Streptococcus pneumoniae
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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:Segregation of replicated chromosomes during cell division is an essential process in all organisms. Chromosome segregation is promoted by the action of the DNA-binding ParB protein in the rod-shaped model bacterium Bacillus subtilis. How oval shaped bacteria, such as the human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes is poorly understood. Here, we show that the pneumococcal homolog of ParB is enriched at four centromere-like DNA sequences (parS sites) that are present near the origin of replication.
2011-06-11 | GSE26839 | GEO
Project description:Bacterial viruses, or bacteriophages, are major contributors to the evolution, pathogenesis and overall biology of their host bacteria. During their life cycle, temperate bacteriophages form stable associations with their host by integrating into the chromosome, a process called lysogeny. Isolates of the human pathogen Streptococcus pneumoniae are frequently lysogenic, and genomic studies have allowed the classification of these phages into distinct phylogenetic groups. Here, we review the recent advances in the characterization of temperate pneumococcal phages, with a focus on their genetic features and chromosomal integration loci. We also discuss the contribution of phages, and specific phage-encoded features, to colonization and virulence. Finally, we discuss interesting research perspectives in this field.
| S-EPMC7600539 | biostudies-literature
Project description:PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for Streptococcus pneumoniae remain a public health priority for every country in world today. The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance.
2011-08-01 | GSE29501 | GEO
Project description:To gain deeper insights into antibacterial mechanisms of NAD+ and bacterial adaptation, we generated and sequenced NAD+ resistant clones of Spn. For this purpose, Spn was cultivated in liquid medium with increasing concentrations (50 µM to 5 mM) of NAD+. After six passages, bacteria were plated on blood agar supplemented with 500 µM NAD+ and three clones were picked
2023-06-11 | E-MTAB-12644 | biostudies-arrayexpress
Project description:Pneumonia is an inflammatory disease of the lung, responsible for high morbidity and mortality worldwide. It is caused by bacteria, viruses, fungi, or other microorganisms. Streptococcus pneumoniae, a gram-positive bacterium with over 90 serotypes, is the most common causative agent. Moreover, comorbid factors including heart failure, renal disease, and pulmonary disease could increase the risk of pneumococcal pneumonia. Since the advent of the pneumococcal vaccine in the 1980s, the incidence of pneumonia has decreased significantly. However, current vaccines confer only limited protection against serotypes included in the vaccine. Thus, to overcome this limitation, new types of pneumococcal vaccines have been sought and under clinical trials. In this review, we discuss pneumonia and summarize the various types of pneumococcal vaccines in progress.
| S-EPMC7090487 | biostudies-literature
Project description:Streptococcus pneumoniae is the causative agent of a multitude of diseases, and further study into its pathogenies is vital. The pneumococcus is genetically malleable, and several tools are available to manipulate this pathogen. In this study, we attempted to utilize one such tool, the Sweet Janus cassette, to replace the capsule locus with other capsule loci in our strain background and found that the efficiency of allelic replacement was low and the number of revertant false-positive colonies was high. We determined that the capacity to recombine capsule varied by the initial isolated colony, suggesting that frequency of reversion is dependent on the bacterial clone. Alternative selection markers may further expand the application of Sweet Janus. We created novel cassettes that utilized chlorinated phenylalanine as an alternative counter-selection agent in conjunction with the Janus or Sweet Janus cassette, providing a new dual or triple selection marker. Moreover, we created cassettes that do not require engineered resistance in the background strain, including both single and dual selection markers. We were able to utilize all constructs in allelic replacement of the capsule loci. These novel constructs provide a new means for generating gene deletions in S. pneumoniae that expand experimental applications.
| S-EPMC7563404 | biostudies-literature
Project description:A nationwide surveillance study was undertaken to monitor antimicrobial resistance among clinical isolates of Streptococcus pneumoniae in Korea, with a special focus on vancomycin tolerance. For the 6-month period from March to August 2002, clinical isolates of S. pneumoniae were collected from 11 university hospitals and 1 reference laboratory. One-hundred eighty-eight isolates were measured for lysis rates after exposure to vancomycin for 4 h. Two vancomycin-tolerant S. pneumoniae (VTSP) strains, S3 and H8, were isolated from sputum cultures of two patients, who had stayed in intensive-care units of different hospitals with long-term antibiotic therapy and were not treated for pneumococcal pneumonia. The penicillin, cefotaxime, and vancomycin MICs for S3 were 8 microg/ml, >16 microg/ml, and 0.5 microg/ml, and those for H8 were 2 microg/ml, 2 microg/ml, and 0.5 microg/ml, respectively. While S3 belonged to serotype 23F and was autolysin defective, H8 belonged to serotype 13F and had intact autolysin. These strains were not clonally related as determined by pulsed-field gel electrophoresis of chromosomal DNA. In agreement with previous reports, both isolates showed pairing of TIGR4 vex2 with R6 pep27 and had two identical amino acid substitutions, Q441K in vncS and N25D in vex2. These findings indicate that two VTSP strains have emerged independently in Korea, suggesting a prevalence rate of 1.1%. The emergence of VTSP would be a serious threat in Korea, where there are significant rates of penicillin resistance in S. pneumoniae. Monitoring of the prevalence of VTSP and further investigation of the clinical relevance of VTSP are warranted.
| S-EPMC1594776 | biostudies-literature
Project description:Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.
| S-EPMC4898793 | biostudies-literature
Project description:Among 34 Streptococcus pneumoniae (Spn) sequential isolates from middle ear fluid, we found a case of a nontypeable S. pneumoniae (NT-Spn) in a child with acute otitis media (AOM). The strain was pneumolysin PCR positive and capsule gene PCR negative. Virulence of the NT-Spn was confirmed in a chinchilla model of AOM.
| S-EPMC3897191 | biostudies-literature