scholarly journals Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth

2021 ◽  
Vol 9 (1) ◽  
pp. 112
Author(s):  
Jiri Vohradsky ◽  
Marek Schwarz ◽  
Olga Ramaniuk ◽  
Olatz Ruiz-Larrabeiti ◽  
Viola Vaňková Hausnerová ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Kinetic Modeling ◽  
Spore Germination ◽  
Meta Analysis ◽  
Promoter Sequence ◽  
Binding Motif ◽  
The Past ◽  
New Information ◽  
Expression Kinetic ◽  
Sequence Characteristics

The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expression kinetic modeling and promoter sequence analysis. This approach allowed us to identify the regulon of Bacillus subtilis sigma factor SigB of RNA polymerase (RNAP) specifically expressed during germination and outgrowth. SigB is critical for the cell’s response to general stress but is also expressed during spore germination and outgrowth, and this specific regulon is not known. This approach allowed us to (i) define a subset of the known SigB regulon controlled by SigB specifically during spore germination and outgrowth, (ii) identify the influence of the promoter sequence binding motif organization on the expression of the SigB-regulated genes, and (iii) suggest additional sigma factors co-controlling other SigB-dependent genes. Experiments then validated promoter sequence characteristics necessary for direct RNAP–SigB binding. In summary, this work documents the potential of computational approaches to unravel new information even for a well-studied system; moreover, the study specifically identifies the subset of the SigB regulon, which is activated during germination and outgrowth.

The Ego Could Be Depleted, Providing Initial Exertion Is Depleting

2017 ◽  
Vol 48 (4) ◽  
pp. 242-245 ◽  
Author(s):  
Junhua Dang ◽  
Ying Liu ◽  
Xiaoping Liu ◽  
Lihua Mao
Keyword(s):  
Stroop Task ◽  
Meta Analysis ◽  
Ego Depletion ◽  
Current Experiment ◽  
The Past ◽  
Depletion Effect

Abstract. The ego depletion effect has been examined by over 300 independent studies during the past two decades. Despite its pervasive influence, recently this effect has been severely challenged and asserted to be a fake. Based on an up-to-date meta-analysis that examined the effectiveness of each frequently used depleting task, we preregistered the current experiment with the aim to examine whether there would be an ego depletion effect when the Stroop task is used as the depleting task. The results demonstrated a significant ego depletion effect. The current research highlights the importance of the depleting task’s effectiveness. That is to say, the “ego” could be “depleted,” but only when initial exertion is “depleting.”

scholarly journals Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis

2021 ◽  
Vol 22 (7) ◽  
pp. 3793
Author(s):  
Sophie Blinker ◽  
Jocelyne Vreede ◽  
Peter Setlow ◽  
Stanley Brul
Keyword(s):  
Bacillus Subtilis ◽  
Membrane Protein ◽  
Spore Germination ◽  
Structural Information ◽  
Transmembrane Protein ◽  
Homology Modelling ◽  
Water Channel ◽  
Md Simulations ◽  
Integral Membrane Protein ◽  
Starting Point

Bacillus subtilis forms dormant spores upon nutrient depletion. Germinant receptors (GRs) in spore’s inner membrane respond to ligands such as L-alanine, and trigger spore germination. In B. subtilis spores, GerA is the major GR, and has three subunits, GerAA, GerAB, and GerAC. L-Alanine activation of GerA requires all three subunits, but which binds L-alanine is unknown. To date, how GRs trigger germination is unknown, in particular due to lack of detailed structural information about B subunits. Using homology modelling with molecular dynamics (MD) simulations, we present structural predictions for the integral membrane protein GerAB. These predictions indicate that GerAB is an α-helical transmembrane protein containing a water channel. The MD simulations with free L-alanine show that alanine binds transiently to specific sites on GerAB. These results provide a starting point for unraveling the mechanism of L-alanine mediated signaling by GerAB, which may facilitate early events in spore germination.

Properties of spores of Bacillus subtilis with or without a transposon that decreases spore germination and increases spore wet heat resistance

2021 ◽  
Author(s):  
Yannong Luo ◽  
George Korza ◽  
Angela M. DeMarco ◽  
Oscar P. Kuipers ◽  
Yong‐qing Li ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Heat Resistance ◽  
Spore Germination ◽  
Wet Heat

scholarly journals Does Neonatal Imitation Exist? Insights From a Meta-Analysis of 336 Effect Sizes

2021 ◽  
pp. 174569162095983
Author(s):  
Jacqueline Davis ◽  
Jonathan Redshaw ◽  
Thomas Suddendorf ◽  
Mark Nielsen ◽  
Siobhan Kennedy-Costantini ◽  
...  
Keyword(s):  
Social Behavior ◽  
Positive Result ◽  
Human Development ◽  
Degrees Of Freedom ◽  
Meta Analysis ◽  
Effect Sizes ◽  
Significant Evidence ◽  
The Past ◽  
Substantial Heterogeneity

