Streptococcus pneumoniae R6
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA98529 | ENA |
REPOSITORIES: ENA
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Project description:The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Separate domains were identified depending of the transcription of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show here that these distinct domains have different expression and conservation tendencies. Microarray fluorescence units under non-relaxation conditions, taken as a measure of gene transcription level, were significantly lower in F genes than in the other domains in the same range of AT content. Transcription level categorization of the domains was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences evidenced conservation of gene composition in the U and D domains and extensive gene interchange in F domains. We tested domain organization by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology works as a general transcriptional regulator, superimposed to other kind of more specific regulatory mechanisms.
2014-12-29 | GSE58186 | GEO
Project description: Not available
| S-EPMC95463 | biostudies-literature
Project description:Streptococcus pneumoniae is a major cause of serious infections such as pneumonia and meningitis in both children and adults worldwide. Here, we describe the development of a high-throughput genome-wide technique, Genomic Array Footprinting (GAF), for the identification of genes essential for this bacterium at various stages during infection. GAF enables negative screens by means of a combination of transposon mutagenesis and microarray technology for the detection of transposon insertion sites. We tested several methods for the identification of transposon insertion sites and found that amplification of DNA adjacent to the insertion site by PCR resulted in non-reproducible results, even when combined with an adapter. However, restriction of genomic DNA followed directly by in vitro transcription circumvented these problems. Analysis of parallel reactions generated with this method on a large mariner transposon library, showed that it was highly reproducible and correctly identified essential genes. Comparison of a mariner library to one generated with the in vivo transposition plasmid pGh:ISS1, showed that both have an equal degree of saturation, but that 9% of the genome is preferentially mutated by either one. The usefulness of GAF was demonstrated in a screen for genes essential for survival of zinc stress. This identified a gene encoding a putative cation efflux transporter, and its deletion resulted in an inability to grow under high zinc conditions. In conclusion, we developed a fast, versatile, specific, and high-throughput method for the identification of conditionally essential genes in S. pneumoniae. Keywords: GAF pGHost vs mariner
2007-06-26 | GSE6912 | GEO
Project description: Not available
| S-EPMC2953539 | biostudies-literature
Project description:Identification of transposon insertion sites using the T7 RNA polymerase promoter
| PRJNA98531 | ENA
Project description:Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells
| PRJNA150365 | ENA
Project description:Reactive oxygen species contribute to the bactericidal effects of the fluoroquinolone moxifloxacin in Streptococcus pneumoniae: metabolic pathways involved
| PRJNA284149 | ENA
Project description:Streptococcus pneumoniae R6 genomic DNA
| PRJNA251531 | ENA