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 An Essential Poison: Synthesis and Degradation of Cyclic Di-AMP in Bacillus subtilis

2015 ◽  
Vol 197 (20) ◽  
pp. 3265-3274 ◽  
Author(s):  
Jan Gundlach ◽  
Felix M. P. Mehne ◽  
Christina Herzberg ◽  
Jan Kampf ◽  
Oliver Valerius ◽  
...  
Keyword(s):  
Cell Wall ◽  
Bacillus Subtilis ◽  
Nitrogen Source ◽  
Second Messengers ◽  
Regulatory Protein ◽  
Control Cell ◽  
Model Organism ◽  
Second Messenger ◽  
Content Type ◽  
Gram Positive Bacteria

ABSTRACTGram-positive bacteria synthesize the second messenger cyclic di-AMP (c-di-AMP) to control cell wall and potassium homeostasis and to secure the integrity of their DNA. In the firmicutes, c-di-AMP is essential for growth. The model organismBacillus subtilisencodes three diadenylate cyclases and two potential phosphodiesterases to produce and degrade c-di-AMP, respectively. Among the three cyclases, CdaA is conserved in nearly all firmicutes, and this enzyme seems to be responsible for the c-di-AMP that is required for cell wall homeostasis. Here, we demonstrate that CdaA localizes to the membrane and forms a complex with the regulatory protein CdaR and the glucosamine-6-phosphate mutase GlmM. Interestingly,cdaA,cdaR, andglmMform a gene cluster that is conserved throughout the firmicutes. This conserved arrangement and the observed interaction between the three proteins suggest a functional relationship. Our data suggest that GlmM and GlmS are involved in the control of c-di-AMP synthesis. These enzymes convert glutamine and fructose-6-phosphate to glutamate and glucosamine-1-phosphate. c-di-AMP synthesis is enhanced if the cells are grown in the presence of glutamate compared to that in glutamine-grown cells. Thus, the quality of the nitrogen source is an important signal for c-di-AMP production. In the analysis of c-di-AMP-degrading phosphodiesterases, we observed that both phosphodiesterases, GdpP and PgpH (previously known as YqfF), contribute to the degradation of the second messenger. Accumulation of c-di-AMP in agdpP pgpHdouble mutant is toxic for the cells, and the cells respond to this accumulation by inactivation of the diadenylate cyclase CdaA.IMPORTANCEBacteria use second messengers for signal transduction. Cyclic di-AMP (c-di-AMP) is the only second messenger known so far that is essential for a large group of bacteria. We have studied the regulation of c-di-AMP synthesis and the role of the phosphodiesterases that degrade this second messenger. c-di-AMP synthesis strongly depends on the nitrogen source: glutamate-grown cells produce more c-di-AMP than glutamine-grown cells. The accumulation of c-di-AMP in a strain lacking both phosphodiesterases is toxic and results in inactivation of the diadenylate cyclase CdaA. Our results suggest that CdaA is the critical diadenylate cyclase that produces the c-di-AMP that is both essential and toxic upon accumulation.

scholarly journals A Modification of Cell-Lysis for High-Quality Intact RNA of Bacillus Subtilis Extracted From the Culture Under Different Physiological Stages

2021 ◽  
Author(s):  
Phetcharat Jaiaue ◽  
Piroonporn Srimong ◽  
Sitanan Thitiprasert ◽  
Somboon Tanasupawat ◽  
Benjamas Cheirsilp ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Rna Extraction ◽  
Model Organism ◽  
Cell Lysis ◽  
Protein Precipitation ◽  
Absolute Ethanol ◽  
Process Conditions ◽  
High Quality ◽  
Gram Positive ◽  
Gram Positive Bacteria

Abstract High quality RNA products from bacterial cells are required for the molecular study. Sample preparation to acquire the high-quality RNA especially the Gram-positive bacteria like Bacillus sp., the model organism, remains a critical burden toward the integration of full molecular downstream analyses although several methods have been proposed including conventional or kit-based protocols. Those techniques were simply developed using the cell samples at certain growth stages unless some molecular studies require RNA samples gathered under different physiological stages of growth and process conditions. Herein, we developed the simple yet effective cell-lysis technique prior to RNA extraction by modifying the commercial kit-based protocols. Bacillus subtilis TL7-3 was used as the model organism in this study. Lysozyme loading (20 mg/mL) as well as the incubation time (30 min) and temperature (37 °C) was responsible for cell lysis and increased RNA concentration in the samples. Invert mixing rather than centrifugation and vortexing prevented RNA damage during protein precipitation by absolute ethanol. This was confirmed by the RNA Integrity Number (RIN) values greater than 8.0 of all RNA extracted from both vegetative cells and endospores of B. subtilis TL7-3. Additionally, absolute ethanol is preferable to our less-than-1-h protocol for protein precipitation as indicated from the higher ratios of A260/A280 and those of A260/A230 of the RNA products than 2.0 and 2.1, respectively. From the findings mentioned above, we successfully developed the modified RNA extraction protocol applicable for the intact cells of Gram-positive bacteria like Bacillus sp. at varied physiological and morphological stages.

