scholarly journals Special Issue “Bacillus subtilis as a Model Organism to Study Basic Cell Processes”

2021 ◽  
Vol 9 (12) ◽  
pp. 2459
Author(s):  
Imrich Barák
Keyword(s):  
Bacillus Subtilis ◽  
Model Organism ◽  
Special Issue ◽  
Basic Cell ◽  
Cell Processes

Bacillus subtilis has served as a model microorganism for many decades [...]

scholarly journals Physiology of guanosine-based second messenger signaling in Bacillus subtilis

2020 ◽  
Vol 401 (12) ◽  
pp. 1307-1322
Author(s):  
Gert Bange ◽  
Patricia Bedrunka
Keyword(s):  
Bacillus Subtilis ◽  
Biofilm Formation ◽  
Second Messengers ◽  
Model Organism ◽  
Physiological Regulation ◽  
Open Questions ◽  
Key Players ◽  
Stress Signals ◽  
Second Messenger Signaling ◽  
Synthesis And Degradation

AbstractThe guanosine-based second messengers (p)ppGpp and c-di-GMP are key players of the physiological regulation of the Gram-positive model organism Bacillus subtilis. Their regulatory spectrum ranges from key metabolic processes over motility to biofilm formation. Here we review our mechanistic knowledge on their synthesis and degradation in response to environmental and stress signals as well as what is known on their cellular effectors and targets. Moreover, we discuss open questions and our gaps in knowledge on these two important second messengers.

scholarly journals Quantification and Isolation ofBacillus subtilisSpores using Cell Sorting and automated Gating

2019 ◽  
Author(s):  
Marianna Karava ◽  
Felix Bracharz ◽  
Johannes Kabisch
Keyword(s):  
Bacillus Subtilis ◽  
Cell Sorting ◽  
Fluorescent Dyes ◽  
Model Organism ◽  
Gaussian Mixture ◽  
Spore Formation ◽  
Gene Encoding ◽  
Knock Out ◽  
Optimal Separation ◽  
Genome Modifications

AbstractThe Gram-positive bacteriumBacillus subtilisis able to form endospores which have a variety of biotechnological applications. Due to this ability,B. subtilisis as well a model organism for cellular differentiation processes. Sporulating cultures ofBacillus subtilisform sub-populations which include vegetative cells, spore forming cells and spores. In order to readily and rapidly quantify spore formation we employed flow cytometric and fluorescence activated cell sorting techniques in combination with nucleic acid fluorescent staining in order to investigate the distribution of sporulating cultures on a single cell level. Moreover we tested different fluorescent dyes as well as different conditions in order to develop a method for optimal separation of distinct populations during sporulation. Automated gating procedures using k-means clustering and thresholding by gaussian mixture modeling were employed to avoid subjective gating and allow for the simultaneous measurement of controls. We utilized the presented method for monitoring sporulation over time in strains harboring different genome modifications. We identified the different subpopulations formed during sporulation by employing sorting and microscopy. Finally, we employed the technique to show that a double knock-out mutant of the phosphatase gene encoding Spo0E and of the spore killing factor SkfA results in faster spore formation.

scholarly journals The Dictyostelium discoideum model system

2019 ◽  
Vol 63 (8-9-10) ◽  
pp. 317-320 ◽  
Author(s):  
Ricardo Escalante ◽  
Elena Cardenal-Muñoz
Keyword(s):  
Cell Motility ◽  
Dictyostelium Discoideum ◽  
Cell Biology ◽  
Model Organism ◽  
Opportunity To Learn ◽  
Model System ◽  
Special Issue ◽  
Complete Understanding ◽  
Single Model ◽  
Present Collection

When we set out to organize this Special Issue, we faced the difficult task of gathering together a large variety of topics with the unique commonality of having been studied in a single model organism, Dictyostelium discoideum. This apparent setback turned into a wonderful opportunity to learn about an organism as a whole, which provides a more complete understanding of life processes, their natural meaning and their changes during evolution. From studies dedicated almost exclusively to cell motility, differentiation and patterning, the versatility of D. discoideum has allowed in recent years the expansion of our knowledge to other areas, including cell biology and many others related to human diseases. The present collection of papers can be considered as a journey throughout the mechanisms of life, where D. discoideum acts as a very special tourist guide.

scholarly journals σIfromBacillus subtilis: Impact on Gene Expression and Characterization of σI-Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements

2018 ◽  
Vol 200 (17) ◽  
Author(s):  
Olga Ramaniuk ◽  
Martin Převorovský ◽  
Jiří Pospíšil ◽  
Dragana Vítovská ◽  
Olga Kofroňová ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Iron Metabolism ◽  
Transcription Initiation ◽  
Iron Homeostasis ◽  
Model Organism ◽  
Content Type ◽  
Σ Factor

