthetic prokaryote.
Sci Adv: 2021, 7(2);
[PubMed:33523996] [WorldCat.org] [DOI] (I e)

• January 2021
  • So far, the role of metabolism in B. subtilis sporulation has remained poorly understood. Now Riley et al. from the lab of Kit Pogliano demonstrate that B. subtilis sporulation entails a marked metabolic differentiation of the forespore and the mother cell. Their data demonstrate that metabolic precursor biosynthesis becomes restricted to the mother cell and that the forespore becomes reliant on mother cell-derived metabolites for protein synthesis. Importantly, arginine is trafficked between the two cells and via proposed proteinaceous channels that mediate small-molecule intercellular transport. Thus, sporulation entails the profound metabolic reprogramming of the forespore, which is depleted of key metabolic enzymes and must import metabolites from the mother cell.
  • Relevant SubtiWiki pages: Kit Pogliano, SpoIIQ, SpoIIIAH, metabolism, biosynthesis/ acquisition of amino acids

Eammon P Riley, Javier Lopez-Garrido, Joseph Sugie, Roland B Liu, Kit Pogliano
Metabolic differentiation and intercellular nurturing underpin bacterial endospore formation.
Sci Adv: 2021, 7(4);
[PubMed:33523946] [WorldCat.org] [DOI] (I e)

2020

• December 2020
  • Single-cell RNA-sequencing has become an essential tool for characterizing gene expression in eukaryotes but current methods are incompatible with bacteria. Now, Kuchina et al. have developed a high-throughput method for single-cell RNA-sequencing that can resolve heterogeneous transcriptional states. They applied the technique to >25,000 B. subtilis cells sampled at different growth stages, and thus created an atlas of changes in metabolism and lifestyle. The authors retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction, and also identified novel and unexpected gene expression states including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities otherwise not amenable to single-cell analysis.

• November 2020
  • Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control. B. subtilis RqcH, a widely conserved ribosome-associated quality control factor, senses the obstruction and recruits tRNAAla(UGC) to modify nascent-chain C termini with a polyalanine degradation signal. However, how RqcH and its eukaryotic homologs synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained enigmatic. Now, two studies by Crowe-McAuliffe et al. and Filbeck et al. report the structures of Bacillus subtilis ribosome-associated quality control complexes. The structures explain how tRNAAla is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNAAla into a hybrid A/P-state associated with peptidyl-transfer. Moreover, the studies identify the Hsp15 homolog RqcP as a novel ribosome-associated quality control component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation.
  • Relevant SubtiWiki pages: RqcH, RqcP, ribosome, translation

• October 2020
  • Bacterial nanotubes have been reported to facilitate the exchange of DNA, proteins, and nutrients. Now, Pospisil et al. show that nanotube formation is associated with stress conditions, and that nanotubes appear to be extruded exclusively from dying cells. Moreover, the study demonstrates that cell-to-cell transfer of non-conjugative plasmids depends strictly on the competence system of the cell, and not on nanotube formation. This study thus suggests that bacterial nanotubes are a post mortem phenomenon involved in cell disintegration, and are unlikely to be involved in cytoplasmic content exchange between live cells.
  • Relevant SubtiWiki pages: Libor Krasny, Imrich Barak, Sigal Ben-Yehuda, SigD, genetic competence

• September 2020
  • It is generally accepted, that transcription and translation are directly coupled in bacteria. This was confirmed by an in vivo protein-protein interaction analysis and cryo-electron tomography for the minimal bacterium Mycoplasma pneumoniae. Now, Johnson et al. show that RNAPs outpace pioneering ribosomes in B. subtilis, and that this 'runaway transcription' creates alternative rules for both global RNA surveillance and translational control of nascent RNA. In particular, uncoupled RNA polymerases in B. subtilis explain the diminished role of Rho-dependent transcription termination, as well as the prevalence of mRNA leaders that use riboswitches and RNA binding regulators. These results show that coupled RNA polymerase-ribosome movement is not a general hallmark of bacteria. Instead, translation-coupled transcription and runaway transcription constitute two principal modes of gene expression that determine genome-specific regulatory mechanisms in prokaryotes.
  • Relevant SubtiWiki pages: transcription, translation, RNA polymerase