Synthesis of Chalcones and Nucleosides Incorporating [1, 3, 4]Oxadiazolenone Core and Evaluation of their Antifungal and Antibacterial Activities

2020 ◽  
Vol 15 (6) ◽  
pp. 665-679
Author(s):  
Alok K. Srivastava ◽  
Lokesh K. Pandey
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Antibacterial Activity ◽  
Bacillus Subtilis ◽  
Antifungal Activity ◽  
Aspergillus Niger ◽  
Gram Negative ◽  
E Coli ◽  
Gram Positive Bacteria ◽  
Good Antibacterial Activity

Background: [1, 3, 4]oxadiazolenone core containing chalcones and nucleosides were synthesized by Claisen-Schmidt condensation of a variety of benzaldehyde derivatives, obtained from oxidation of substituted 5-(3/6 substituted-4-Methylphenyl)-1, 3, 4-oxadiazole-2(3H)-one and various substituted acetophenone. The resultant chalcones were coupled with penta-O-acetylglucopyranose followed by deacetylation to get [1, 3, 4] oxadiazolenone core containing chalcones and nucleosides. Various analytical techniques viz IR, NMR, LC-MS and elemental analysis were used to confirm the structure of the synthesised compounds.The compounds were targeted against Bacillus subtilis, Staphylococcus aureus and Escherichia coli for antibacterial activity and Aspergillus flavus, Aspergillus niger and Fusarium oxysporum for antifungal activity. Methods: A mixture of Acid hydrazides (3.0 mmol) and N, Nʹ- carbonyl diimidazole (3.3 mmol) in 15 mL of dioxane was refluxed to afford substituted [1, 3, 4]-oxadiazole-2(3H)-one. The resulted [1, 3, 4]- oxadiazole-2(3H)-one (1.42 mmol) was oxidized with Chromyl chloride (1.5 mL) in 20 mL of carbon tetra chloride and condensed with acetophenones (1.42 mmol) to get chalcones 4. The equimolar ratio of obtained chalcones 4 and β -D-1,2,3,4,6- penta-O-acetylglucopyranose in presence of iodine was refluxed to get nucleosides 5. The [1, 3, 4] oxadiazolenone core containing chalcones 4 and nucleosides 5 were tested to determined minimum inhibitory concentration (MIC) value with the experimental procedure of Benson using disc-diffusion method. All compounds were tested at concentration of 5 mg/mL, 2.5 mg/mL, 1.25 mg/mL, 0.62 mg/mL, 0.31 mg/mL and 0.15 mg/mL for antifungal activity against three strains of pathogenic fungi Aspergillus flavus (A. flavus), Aspergillus niger (A. niger) and Fusarium oxysporum (F. oxysporum) and for antibacterial activity against Gram-negative bacterium: Escherichia coli (E. coli), and two Gram-positive bacteria: Staphylococcus aureus (S. aureus) and Bacillus subtilis(B. subtilis). Result: The chalcones 4 and nucleosides 5 were screened for antibacterial activity against E. coli, S. aureus and B. subtilis whereas antifungal activity against A. flavus, A. niger and F. oxysporum. Compounds 4a-t showed good antibacterial activity whereas compounds 5a-t containing glucose moiety showed better activity against fungi. The glucose moiety of compounds 5 helps to enter into the cell wall of fungi and control the cell growth. Conclusion: Chalcones 4 and nucleosides 5 incorporating [1, 3, 4] oxadiazolenone core were synthesized and characterized by various spectral techniques and elemental analysis. These compounds were evaluated for their antifungal activity against three fungi; viz. A. flavus, A. niger and F. oxysporum. In addition to this, synthesized compounds were evaluated for their antibacterial activity against gram negative bacteria E. Coli and gram positive bacteria S. aureus, B. subtilis. Compounds 4a-t showed good antibacterial activity whereas 5a-t showed better activity against fungi.