ABSTRACTThe σIsigma factor fromBacillus subtilisis a σ factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and σI-null strains at 37°C and 52°C, we identified ∼130 genes affected by the absence of σI. Further analysis revealed that the majority of these genes were affected indirectly by σI. The σIregulon, i.e., the genes directly regulated by σI, consists of 16 genes, of which eight (thedhbandykuoperons) are involved in iron metabolism. The involvement of σIin iron metabolism was confirmed phenotypically. Next, we set up anin vitrotranscription system and defined and experimentally validated the promoter sequence logo that, in addition to −35 and −10 regions, also contains extended −35 and −10 motifs. Thus, σI-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored σ factor from the industrially important model organismB. subtilis.IMPORTANCEIn bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the σIregulon from the industrially important model Gram-positive bacteriumBacillus subtilis. We reveal that σIaffects expression of ∼130 genes, of which 16 are directly regulated by σI, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σI-dependent transcription. This study thus provides a comprehensive view on this underexplored component of theB. subtilistranscription machinery.

scholarly journals Dynamic Membrane Localization of RNase Y in Bacillus subtilis

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Lina Hamouche ◽  
Cyrille Billaudeau ◽  
Anna Rocca ◽  
Arnaud Chastanet ◽  
Saravuth Ngo ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Active Form ◽  
Model Organism ◽  
Living Cells ◽  
Cell Periphery ◽  
Rnase E ◽  
Content Type ◽  
Endonucleolytic Cleavage ◽  
Rnase Y

ABSTRACT Metabolic turnover of mRNA is fundamental to the control of gene expression in all organisms, notably in fast-adapting prokaryotes. In many bacteria, RNase Y initiates global mRNA decay via an endonucleolytic cleavage, as shown in the Gram-positive model organism Bacillus subtilis. This enzyme is tethered to the inner cell membrane, a pseudocompartmentalization coherent with its task of initiating mRNA cleavage/maturation of mRNAs that are translated at the cell periphery. Here, we used total internal reflection fluorescence microscopy (TIRFm) and single-particle tracking (SPT) to visualize RNase Y and analyze its distribution and dynamics in living cells. We find that RNase Y diffuses rapidly at the membrane in the form of dynamic short-lived foci. Unlike RNase E, the major decay-initiating RNase in Escherichia coli, the formation of foci is not dependent on the presence of RNA substrates. On the contrary, RNase Y foci become more abundant and increase in size following transcription arrest, suggesting that they do not constitute the most active form of the nuclease. The Y-complex of three proteins (YaaT, YlbF, and YmcA) has previously been shown to play an important role for RNase Y activity in vivo. We demonstrate that Y-complex mutations have an effect similar to but much stronger than that of depletion of RNA in increasing the number and size of RNase Y foci at the membrane. Our data suggest that the Y-complex shifts the assembly status of RNase Y toward fewer and smaller complexes, thereby increasing cleavage efficiency of complex substrates like polycistronic mRNAs. IMPORTANCE All living organisms must degrade mRNA to adapt gene expression to changing environments. In bacteria, initiation of mRNA decay generally occurs through an endonucleolytic cleavage. In the Gram-positive model organism Bacillus subtilis and probably many other bacteria, the key enzyme for this task is RNase Y, which is anchored at the inner cell membrane. While this pseudocompartmentalization appears coherent with translation occurring primarily at the cell periphery, our knowledge on the distribution and dynamics of RNase Y in living cells is very scarce. Here, we show that RNase Y moves rapidly along the membrane in the form of dynamic short-lived foci. These foci become more abundant and increase in size following transcription arrest, suggesting that they do not constitute the most active form of the nuclease. This contrasts with RNase E, the major decay-initiating RNase in E. coli, where it was shown that formation of foci is dependent on the presence of RNA substrates. We also show that a protein complex (Y-complex) known to influence the specificity of RNase Y activity in vivo is capable of shifting the assembly status of RNase Y toward fewer and smaller complexes. This highlights fundamental differences between RNase E- and RNase Y-based degradation machineries.

scholarly journals Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis

Microbiology ◽  
2010 ◽  
Vol 156 (3) ◽  
pp. 849-859 ◽  
Author(s):  
Christoph R. Lammers ◽  
Lope A. Flórez ◽  
Arne G. Schmeisky ◽  
Sebastian F. Roppel ◽  
Ulrike Mäder ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Model Organism ◽  
Online Tool ◽  
Gram Positive Bacteria ◽  
Web Resource ◽  
Link Type ◽  
Pathway Annotation ◽  
Online Databases ◽  
Online Tools ◽  
Intuitive Interface

