Regulons and protein–protein interactions of PRD-containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA639101 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: Bacillus anthracis produces three regulators, AtxA, AcpA and AcpB, which control virulence gene transcription and belong to an emerging class of regulators termed ‘PCVRs’ (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA, named for its control of toxin gene expression, is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. Reports of PCVR activity suggest overlapping function. We used RNA-Seq to assess the regulons of the paralogous regulators in strains constructed to express individual PCVRs at native levels. Methods: Cultures were incubated in toxin-inducing conditions, and expression of each PCVR in the atxAacpAacpB-null background strain was induced with an IPTG concentration that yielded native protein levels for each PCVR. RNA was extracted when cultures reached late-exponential phase using saturated acid phenol extraction, followed by RNA precipitation from the aqueous phase. Creation of libraries for NGS analysis used total RNA (1.0 μg). Samples were treated with Ribo-Zero (Epicentre) to remove ribosomal RNA prior to fragmentation using divalent cations and heat. Libraries were created using an Illumina TruSeq sample preparation kit following the protocol as recommended by the manufacturer. NGS sequencing was performed as a paired-end 50 base sequence using an Illumina HiSeq 1500 following the protocol recommended by the manufacturer. Results: Plasmid and chromosome-borne genes were PCVR controlled, with AtxA, AcpA and AcpB having a ≥4-fold effect on transcript levels of 145, 130 and 49 genes respectively. Several genes were coregulated by two or three PCVRs. Of the 203 transcripts associated with pXO1, 15 were altered at least fourfold: 13 by AtxA and 2 by AcpA. No pXO1-derived transcripts were affected fourfold or greater by AcpB. Read maps revealed that many of the regulated transcripts from pXO1 were associated with the 35 kb region that lies within a larger 44.8 kb pathogenicity island (PAI) (Thorne, 1993). We detected transcripts for 110 genes on pXO2, of which 21 were regulated fourfold or greater by at least one of the three PCVRs. The highly regulated genes clustered within a 35.5 kb region of the plasmid, which includes the capsule biosynthetic operon capBCADE followed by the weakly co-transcribed acpB gene. A significantly smaller proportion of PCVR-regulated genes mapped to the chromosome. Of the 5593 transcripts, 198 were altered fourfold or greater by one or more PCVRs. Clustering of PCVR-regulated chromosome genes was not apparent. Among the most highly regulated chromosomal genes were many genes associated with branched chain amino acid (BCAA) synthesis and uptake. Of the 17 genes implicated in BCAA biosynthesis, expression of 13 of these genes is repressed by AtxA and AcpB. In this work, we have shown that the three PRD-containing virulence regulators of B. anthracis exhibit overlapping and divergent target gene specificities. Conclusions: In this work, we show the relative activities of the PCVRs for specific and co-regulated genes. The results reveal the vast effects of the PCVRs on B. anthracis gene expression and indicate a high degree of functional similarity among the regulators. Our investigations provide insight into control of B. anthracis gene expression and expand our knowledge of structure and function of this emerging class of virulence gene regulators.
2020-06-13 | GSE152357 | GEO
Project description:AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins that are required for the pathogenicity of Bacillus anthracis. Recent transcriptome analyses also showed that AtxA affects a large number of genes on both chromosome and plasmid, suggesting its role as a global regulator. Its mechanism of gene regulation nor binding target in vivo was, however, not well understood. In this work, we conducted ChIP-seq for cataloging binding sites of AtxA in vivo and Cappable-seq for catalogging the transcription start sites on the B. anthracis genome. For detected regulons, single knockout strains were constructed and RNA-seq was conducted for each strain.
