Micromonospora soli strain:SL3-70
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ABSTRACT:
PROVIDER: PRJNA1302119 | ENA |
REPOSITORIES: ENA
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Project description:Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenicity. To date, the complete genome sequences have been reported for only two S. pneumoniae strains; TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report herein the genome sequences of two different isolates of strain D39 and the corrected sequence and updated annotation of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only 5 relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single base pair changes, 6 deletions, 4 insertions, and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed. Keywords: bacterial strain comparison, bacterial isolate comparison
2006-10-09 | GSE5375 | GEO
Project description:Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase center (PTC), is thought to be nearly universally conserved. Here, we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify a previously undescribed archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome
2025-06-17 | PXD064958 | Pride
Project description:Chemical communication is crucial in ecosystems with complex microbial assemblages. However, due to archaeal cultivation challenges, our understanding of the structure diversity and function of secondary metabolites (SMs) within archaeal communities is limited compared to the extensively studied and well-documented bacterial counterparts. Our comprehensive investigation into the biosynthetic potential of archaea, combined with metabolic analyses and the first report of heterologous expression in archaea, has unveiled the previously unexplored biosynthetic capabilities and chemical diversity of archaeal ribosomally synthesized and post-translationally modified peptide (RiPP). We have identified twenty-four new lanthipeptides of RiPPs exhibiting unique chemical characteristics, including a novel subfamily featuring an unexplored type with diamino-dicarboxylic (DADC) termini, largely expanding the chemical landscape of archaeal SMs. This sheds light on the chemical novelty of archaeal metabolites and emphasizes their potential as an untapped resource for natural product discovery. Additionally, archaeal lanthipeptides demonstrate specific antagonistic activity against haloarchaea, mediating the unique biotic interaction in the halophilic niche. Furthermore, they showcased a unique ecological role in enhancing the host's motility by inducing the rod-shaped cell morphology and upregulating the archaellum gene flgA1, facilitating the archaeal interaction with abiotic environments. These discoveries broaden our understanding of archaeal chemical language and provide promising prospects for future exploration of SM-mediated interaction.
2024-11-09 | GSE281021 | GEO
Project description:We describe the complete synthesis, assembly, debugging and characterization of a synthetic 404,963 bp yeast chromosome, synIX. Combined chromosome construction methods were used to synthesize the left arm of synIX (synIXL) and retrofit previously described synIXR. During synIX strain characterization, we identified and resolved a bug related to EST3, a gene involved in telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. We found that both synIX transfer via chromoduction and wild-type IX destabilization were efficient methods. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these two chromosomes.
2023-10-02 | GSE244153 | GEO
Project description:To reveal the functional consequences of H-NS modifications, we performed proteome and secretome of Salmonella wild-type and H-NS mutant strains to analyze how phosphorylation impacts the landscape of H-NS-regulated bacterial proteins.
2024-04-25 | PXD051752 |
Project description:Weissella soli strain DB-2 is a lactic acid bacterium that was isolated from nukadoko in Japan. We report the draft genome sequence of Weissella soli strain DB-2 to determine the presence of the genes responsible for exopolysaccharide biosynthesis, with the aim of further probiotic evaluation.
| S-EPMC8800448 | biostudies-literature
Project description:Francisella tularensis is one of three bacterial species designated as a Category A select agent by the Centre for Disease Control (CDC), a category indicating agents most likely to be employed as a biological weapon. F. tularensis can be divided into four different subspecies, and it is well known that the type, severity and duration of the disease can differ substantially depending on what subspecies is responsible for the infection. Of the four subspecies, subsp. tularensis (Type A) and subsp. holartica (Type B) are of primary clinical significance, and account for nearly all recorded incidences of the disease in humans. Though Type A is considered to be more virulent than Type B, recent reports have shown that Type A can be further sub-divided into two genetically distinct populations, termed A.I and A.II, which differ with respect to geographical location, disease outcome and source of recovered isolates. Of these two subpopulations, clinical data suggests that Type A.I strains are significantly more virulent than Type A.II, and Type A.II strains appear to have a disease outcome similar to infections with Type B. During natural infections, host mononuclear phagocytes appear to be the primary target of all F. tularensis subsp. Despite the differences in disease outcome between different subspecies, the mechanisms involved in phagosomal escape, the modulation of phagosomal biogenesis, phagosomal disruption and bacterial egress appears to be indistinguishable between subspecies, at least at a physiological level. In collaboration with Dr. Patrick McGann at Walter Reed Army Institute of Research (WRAIR) we have been studying the differential gene expression of F. tularensis during macrophage infection. Dr. McGann provided the PFGRC with RNA samples from F. tularensis strains LVS and Shuh4 isolated from infected macrophages. Samples were interrogated using high throughput qRT-PCR using 1,067 primer pairs.
2011-06-08 | GSE29755 | GEO
Project description:To date, a number of bacteriophages (phages) infecting Acinetobacter species have been reported and characterized. However, Acinetobacter phages which infect A. soli have not been investigated yet. Here, we report the complete genome sequence of Acinetobacter phage phiAC-1, which belongs to the Myoviridae, infecting Acinetobacter soli strain KZ-1.
| S-EPMC3497645 | biostudies-literature