• August 2020
  • Many bacteria can form L-forms, that do not require the FtsZ-based cell division machinery. Now, Wu et al. from the lab of Jeff Errington performed microfluidic analyses of the growth, chromosome cycle and division mechanism of B. subtilis L-forms. Their results support the view that L-form division is driven by an excess accumulation of surface area over volume. Cell geometry also plays a dominant role in controlling the relative positions and movement of segregating chromosomes. Furthermore, the presence of the nucleoid appears to influence division both via a cell volume effect and by nucleoid occlusion, even in the absence of FtsZ. The study emphasises the importance of geometric effects for a range of crucial cell functions, and is highly relevant for efforts to develop artificial or minimal cell systems.
  • Relevant SubtiWiki pages: cell division, FtsZ, Jeff Errington

Ling Juan Wu, Seoungjun Lee, Sungshic Park, Lucy E Eland, Anil Wipat, Séamus Holden, Jeff Errington
Geometric principles underlying the proliferation of a model cell system.
Nat Commun: 2020, 11(1);4149
[PubMed:32811832] [WorldCat.org] [DOI] (I e)

• June 2020
  • Peptidoglycan is essential for viability of most bacteria and its synthesis is the target for crucial antibiotics. In B. subtilis, peptidoglycan is generally regarded as a homogeneous structure that provides mechanical strength. Now, Pasquina-Lemonche et al. interrogate B. subtilis peptidoglycan structure, using live cells and purified peptidoglycan. The mature surface of live cells is characterized by a landscape of large (up to 60 nm in diameter), deep (up to 23 nm) pores constituting a disordered gel of peptidoglycan. The inner peptidoglycan surface, consisting of more nascent material, is much denser, with glycan strand spacing typically less than 7 nm. The inner surface architecture is location dependent; the cylinder of B. subtilis has dense circumferential orientation, while in division septa, peptidoglycan is dense but randomly oriented. Revealing the molecular architecture of the cell envelope frames our understanding of its mechanical properties and role as the environmental interface, providing information complementary to traditional structural biology approaches.
  • Relevant SubtiWiki pages: cell wall synthesis, Simon Foster, divisome

• May 2020
  • The synthesis of the cell wall is an essential and highly controlled function in B. subtilis and most other bacteria. Now, Alexander Egan, Jeff Errington, and Waldemar Vollmer provide an authorative overview on the regulation of peptidoglycan biosynthetic enzymes by interactions with morphogenetic proteins.
  • Relevant SubtiWiki pages: cell wall synthesis, Jeff Errington, Waldemar Vollmer, divisome, elongasome

2019

• March 2019
  • Lysine acetylation is an abundant yet poorly characterized posttranslational modification in bacteria. Now, Carabetta et al. from the lab of David Dubnau report that acetylation is a regulatory component of the function of HBsu in nucleoid compaction. Genetic experiments demonstrated that two potential members of the acetyltransferase family, YfmK and YdgE, can acetylate HBsu, and their potential acetylation sites of action on HBsu were identified. Additionally, purified YfmK was able to directly acetylate HBsu in vitro, suggesting that it is the second identified protein acetyltransferase in B. subtilis. The authors propose that at least one physiological function of the acetylation of HBsu at key lysine residues is to regulate nucleoid compaction, analogous to the role of histone acetylation in eukaryotes.
  • Relevant SubtiWiki pages: David Dubnau, HBsu, YfmK, YdgE, acetyltransferase family

