11 research outputs found
Functional Redundancy and Specialization of the Conserved Cold Shock Proteins in Bacillus subtilis
No full textFaßhauer P, Busche T, Kalinowski J, et al. Functional Redundancy and Specialization of the Conserved Cold Shock Proteins in Bacillus subtilis. Microorganisms. 2021;9(7): 1434.Many bacteria encode so-called cold shock proteins. These proteins are characterized by a conserved protein domain. Often, the bacteria have multiple cold shock proteins that are expressed either constitutively or at low temperatures. In the Gram-positive model bacterium Bacillussubtilis, two of three cold shock proteins, CspB and CspD, belong to the most abundant proteins suggesting a very important function. To get insights into the role of these highly abundant proteins, we analyzed the phenotypes of single and double mutants, tested the expression of the csp genes and the impact of CspB and CspD on global gene expression in B. subtilis. We demonstrate that the simultaneous loss of both CspB and CspD results in a severe growth defect, in the loss of genetic competence, and the appearance of suppressor mutations. Overexpression of the third cold shock protein CspC could compensate for the loss of CspB and CspD. The transcriptome analysis revealed that the lack of CspB and CspD affects the expression of about 20% of all genes. In several cases, the lack of the cold shock proteins results in an increased read-through at transcription terminators suggesting that CspB and CspD might be involved in the control of transcription termination
Der Datenpool eines frühneuzeitlichen Self-Trackers, oder: Johann Christian Senckenbergs "Observationes". Ein Distant Reading-Zugang
No full textA single abstract from the DHd-2020 Book of Abstracts.Sofern eine editorische Arbeit an dieser Publikation stattgefunden hat, dann bestand diese aus der Eliminierung von Bindestrichen in Überschriften, die aufgrund fehlerhafter Silbentrennung entstanden sind, der Vereinheitlichung von Namen der Autor*innen in das Schema "Nachname, Vorname" und/oder der Trennung von Überschrift und Unterüberschrift durch die Setzung eines Punktes, sofern notwendig
Functions of the Cold Shock Proteins in Bacillus Subtilis
No full textRNA binding proteins are fundamental to the proper functioning of all cells. They are structural components in larger complexes such as ribosomes or regulate cellular processes that involve RNA such as transcription, translation, or the modification, processing, and decay of RNA. Some RNA binding proteins contain the cold shock domain which is highly conserved from bacteria to mammals. Bacterial cold shock proteins consist of a single cold shock domain that binds RNA and single stranded DNA. They have been extensively studied in various species and some act as RNA chaperones that destabilize secondary RNA structures to regulate transcriptional termination, RNA stability and processing, as well as translation. In the Gram-positive model organism Bacillus subtilis, the function(s) and targets of cold shock proteins have not been elucidated so far. This work identified the regulon of the cold shock proteins in B. subtilis and uncovered their involvement in many biological processes. The B. subtilis genome encodes the three cold shock protein paralogs CspB, CspC, and CspD. While csp single-mutants did not exhibit any obvious phenotype and a triple knockout was not possible, the cspB cspD double-knockout led to the loss of genetic competence, impairment of biofilm formation, aberrant gene expression, and a strong impairment of growth. This suggests CspC cannot fully replace the function of CspB and CspD. The cspB cspD double mutant formed suppressor mutants, which often harbored a point mutation that leads to upregulation of CspC. The overexpression of CspC in these suppressor mutants improved growth and genetic stability but did not restore genetic competence. This suggests CspC is functionally different from CspB and CspD. CspC was the only paralog that was induced at 15°C further highlighting the functional specialization. Comparison of the amino acid residue at position 58 which is important for functional specificity in Staphylococcus aureus, revealed that CspC harbors an alanine residue while CspB and CspD carry a proline residue at this position. Therefore, a CspC(A58P) variant was expressed in the cspB cspD double mutant background which improved genetic stability, growth, and also restored genetic competence. Hence, a single amino acid is responsible for the functional specificity of the cold shock proteins. Analysis of the cspB cspD double mutant transcriptome uncovered up- or downregulation for as many as 21% of genes suggesting numerous potential targets of CspB and CspD. One of these targets is the cspC 5’-UTR at which CspB and CspD but not CspC negatively regulated expression. Other targets were identified by analysis of read-through transcription at intergenic regions in the cspB cspD double mutant. An increased transcriptional read-through was found at the manR and liaH terminators. Conversely, transcriptional read-through was decreased at the terminator/ antiterminator switches between the pyrR-pyrP and pyrP-pyrB genes. These results demonstrate that the B. subtilis cold shock proteins have different biological functions and influence gene expression globally at least by regulation of transcription. This study may serve as a starting point for future research on cold shock protein function in B. subtilis. It presents methods and interesting targets to further explore the function of cold shock proteins.2021-07-1
Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis
No full textAbstract RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.Abstract RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells
Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis
No full textThe Bacillus subtilis Minimal Genome Compendium
No full textTo better understand
cellular life, it is essential to decipher
the contribution of individual components and their interactions.