Neonatal imitation is a cornerstone in many theoretical accounts of human development and social behavior, yet its existence has been debated for the past 40 years. To examine possible explanations for the inconsistent findings in this body of research, we conducted a multilevel meta-analysis synthesizing 336 effect sizes from 33 independent samples of human newborns, reported in 26 articles. The meta-analysis found significant evidence for neonatal imitation ( d = 0.68, 95% CI = [0.39, 0.96], p < .001) but substantial heterogeneity between study estimates. This heterogeneity was not explained by any of 13 methodological moderators identified by previous reviews, but it was associated with researcher affiliation, test of moderators ( QM) (15) = 57.09, p < .001. There are at least two possible explanations for these results: (a) Neonatal imitation exists and its detection varies as a function of uncaptured methodological factors common to a limited set of studies, and (2) neonatal imitation does not exist and the overall positive result is an artifact of high researcher degrees of freedom.

scholarly journals 165 A Review of The Current Literature on LMWH Administered at Different Times in Relation to MOS (Major Orthopaedic Surgery): Assessment of The Safety and Efficacy of The Different Proposed Strategies

2021 ◽  
Vol 108 (Supplement_2) ◽  
Author(s):  
G Placella ◽  
V Pace ◽  
P Antinolfi ◽  
V Salini
Keyword(s):  
Meta Analysis ◽  
Convincing Evidence ◽  
Just In Time ◽  
Medical Complications ◽  
Randomized Controlled ◽  
The Past ◽  
Cochrane Database ◽  
Major Orthopedic Surgery ◽  
Major Orthopaedic Surgery ◽  
The One

Abstract Nowadays venous VTE represents an important perioperative and postoperative complication in patients undergoing elective Major Orthopedic Surgery (MOS). There are significant discrepancies between clinical practice, international recommendations, and published guidelines. Although thromboembolic events may be less common these days than in the past, they can still lead to serious medical complications. Therefore, most patients undergoing MOS procedures are provided with one of the thromboprophylactic treatments. The optimum timing of LMWH administrations remains debated. Customized structured electronic searches in PubMed and Cochrane database. Meta-Analysis, Randomized Controlled Trials, Systematic Reviews on different strategies of the use of LMWH for MOS. Studies on prophylactic regimens showed that subcutaneous LMWH plays a key role in the management of thromboprophylaxis in MOS. However, some controversies still stand. Among those most relevant, it remains unclear whether to start thromboprophylaxis before or after MOS to better balance the risks of clotting and bleeding. With regards to different times of LMWH administration, there is no convincing evidence that starting prophylaxis 12 hours preoperatively is associated with lower risks of VTE compared to prophylaxis started 12 to 24 hours postoperatively. Furthermore, it seems that the most safe and efficient LMWH regimen is the one called “Just-in-time” (LMWH started 6 hours post-op).

scholarly journals Not Just Transporters: Alternative Functions of ABC Transporters in Bacillus subtilis and Listeria monocytogenes

2021 ◽  
Vol 9 (1) ◽  
pp. 163
Author(s):  
Jeanine Rismondo ◽  
Lisa Maria Schulz
Keyword(s):  
Bacillus Subtilis ◽  
Listeria Monocytogenes ◽  
Abc Transporters ◽  
Organic Molecules ◽  
Atp Hydrolysis ◽  
The Past ◽  
Wide Range ◽  
Regulatory Functions ◽  
Complex Organic ◽  
Detoxification Mechanisms

ATP-binding cassette (ABC) transporters are usually involved in the translocation of their cognate substrates, which is driven by ATP hydrolysis. Typically, these transporters are required for the import or export of a wide range of substrates such as sugars, ions and complex organic molecules. ABC exporters can also be involved in the export of toxic compounds such as antibiotics. However, recent studies revealed alternative detoxification mechanisms of ABC transporters. For instance, the ABC transporter BceAB of Bacillus subtilis seems to confer resistance to bacitracin via target protection. In addition, several transporters with functions other than substrate export or import have been identified in the past. Here, we provide an overview of recent findings on ABC transporters of the Gram-positive organisms B. subtilis and Listeria monocytogenes with transport or regulatory functions affecting antibiotic resistance, cell wall biosynthesis, cell division and sporulation.

pGR71 plasmid promotor sequence temporally regulated in Bacillus subtilis

1998 ◽  
Vol 44 (12) ◽  
pp. 1186-1192
Author(s):  
Guy Daxhelet ◽  
Philippe Gilot ◽  
Etienne Nyssen ◽  
Philippe Hoet
Keyword(s):  
Bacillus Subtilis ◽  
Binding Site ◽  
Transcription Initiation ◽  
Promoter Sequence ◽  
Initiation Site ◽  
Chloramphenicol Acetyltransferase ◽  
Ribosome Binding Site ◽  
Chloramphenicol Resistance ◽  
E Coli ◽  
Ribosome Binding