• February 2019
  • B. subtilis can form spores when cells are starved for nutrients. Now, Gray et al. from the lab of Leendert Hamoen describe that non-sporulating B. subtilis cells can survive deep starvation conditions for many months. During this period, cells become tolerant to antibiotics. These starved cells are not dormant but are growing and dividing, albeit with a doubling time close to 4 days. The authors call this extreme slow growth the 'oligotrophic growth state'. The sporulation genes mmgB, ydfR, and yisJ are strongly expressed during oligotrophic growth, whereas the unknown ywpE gene is severely repressed.
  • Relevant SubtiWiki pages: Leendert Hamoen, mmgB, ydfR, yisJ, ywpE

• January 2019
  • Glyphosate is widely used herbicide that targets the EPSP synthase, an enzyme required for aromatic amino acid biosynthesis. However, the use of glyphosate is highly controversial, and the producing company has been accused to be responsible for the development of cancer in people that have used the compound. Interestingly, despite the wide use of this weed killer, only little is known about its uptake by cells. Now, Wicke et al. from the lab of Fabian Commichau and the iGEM team Göttingen have identified the first glyphosate transporter. Using suppressor screens with strains adapted to high concentrations of glyphosate, the team found that the glutamate transporter GltT does also transport glyphosate. In addition, the GltP protein is a minor glyphosate transporter.
  • Relevant SubtiWiki pages: Fabian Commichau, GltT, GltP, AroE, Biosynthesis/ acquisition of amino acids

2018

• December 2018
  • The essential DnaD protein is known to interact with the bacterial master replication initiation protein DnaA at the oriC, but structural and functional details of this interaction are lacking. Now, Martin et al. from the lab of Panos Soultanas demonstrate that both the N- and C-terminal domains of DnaD interact with the N-terminal domain I of DnaA. The study shows that the DnaA-interaction patch of DnaD is distinct from the DNA-interaction patch, suggesting that DnaD can bind simultaneously DNA and DnaA. The data suggest that DnaA and DnaD are working collaboratively in the oriC to locally melt the DNA duplex during replication initiation.
  • Relevant SubtiWiki pages: Panos Soultanas, DNA replication, DnaA, DnaD

• November 2018
  • Even though B. subtilis is one of the best-characterized bacterial model organisms, recent proteomics studies identified only about 50% of its theoretical protein count. Now, Ravikumar et al. from the labs of Boris Macek and Ivan Mijakovic generated a comprehensive map of the proteome, phosphoproteome and acetylome of B. subtilis. The study covers 75% of the theoretical proteome (3,159 proteins), detected 1,085 phosphorylation and 4,893 lysine acetylation sites and performed a systematic bioinformatic characterization of the obtained data. A proteogenomic analysis identified 19 novel ORFs. The study provides the most extensive overview of the proteome and post-translational modifications for B. subtilis to date, with insights into functional annotation and evolutionary aspects of the B. subtilis genome.
  • Relevant SubtiWiki pages: Ivan Mijakovic, Boris Macek, phosphoproteins, protein modification

Vaishnavi Ravikumar, Nicolas C Nalpas, Viktoria Anselm, Karsten Krug, Maša Lenuzzi, Martin Sebastijan Šestak, Tomislav Domazet-Lošo, Ivan Mijakovic, Boris Macek
In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins.
Sci Rep: 2018, 8(1);17246
[PubMed:30467398] [WorldCat.org] [DOI] (I e)

• October 2018
  • Membrane-bound O-acyltransferases (MBOATs) are a superfamily of integral transmembrane enzymes present in all domains of life. In bacteria, they modify protective cell-surface polymers. Although many MBOAT proteins are important drug targets, little is known about their molecular architecture and functional mechanisms. Now, Ma et al. present the crystal structures of DltB, an MBOAT responsible for the D-alanylation of cell-wall teichoic acid, both alone and in complex with the D-alanyl donor protein DltC. The conserved catalytic histidine residue is located at the bottom of a highly conserved extracellular structural funnel and is connected to the intracellular DltC through a narrow tunnel.
  • Relevant SubtiWiki pages: DltB, DltC biosynthesis of teichoic acid