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 In Vitro Characterization of the Bacillus subtilis Protein Tyrosine Phosphatase YwqE

2005 ◽  
Vol 187 (10) ◽  
pp. 3384-3390 ◽  
Author(s):  
Ivan Mijakovic ◽  
Lucia Musumeci ◽  
Lutz Tautz ◽  
Dina Petranovic ◽  
Robert A. Edwards ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Tyrosine Phosphatase ◽  
Protein Tyrosine Phosphatases ◽  
Class Ii ◽  
Gram Positive ◽  
Protein Tyrosine ◽  
Gram Positive Bacteria ◽  
New Family ◽  
In Vitro Characterization

ABSTRACT Both gram-negative and gram-positive bacteria possess protein tyrosine phosphatases (PTPs) with a catalytic Cys residue. In addition, many gram-positive bacteria have acquired a new family of PTPs, whose first characterized member was CpsB from Streptococcus pneumoniae. Bacillus subtilis contains one such CpsB-like PTP, YwqE, in addition to two class II Cys-based PTPs, YwlE and YfkJ. The substrates for both YwlE and YfkJ are presently unknown, while YwqE was shown to dephosphorylate two phosphotyrosine-containing proteins implicated in UDP-glucuronate biosynthesis, YwqD and YwqF. In this study, we characterize YwqE, compare the activities of the three B. subtilis PTPs (YwqE, YwlE, and YfkJ), and demonstrate that the two B. subtilis class II PTPs do not dephosphorylate the physiological substrates of YwqE.

scholarly journals AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens

Microbiology ◽  
2020 ◽  
Vol 166 (1) ◽  
pp. 73-84 ◽  
Author(s):  
Cristina Bez ◽  
Sree Gowrinadh Javvadi ◽  
Iris Bertani ◽  
Giulia Devescovi ◽  
Corrado Guarnaccia ◽  
...  
Keyword(s):  
Azelaic Acid ◽  
Type Species ◽  
Isocitrate Lyase ◽  
Model Organism ◽  
Transcriptional Regulator ◽  
Sole Source ◽  
Bacterial Degradation ◽  
Content Type ◽  
Link Type ◽  
Pseudomonas Nitroreducens

Azelaic acid is a dicarboxylic acid that has recently been shown to play a role in plant-bacteria signalling and also occurs naturally in several cereals. Several bacteria have been reported to be able to utilize azelaic acid as a unique source of carbon and energy, including Pseudomonas nitroreducens . In this study, we utilize P. nitroreducens as a model organism to study bacterial degradation of and response to azelaic acid. We report genetic evidence of azelaic acid degradation and the identification of a transcriptional regulator that responds to azelaic acid in P. nitroreducens DSM 9128. Three mutants possessing transposons in genes of an acyl-CoA ligase, an acyl-CoA dehydrogenase and an isocitrate lyase display a deficient ability in growing in azelaic acid. Studies on transcriptional regulation of these genes resulted in the identification of an IclR family repressor that we designated as AzeR, which specifically responds to azelaic acid. A bioinformatics survey reveals that AzeR is confined to a few proteobacterial genera that are likely to be able to degrade and utilize azelaic acid as the sole source of carbon and energy.

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.

Using Online Tools to Support Technology Integration in Education

2009 ◽  
pp. 389-402 ◽  
Author(s):  
Jo Tondeur ◽  
Arno Coenders ◽  
Johan van Braak ◽  
Alfons ten Brummelhuis ◽  
Ruben Vanderlinde
Keyword(s):  
Technology Integration ◽  
Primary Education ◽  
Assessment Tool ◽  
Online Tool ◽  
Good Education ◽  
Knowledge And Skills ◽  
Online Tools ◽  
Information And Communication ◽  
Insight Into ◽  
Selection Of

This chapter explores the possibilities of online tools to support ICT (Information and Communication Technology) integration in primary education. Before describing three valuable tools, a framework will be discussed which gives schools insight into the most important preconditions for successful use of ICT in relation to the selection of a specific tool. Consequently, three specific tools are described: (1) the “Four in Balance” tool measures a school’s current use of ICT, (2) the “ICT-Assessment tool” focuses on teachers’ knowledge and skills and corresponds with the school’s vision on ‘good’ education, and (3) “pICTos”, an online tool that supports the process of ICT planning in schools. These examples illustrate how the tools operate and their many possibilities.

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