Bacillus subtilis is the model organism for a large group of Gram-positive bacteria, the Firmicutes. Several online databases have been established over time to manage its genetic and metabolic information, but they differ greatly in their rate of update and their focus on B. subtilis. Therefore, a European systems biology consortium called for an integrated solution that empowers its users to enrich online content. To meet this goal we created SubtiWiki and SubtiPathways, two complementary online tools for gene and pathway information on B. subtilis 168. SubtiWiki (http://subtiwiki.uni-goettingen.de/) is a scientific wiki for all genes of B. subtilis and their protein or RNA products. Each gene page contains a summary of the most important information; sections on the gene, its product and expression; sections concerning biological materials and laboratories; and a list of references. SubtiWiki has been seeded with key content and can be extended by any researcher after a simple registration, thus keeping it always up to date. As a complement, SubtiPathways (http://subtipathways.uni-goettingen.de/) is an online tool for navigation of the metabolism of B. subtilis and its regulation. Each SubtiPathways diagram presents a metabolic pathway with its participating enzymes, together with the regulatory mechanisms that act on their expression and activity, in an intuitive interface that is based on Google Maps. Together, SubtiWiki and SubtiPathways provide an integrated view of the processes that make up B. subtilis and its components, making it the most comprehensive web resource for B. subtilis researchers.

scholarly journals Thio Derivatives of 2(5H)-Furanone As Inhibitors against Bacillus subtilis Biofilms

Acta Naturae ◽  
2015 ◽  
Vol 7 (2) ◽  
pp. 102-107 ◽  
Author(s):  
E. Yu. Trizna ◽  
E. N. Khakimullina ◽  
L. Z. Latypova ◽  
A. R. Kurbangalieva ◽  
I. S. Sharafutdinov ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Biofilm Formation ◽  
Wide Spectrum ◽  
Model Organism ◽  
Human Immune System ◽  
Gram Positive ◽  
Bacterium Bacillus Subtilis ◽  
Bacterial Sensitivity ◽  
Bacterium Bacillus ◽  
Derivatives Of

Gram-positive bacteria cause a wide spectrum of infectious diseases, including nosocomial infections. While in the biofilm, bacteria exhibit increased resistance to antibiotics and the human immune system, causing difficulties in treatment. Thus, the development of biofilm formation inhibitors is a great challenge in pharmacology. The gram-positive bacterium Bacillus subtilis is widely used as a model organism for studying biofilm formation. Here, we report on the effect of new synthesized 2(5Н)-furanones on the biofilm formation by B.subtilis cells. Among 57 compounds tested, sulfur-containing derivatives of 2(5H)-furanone (F12, F15, and F94) repressed biofilm formation at a concentration of 10 g/ml. Derivatives F12 and F94 were found to inhibit the biosynthesis of GFP from the promoter of the eps operon encoding genes of the biofilm exopolysaccharide synthesis (EPS). Using the differential fluorescence staining of alive/dead cells, we demonstrated an increased bacterial sensitivity to antibiotics (kanamycin and chloramphenicol) in the presence of F12, F15, and F94, with F12 being the most efficient one. The derivative F15 was capable of disrupting an already formed biofilm and thereby increasing the efficiency of antibiotics.

scholarly journals Dynamics of the Bacillus subtilis Min system

2020 ◽  
Author(s):  
Helge Feddersen ◽  
Laeschkir Würthner ◽  
Erwin Frey ◽  
Marc Bramkamp
Keyword(s):  
Bacillus Subtilis ◽  
Active Sites ◽  
Dynamic Equilibrium ◽  
Model Organism ◽  
Physical Modelling ◽  
Division Site ◽  
Diffusion Constants ◽  
Dynamic Equilibrium State ◽  
Min Proteins

SummaryDivision site selection is a vital process to ensure generation of viable offspring. In many rod-shaped bacteria a dynamic protein system, termed the Min system, acts as a central regulator of division site placement. The Min system is best studied in Escherichia coli where it shows a remarkable oscillation from pole to pole with a time-averaged density minimum at midcell. Several components of the Min system are conserved in the Gram-positive model organism Bacillus subtilis. However, in B. subtilis it is believed that the system forms a stationary bipolar gradient from the cell poles to midcell. Here, we show that the Min system of B. subtilis localizes dynamically to active sites of division, often organized in clusters. We provide physical modelling using measured diffusion constants that describe the observed enrichment of the Min system at the septum. Modelling suggests that the observed localization pattern of Min proteins corresponds to a dynamic equilibrium state. Our data provide evidence for the importance of ongoing septation for the Min dynamics, consistent with a major role of the Min system to control active division sites, but not cell pole areas.

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