• September 2018
  • Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N4-acetylcytidine (ac4C) is present at the anticodon first position (position 34) of bacterial elongator tRNAMet. Now, Taniguchi et al. identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac4C34 formation, determined te structure of the protein and unraveled the unusual the molecular basis of ac4C34 formation. The ΔylbM strain displayed a cold-sensitive phenotype and a strong genetic interaction with TilS, the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNAIle to facilitate AUA decoding.
  • Relevant SubtiWiki pages: YlbM, TilS, tRNA modification/ maturation

Takaaki Taniguchi, Kenjyo Miyauchi, Yuriko Sakaguchi, Seisuke Yamashita, Akiko Soma, Kozo Tomita, Tsutomu Suzuki
Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.
Nat Chem Biol: 2018, 14(11);1010-1020
[PubMed:30150682] [WorldCat.org] [DOI] (I p)

• August 2018
  • Structural maintenance of chromosomes (SMC) complexes shape the genomes of virtually all organisms, but how they function remains incompletely understood. The condensin complexes act along contiguous DNA segments, thus processively enlarging DNA loops. Now, Wang et al. from the lab of David Rudner show that point mutants in the Smc nucleotide-binding domain that impair but do not eliminate ATPase activity not only exhibit delays in de novo loop formation but also have reduced rates of processive loop enlargement. These data provide in vivo evidence that SMC complexes function as loop extruders.
  • Relevant SubtiWiki pages: condensin, David Rudner, Smc, ParB

Xindan Wang, Anna C Hughes, Hugo B Brandão, Benjamin Walker, Carrie Lierz, Jared C Cochran, Martha G Oakley, Andrew C Kruse, David Z Rudner
In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Complex.
Mol Cell: 2018, 71(5);841-847.e5
[PubMed:30100265] [WorldCat.org] [DOI] (I p)

• July 2018
  • Making the right choice for nutrient consumption is essential for bacteria for evolutionary success in a highly competetive environment. Now, Buffing et al. from the lab of Uwe Sauer have studied the regulatory mechanisms that allow dynamic adaptation between non-preferred and preferred carbon sources for Escherichia coli and Bacillus subtilis. The authors show that flux reversal from the preferred glucose to non-preferred pyruvate as the sole carbon source is primarily transcriptionally regulated. In the opposite direction, however, E. coli can reverse its flux instantaneously by means of allosteric regulation, whereas in B. subtilis this flux reversal is transcriptionally regulated.
  • Relevant SubtiWiki pages: metabolism, Uwe Sauer, GlcT, CggR, carbon core metabolism

Marieke F Buffing, Hannes Link, Dimitris Christodoulou, Uwe Sauer
Capacity for instantaneous catabolism of preferred and non-preferred carbon sources in Escherichia coli and Bacillus subtilis.
Sci Rep: 2018, 8(1);11760
[PubMed:30082753] [WorldCat.org] [DOI] (I e)

• June 2018
  • Individual microbial species are occupy distinct metabolic niches within multi-species communities. However, it has remained largely unclear whether metabolic specialization can similarly occur within a clonal bacterial population. More specifically, it is not clear what functions such specialization could provide and how specialization could be coordinated dynamically. Now, Rosenthal et al. from the lab of Michael Elowitz have shown that exponentially growing B. subtilis cultures divide into distinct interacting metabolic subpopulations. These subpopulations exhibit distinct growth rates and dynamic interconversion between states. Their results show that clonal populations can use metabolic specialization to control the environment through a process of dynamic, environmentally-sensitive state-switching.
  • Relevant SubtiWiki pages: metabolism, Michael Elowitz

• May 2018
  • The YaaT, YlbF, and YmcA proteins form a complex that has been implicated in biofilm formation and the control of the phosphorelay. Now, DeLougheri et al. have shown that this complex acts as a specificity factor for RNase Y. The complex is required for the maturation of mRNAs of polycistronic mRNAs (including the well-studied cggR-gapA operon) and for the degradation of many riboswitch RNAs but not for the processing of small ncRNAs
  • Relevant SubtiWiki pages: RNase Y, cggR, gapA, riboswitch, Richard Losick