Minimal genomes are an important tool to investigate these interactions.
Here, we provide a database of 105 fully annotated genomes of a series
of strains with sequential deletion steps of the industrially relevant
model bacterium Bacillus subtilis starting with the
laboratory wild type strain B. subtilis 168 and ending
with B. subtilis PG38, which lacks approximately
40% of the original genome. The annotation is supported by sequencing
of key intermediate strains as well as integration of literature knowledge
for the annotation of the deletion scars and their potential effects.
The strain compendium presented here represents a comprehensive genome
library of the entire MiniBacillus project. This
resource will facilitate the more effective application of the different
strains in basic science as well as in biotechnology
The <i>Bacillus subtilis</i> Minimal Genome Compendium
No full textTo better understand
cellular life, it is essential to decipher
the contribution of individual components and their interactions.
Minimal genomes are an important tool to investigate these interactions.
Here, we provide a database of 105 fully annotated genomes of a series
of strains with sequential deletion steps of the industrially relevant
model bacterium Bacillus subtilis starting with the
laboratory wild type strain B. subtilis 168 and ending
with B. subtilis PG38, which lacks approximately
40% of the original genome. The annotation is supported by sequencing
of key intermediate strains as well as integration of literature knowledge
for the annotation of the deletion scars and their potential effects.
The strain compendium presented here represents a comprehensive genome
library of the entire MiniBacillus project. This
resource will facilitate the more effective application of the different
strains in basic science as well as in biotechnology
The Bacillus subtilis Minimal Genome Compendium
No full textTo better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology.</p
Clinical efficacy of SARS-CoV-2 Omicron-neutralizing antibodies in immunoglobulin preparations for the treatment of agammaglobulinemia in patients with primary antibody deficiency
No full textImmunocompromised individuals are at significantly elevated risk for severe courses of coronavirus disease 2019 (COVID-19). In addition to vaccination, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies (nAbs) have been applied throughout the pandemic, with time of treatment onset and potency against the currently prevailing virus variant identified as relevant factors for medical benefit. Using data from the European Society for Immunodeficiencies (ESID) registry, the present study evaluated COVID-19 cases in three groups of patients with inborn errors of immunity (IEI; 981 agammaglobulinemia patients on immunoglobulin replacement therapy (IGRT); 8960 non-agammaglobulinemia patients on IGRT; 14 428 patients without IGRT), and the neutralizing capacity of 1100 immunoglobulin lots against SARS-CoV-2 (“Wuhan” and Omicron strains), throughout 3 years. From the first (2020/2021) to the second (2021/2022) cold season, i.e., during the virus drift to the more contagious Omicron variants, an increase in case numbers was recorded that was comparable (~2- to 3-fold) for all three study groups. During the same period, immunoglobulin lots showed a profound nAb increase against the archetypal SARS-CoV-2 strain, yet only low levels of Omicron nAbs. Notably, shortly before the third (2022/2023) cold season, Omicron-neutralizing capacity of released immunoglobulin lots had plateaued at high levels. From the second to the third cold season, COVID-19 cases dropped markedly. While a ~6-fold case reduction was recorded for the groups of non-agammaglobulinemia patients on IGRT and IEI patients not receiving IGRT, the decline was ~30-fold for the group of agammaglobulinemia patients on IGRT. These findings suggest a substantial COVID-19-protective effect of IGRT, at least for distinct groups of antibody-deficient patients.Peer reviewe