pGR71, a composite of plasmids pUB110 and pBR322, replicates in Escherichia coli and in Bacillus subtilis. It carries the chloramphenicol resistance gene (cat) from Tn9, which is not transcribed in either host by lack of a promoter. The cat gene is preceded by a Shine-Dalgarno sequence functional in E. coli but not in B. subtilis. Deleted pGR71 plasmids were obtained in B. subtilis when cloning foreign viral DNA upstream of this cat sequence, as well as by BAL31 exonuclease deletions extending upstream from the cat into the pUB110 moiety. These mutant plasmids expressed chloramphenicol acetyltransferase (CAT), conferring on B. subtilis resistance to high chloramphenicol concentrations. CAT expression peaked at the early postexponential phase of B. subtilis growth. The transcription initiation site of cat, determined by primer extension, was located downstream of a putative promoter sequence within the pUB110 moiety. N-terminal amino acid sequencing showed that native CAT was produced by these mutant plasmids. The cat ribosome-binding site, functional in E. coli, was repositioned within the pUB110 moiety and had consequently an extended homology with B. subtilis 16S rRNA, explaining the production of native enzyme.Key words: chloramphenicol acetyltransferase, Bacillus subtilis, postexponential gene expression, plasmid pUB110, ribosome-binding site, transcriptional promoter.

scholarly journals Role of SpoVA Proteins in Release of Dipicolinic Acid during Germination of Bacillus subtilis Spores Triggered by Dodecylamine or Lysozyme

2006 ◽  
Vol 189 (5) ◽  
pp. 1565-1572 ◽  
Author(s):  
Venkata Ramana Vepachedu ◽  
Peter Setlow
Keyword(s):  
Bacillus Subtilis ◽  
Small Molecules ◽  
Spore Germination ◽  
Dipicolinic Acid ◽  
Temperature Sensitive ◽  
Wild Type ◽  
Ph Optimum ◽  
Inner Membrane ◽  
Temperature Sensitive Mutants

ABSTRACT The release of dipicolinic acid (DPA) during the germination of Bacillus subtilis spores by the cationic surfactant dodecylamine exhibited a pH optimum of ∼9 and a temperature optimum of 60°C. DPA release during dodecylamine germination of B. subtilis spores with fourfold-elevated levels of the SpoVA proteins that have been suggested to be involved in the release of DPA during nutrient germination was about fourfold faster than DPA release during dodecylamine germination of wild-type spores and was inhibited by HgCl2. Spores carrying temperature-sensitive mutants in the spoVA operon were also temperature sensitive in DPA release during dodecylamine germination as well as in lysozyme germination of decoated spores. In addition to DPA, dodecylamine triggered the release of amounts of Ca2+ almost equivalent to those of DPA, and at least one other abundant spore small molecule, glutamic acid, was released in parallel with Ca2+ and DPA. These data indicate that (i) dodecylamine triggers spore germination by opening a channel in the inner membrane for Ca2+-DPA and other small molecules, (ii) this channel is composed at least in part of proteins, and (iii) SpoVA proteins are involved in the release of Ca2+-DPA and other small molecules during spore germination, perhaps by being a part of a channel in the spore's inner membrane.

scholarly journals In Bacillus subtilis, the Sirtuin Protein Deacetylase, Encoded by the srtN Gene (Formerly yhdZ), and Functions Encoded by the acuABC Genes Control the Activity of Acetyl Coenzyme A Synthetase

2009 ◽  
Vol 191 (6) ◽  
pp. 1749-1755 ◽  
Author(s):  
Jeffrey G. Gardner ◽  
Jorge C. Escalante-Semerena
Keyword(s):  
Bacillus Subtilis ◽  
Coenzyme A ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
New Information ◽  
Low Concentrations ◽  
Dependent Protein ◽  
Protein Deacetylase

ABSTRACT This report provides in vivo evidence for the posttranslational control of the acetyl coenzyme A (Ac-CoA) synthetase (AcsA) enzyme of Bacillus subtilis by the acuA and acuC gene products. In addition, both in vivo and in vitro data presented support the conclusion that the yhdZ gene of B. subtilis encodes a NAD+-dependent protein deacetylase homologous to the yeast Sir2 protein (also known as sirtuin). On the basis of this new information, a change in gene nomenclature, from yhdZ to srtN (for sirtuin), is proposed to reflect the activity associated with the YdhZ protein. In vivo control of B. subtilis AcsA function required the combined activities of AcuC and SrtN. Inactivation of acuC or srtN resulted in slower growth and cell yield under low-acetate conditions than those of the wild-type strain, and the acuC srtN strain grew under low-acetate conditions as poorly as the acsA strain. Our interpretation of the latter result was that both deacetylases (AcuC and SrtN) are needed to maintain AcsA as active (i.e., deacetylated) so the cell can grow with low concentrations of acetate. Growth of an acuA acuC srtN strain on acetate was improved over that of the acuA + acuC srtN strain, indicating that the AcuA acetyltransferase enzyme modifies (i.e., inactivates) AcsA in vivo, a result consistent with previously reported in vitro evidence that AcsA is a substrate of AcuA.

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