• April 2018
  • Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. Now, Lalanne et al. have shown that the relative abundance of co-regulated proteins requires precise tuning. Their work demonstrates that many bacterial gene clusters encoding conserved pathways have undergone massive divergence in transcript abundance and architectures via remodeling of internal promoters and terminators. Remarkably, these evolutionary changes are compensated post-transcriptionally to maintain preferred stoichiometry of protein synthesis rates.
  • Relevant SubtiWiki pages: carbon core metabolism, translation

• March 2018
  • ß-lactam antibiotics interfere with cell wall synthesis, and result in cell death. The study by Kawai et al. from the lab of Jeff Errington shows that under conditions of higher osmolarity cell lysis is delayed. Moreover, the cells are additionally protected by lysozyme under these conditions. Lysozyme promotes the formation of L-forms making the bacteria resistant to ß-lactam antibiotics.
  • Relevant SubtiWiki pages: Jeff Errington, cell wall synthesis, penicillin-binding proteins

• February 2018
  • Mutlu et al. discover a "phenotypic memory" which results from the carry-over of nutrients from the vegetative cell into the spore and which links sporulation timing and spore revival. The authors suggest that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits.
  • Relevant SubtiWiki pages: sporulation, Ilka Bischofs, Ald

• January 2018
  • Rojas et al. discover an elegant feedback mechanism ensuring balanced membrane and cell-wall growth in Bacillus subtilis through mechanically induced electrical depolarization that transiently halts wall synthesis.
  • Relevant SubtiWiki pages: cell wall synthesis, cell shape, Mbl

2016

• June 2016
  • The analysis of the functions of essential genes and proteins is hampered by the intrinsic impossibility to construct deletion mutants. Now Peters et al. from the lab of Carol Gross have constructed a library of knock-down strains for all essential genes of B. subtilis.
  • Relevant SubtiWiki pages: Carol Gross, essential genes

• 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

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

• See comments on this issue:

• August 2015
  • The cells in a biofilm experience very different conditions: While the inner cells are well protected from any harm from the environment, they have on the other hand only poor access to nutrients. For the cells on the edge of the biofilm, it is just the other way round. Now, Liu et al. from the lab of Gürol M. Süel have discovered oscillation in the growth of the biofilm. These oscillations serve to provide the inner cells with access to nutrients. These oscillations are caused by metabolic co-dependence between cells in the biofilm periphery and interior that is driven by glutamate consumption and ammonium production, respectively.
  • Relevant SubtiWiki pages: Gürol M. Süel, glutamate consumption and ammonium production, biofilm formation
  • see a blog presenting this paper

• July 2015
  • The precise functions of serine protein kinases in B. subtilis have largely remained enigmatic until very recently. Now, two studies from the lab of Jonathan Dworkin describe functions and molecular targets for two of these kinases, PrkC and YabT. Pereira et al. have identified the universally conserved elongation factor Tu as a target for the protein kinase YabT. In srarving cells, YabT phosphorylates EF-Tu at a conserved threonine residue. Phosphorylation impairs the essential GTPase activity of EF-Tu, thereby preventing its release from the ribosome. As a consequence, phosphorylated EF-Tu has a dominant-negative effect in translation elongation, resulting in the overall inhibition of protein synthesis. Importantly, this mechanism allows a quick and robust regulation of one of the most abundant cellular proteins. Libby et al. have uncovered that phosphorylation by PrkC stimulates the activity of the essential two-component transcription factor WalR. This mechanism links the presence of muropeptides that trigger PrkC activity to the expression of the genes of the WalR regulon that are involved in cell wall metabolism.
  • Relevant SubtiWiki pages: Jonathan Dworkin, protein kinases, YabT, EF-Tu, PrkC, WalR, cell wall metabolism