2021-06-28 | GSE167871 | GEO
Project description:Bacillus anthracis produces three regulators, AtxA, AcpA and AcpB, which control virulence gene transcription and belong to an emerging class of regulators termed 'PCVRs' (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA, named for its control of toxin gene expression, is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. Reports of PCVR activity suggest overlapping function. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA level or activity result in capBCADE transcription in strains lacking acpA and acpB. We used RNA-Seq to assess the regulons of the paralogous regulators in strains constructed to express individual PCVRs at native levels. Plasmid and chromosome-borne genes were PCVR controlled, with AtxA, AcpA and AcpB having a ? 4-fold effect on transcript levels of 145, 130 and 49 genes respectively. Several genes were coregulated by two or three PCVRs. We determined that AcpA and AcpB form homomultimers, as shown previously for AtxA, and we detected AtxA-AcpA heteromultimers. In co-expression experiments, AcpA activity was reduced by increased levels of AtxA. Our data show that the PCVRs have specific and overlapping activity and that PCVR stoichiometry and potential heteromultimerization can influence target gene expression.
| S-EPMC6167206 | biostudies-literature
Project description:Direct regulons of the master virulence regulator AtxA of Bacillus anthracis
| PRJNA705366 | ENA
Project description:The spore forming pathogen Bacillus anthracis is the etiologic agent of anthrax in humans and animals. It cycles through infected hosts as vegetative cells and is eventually introduced into the environment where it generates an endospore resistant to many harsh conditions. The endospores are subsequently ingested by the next host to begin the next cycle. Outbreaks of anthrax occur regularly worldwide in wildlife and livestock, and the potential for human infection exists whenever humans encounter infected animals. It is also possible to encounter intentional releases of anthrax spores, as was the case in October 2001. Consequently, it is important to be able to rapidly establish the provenance of infectious strains of B. anthracis. Here, we compare protein expression in seven low-passage wild isolates and four laboratory strains of B. anthracis grown under identical conditions using LC-MS/MS proteomic analysis. Of the 1,023 total identified proteins, 96 had significant abundance differences between wild and laboratory strains. Of those, 28 proteins directly related to sporulation were upregulated in wild isolates, with expression driven by Spo0A, CodY, and AbrB/ScoC. In addition, we observed evidence of changes in cell division and fatty acid biosynthesis between the two classes of strains, despite being grown under identical experimental conditions. These results suggest wild B. anthracis cells are more highly tuned to sporulate than their laboratory cousins, and this difference should be exploited as a method to differentiate between laboratory adapted cultures and low passage wild strains isolated during an anthrax outbreak. This knowledge should distinguish between intentional releases and exposure to strains in nature providing a basis for the type of response by public health officials and investigators.
2018-12-04 | PXD010120 | Pride
Project description:Timecourse from log phase growth to sporulation in Bacillus anthracis Stern 34F2 Keywords: time-course
2004-01-08 | GSE840 | GEO
Project description:Bacillus anthracis causes anthrax infections in mammals. Large-scale mortality resulting from the intentional release of B. anthracis spores represents a potential bioterrorism threat. Inhalational anthrax almost invariably proceeds to fatal systemic infection, characterized by massive bacteremia. A better understanding of host-pathogen interactions is urgently needed for effective treatment of this lethal disease. However, virulence mechanisms used by B. anthracis to survive and multiply in human blood are not completely understood. Identification of genes that are differentially expressed during the growth of B. anthracis in human serum can elucidate how this pathogen successfully colonizes the bloodstream. We compared the transcriptional profile of B. anthracis growing in heat-inactivated human serum to that in LB medium. Genes involved in the biosynthesis of purines, certain amino acids and riboflavin and lipid metabolism, genes encoding ABC transporters, respiratory enzymes and several genes with hypothetical function were identified as being upregulated during growth in serum.
2022-12-01 | GSE97567 | GEO
Project description:Timecourse from log phase growth to sporulation in Bacillus anthracis Stern 34F2
2010-06-09 | E-GEOD-840 | biostudies-arrayexpress
Project description:The aim of the study was to carry out a CGH study utilizing a set of 39 diverse Bacillus isolates. Thirty four B. cereus and five B. anthracis strains and isolates were chosen so as to represent different lineages based on previous characterizations, including MLEE and MLST (Helgason, Okstad et al. 2000; Helgason, Tourasse et al. 2004). They represent the spectrum of B. cereus phenotypic diversity by including soil, dairy and periodontal isolates in addition to virulent B. anthracis strains.
2009-11-25 | GSE19068 | GEO
Project description:PRD class homeobox genes in bovine early embryos: function, evolution and overlapping roles
| PRJNA791233 | ENA