• 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

• 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

• April 2015
  • In a groundbreaking study from 2004, several candidate riboswitches have been discovered in Bacillus subtilis. While the ydaO riboswitch has recently been discovered to be a target of the second messenger c-di-AMP, two new studies identify manganese ions as the ligand of the yybP-ykoY motif that controls the expression of the yybP and ykoY genes. Both genes are induced in the presence of Mn²⁺, due to the interaction of the ion with the riboswitch. This finding implies that YybP and YkoY, which have not yet been functionally studied, are implicated in the control of manganese homeostasis.
  • Relevant SubtiWiki pages: yybP-ykoY motif, riboswitch, yybP, ykoY, John Helmann

• March 2015
  • In Bacillus subtilis, nitrogen acquisition is controlled by protein-protein interactions. Regulation is brought about by interactions of the trigger enzymes glutamine synthetase with the transcription factors TnrA and GlnR to inhibit or trigger their DNA-binding activity, respectively, and by the PII protein NrgB that also interacts with TnrA. Now, Schumacher et al. have solved the structures of several complexes involved in nitrogen sensing. The results unravel so far unprecendented mechanisms for metabolic reprogramming of the cell in response to nitrogen availability.
  • Relevant SubtiWiki pages: GlnA, trigger enzymes, TnrA, GlnR, NrgB

• 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

• 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

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

• 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

• • See also:

• 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

• September 2014
  • Cyclic di-AMP is the only known essential second messenger. In B. subtilis, it binds the potassium transporter KtrA and the ydaO riboswitch. This riboswitch occurs twice in the genome of B. subtilis: in the untranslated regions of the ydaO gene and the ktrA-ktrB operon. Now, two studies by Ren and Patel and Gao and Serganov report the structure of ydaO riboswitch bound to c-di-AMP. Unexpectedly, the riboswitch structure features two three-way junctions, a turn and a pseudoknot and binds two stapled c-di-AMP molecules.
  • Relevant SubtiWiki pages: riboswitch, YdaO riboswitch, ktrA, metabolism of signalling nucleotides

• 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

• 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

• 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

• See a comment on this issue:

• May 2014
  • The knowledge about absolute numbers of molecules of a given protein is often important, e. g. in the context of systems biology or to evaluate the relevance of experimentally observed protein-protein interactions. Muntel et al. from the lab of Dörte Becher have now determined absolute protein concentrations for about 1,000 cytosolic proteins. The results of this study have been added to the SubtiWiki gene pages (see # Expression and regulation). In this study, flagellin was found to be the most abundant protein of B. subtilis.
  • Relevant SubtiWiki pages: Dörte Becher, Michael Hecker, Vincent Fromion, Ulrike Mäder, genome-wide analyses, protein-protein interactions, most abundant proteins

• April 2014
  • DNA repair and recombination involve the unwinding and digestion of the DNA duplex by the AddA-AddB complex from the broken end until they encounter a χ sequence, whereupon the proteins produce a 3′ single-stranded DNA tail onto which they initiate loading of the RecA protein. Now, two studies from the lab of Mark Dillingham address the structure of AddA-AddB complexed to a χ sequence, and the effect of χ binding for processivity and ATP hydrolysis by AddA-AddB.
  • Relevant SubtiWiki pages: Mark Dillingham, DNA repair/ recombination, AddA, AddB

• March 2014
  • In a retracted paper from the labs of Roberto Kolter and Richard Losick PubMed it was reported that B. subtilis synthesizes norspermidine and that this compound is involved in biofilm disassembly. Now, Hobley et al. from the lab of Nicola Stanley-Wall provide compelling evidence that B. subtilis does not produce norspermidine, that previous function annotations of a norspermidine biosynthetic pathway were made in error, and that norspermidine stimulates biofilm formation.
  • Relevant SubtiWiki pages: Nicola Stanley-Wall, biofilm formation, YaaO, GabT

• February 2014
  • Bacteria use quorum sensing to coordinate their behaviour. In B. subtilis, quorum sensing requires the ComX peptide which is sensed by the ComP-ComA two-component system. Now, Oslizlo et al. from the lab of Ines Mandic-Mulec demonstrate that ComQ combines intra- and extracellular sensing, and the authors suggest that this ensures the generation of evolutionarily stable quorum sensing systems.
  • Relevant SubtiWiki pages: Ines Mandic-Mulec, quorum sensing, ComX, ComQ, ComP, ComA

• January 2014
  • The expression of ribosomal proteins is often subject to feedback regulation by the binding of ribosomal proteins to their mRNA leaders. A new study by Fu et al. demonstrate that a heterodimer of RpsF and RpsR binds a structure in the mRNA leader of the rpsF-ssbA-rpsR operon and suggests autoregulation
  • Relevant SubtiWiki pages: ribosomal proteins, RpsF, RpsR

2013

• December 2013
  • Intercellular signaling requires the transfer of information between two different cells. Now, Mastny et al. from the labs of David Rudner and Tim Clausen show how the protease CtpB is activated by substrate binding to cleave off the inhibitory domain of SpoIVFA to allow ultimately allow processing of pro-SigK by SpoIVFB.
  • Relevant SubtiWiki pages: David Rudner, sporulation, CtpB, SpoIVB, SpoIVFA, SpoIVFB

• 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

• October 2013
  • To initiate DNA replication, the DNA helicase has to bind the oriC region of the chromosome. This binding is assisted by the helicase loader protein. Moreover, the DNA helicase recruits the DNA primase to synthesize RNA primers. Now, Liu et al. determined the structure of the DnaC-DnaI-DnaG complex and present novel insights into insights the mechanism of bacterial primosome assembly.
  • Relevant SubtiWiki pages: DnaC, DnaI, DnaG, SubtInteract, replisome, DNA replication

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

• • A comment on this paper:

• 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)

• 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

• 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)

• April 2013
  • Usually, cell wall synthesis is regarded as being essential for B. subtilis. Now, Mercier et al. from the lab of Jeff Errington show that excess biosynthesis of membranes is sufficient to drive the formation of cell wall-less L-forms in B. subtilis. Interestingly, this cell form is even independent of the essential cell division protein FtsZ.
  • Relevant SubtiWiki pages: Jeff Errington, biosynthesis of lipids, cell wall synthesis, cell division, FtsZ

• 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

• 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)

• February 2013
  • For many essential genes of B. subtilis, it is not clear why they are essential in B. subtilis but not in closely related species. Strikingly, this is the case for RNases such as RNases III and Y. Now, Durand et al. from the lab of Ciaran Condon have identified the reason for the essentiality of RNase III: This enzyme is required to degrade phage encoded toxin mRNA molecules thus protecting the cell from lysis caused by the encoded toxins. Indeed, RNase III is dispensable in a strain lacking the Skin element and the SPß prophage that harbor the corresponding toxin genes.
  • Relevant SubtiWiki pages: Ciaran Condon, RNase III, essential genes, yonT, txpA, toxins, antitoxins and immunity against toxins

• 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:

• January 2013
  • Castaing et al. from the lab of Kumaran Ramamurthi show how ATP hydrolysis drives the self-association of SpoIVA into nucleotide-free filaments which then serve as a platform for the assembly of the spore coat starting with SpoVM. Together with the december's paper of the month these works demonstrate how ATP hydrolysis may contribute to different processes within a protein such as global conformational changes and self-assembly.
  • Relevant SubtiWiki pages: Kumaran Ramamurthi, SpoIVA, sporulation

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

• 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

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)

• 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 report that D-amino acids and norspermidine act together in preventing biofilm formation and triggering biofilm disassembly. However, this was shown to be wrong in February 2014 (see Paper of the month, Feb. 2014) and the paper has been retracted.

• 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

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)

• 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

• A comment on these papers:

• 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

• 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

2011

• December 2011
  • Bange et al. from the lab of Irmgard Sinning show how the FlhG 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, FlhG, signal recognition particle, motility and chemotaxis

• 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

• 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)

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)

• 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:

• 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

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)