28 research outputs found
The potential mRNA target sites for the ribosomal protein L10 found in Streptomyces griseus and S. coelicolor give evidence for the autogenous regulation of expression of the rplJL genes
On the basis of structural similarity between the m- and rRNA binding sites which underlies the molecular mechanism of the autogenous control of expression of the rplJL genes, mediated in prokaryotic organisms by ribosomal protein L10, we attempted to find the potential mRNA target sites in S. griseus and S. coelicolor. The potential targets found in both species of Streptomyces are of highly conserved structure and contain elements similar with the L10 binding domain of the 23S RNA. Compared to the L10, mRNA targets of Enterobacteria, Thermotoga maritima and Synechocystis, the target sites of Streptomyces contain a larger number of conserved and specific structural elements, similar in both analyzed species. Comparison of the structural organization of the "Streptomyces" and "Enterobacterial" types of the L10 mRNA targets with the structure of the L10 binding domain in the 23S RNA reveals that the elements, conserved in all the mentioned targets, are located in the ssA and dsA regions. The structure of the potential L10 mRNA target sites, which mimic the rRNA target of the regulatory ribosomal protein L10, gives evidence for the autogenous L1-0mediated control of expression of the rplJL genes in Streptomyces.Описано структурові особливості виявленого у представників Streptomyces постійного сайта зв'язування рибосомного білка L10, який розміщується в лідерній послідовності, що передує генам rplJL. Консервативність структурової організації сайта у двох видів Streptomyces і значна подібність структури до 23S мРНК свідчать про аутогенну регуляцію генів rplJL стрептоміцетів рибосомним білком L10.Описаны структурные особенности обнаруженного у представителей Streptomyces (Streptomyces griseus и Streptomyces coelicolor) потенциального сайта связывания рибосомного белка L10. расположенного в лидерной последовательности, предшествующей генам rplJL. Консервативность структурной организации сайта у двух видов Streptonmyces и высокое подобие структуры с 23S мРНК свидетельствуют об аутогенной регуляции экспрессии генов rplJL стриптомицетов рибосомным белком L10
The Role of luxS in the Middle Ear Streptococcus pneumoniae Isolate 947
The LuxS protein, encoded by luxS, is required for the production of autoinducer 2 (AI-2) in Streptococcus pneumoniae. The AI-2 molecule serves as a quorum sensing signal, and thus regulates cellular processes such as carbohydrate utilisation and biofilm formation, as well as impacting virulence. The role of luxS in S. pneumoniae biology and lifestyle has been predominantly assessed in the laboratory strain D39. However, as biofilm formation, which is regulated by luxS, is critical for the ability of S. pneumoniae to cause otitis media, we investigated the role of luxS in a middle ear isolate, strain 947. Our results identified luxS to have a role in prevention of S. pneumoniae transition from colonisation of the nasopharynx to the ear, and in facilitating adherence to host epithelial cells.Alexandra Tikhomirova, Erin B. Brazel, Kimberley T. McLean, Hannah N. Agnew, James C. Paton and Claudia Trappett
Streptococcus pneumoniae Strains Isolated From a Single Pediatric Patient Display Distinct Phenotypes
Streptococcus pneumoniae is the leading cause of bacterial paediatric meningitis after the neonatal period worldwide, but the bacterial factors and pathophysiology that drive pneumococcal meningitis are not fully understood. In this work, we have identified differences in raffinose utilization by S. pneumoniae isolates of identical serotype and sequence type from the blood and cerebrospinal fluid (CSF) of a single pediatric patient with meningitis. The blood isolate displayed defective raffinose metabolism, reduced transcription of the raffinose utilization pathway genes, and an inability to grow in vitro when raffinose was the sole carbon source. The fitness of these strains was then assessed using a murine intranasal infection model. Compared with the CSF isolate, mice infected with the blood isolate displayed higher bacterial numbers in the nose, but this strain was unable to invade the ears of infectedmice. A premature stop codon was identified in the aga gene in the raffinose locus, suggesting that this protein likely displays impaired alpha-galactosidase activity. These closely related strains were assessed by Illumina sequencing, which did not identify any single nucleotide polymorphisms (SNPs) between the two strains. However, these wider genomic analyses identified the presence of an alternative alpha-galactosidase gene that appeared to display altered sequence coverage between the strains, which may account for the observed differences in raffinose metabolic capacity. Together, these studies support previous findings that raffinose utilization capacity contributes to disease progression, and provide insight into a possible alternative means by which perturbation of this pathway may influence the behavior of pneumococci in the host environment, particularly in meningitis.Hannah N. Agnew, Erin B. Brazel, Alexandra Tikhomirova, Mark van der Linden, Kimberley T. McLean, James C. Paton, and Claudia Trappett
To make or take: bacterial lipid homeostasis during Infection
Bacterial fatty acids are critical components of the cellular membrane. A shift in environmental conditions or in the bacterium’s lifestyle may result in the requirement for a distinct pool of fatty acids with unique biophysical properties. This can be achieved by the modification of existing fatty acids or via de novo synthesis. Furthermore, bacteria have evolved efficient means to acquire these energy-rich molecules from their environment. However, the balance between de novo fatty acid synthesis and exogenous acquisition during pathogenesis is poorly understood. Here, we studied the mouse fatty acid landscape prior to and after infection with Acinetobacter baumannii, a Gram-negative, opportunistic human pathogen. The lipid fluxes observed following infection revealed fatty acid- and niche-specific changes. Lipidomic profiling of A. baumannii isolated from the pleural cavity of mice identified novel A. baumannii membrane phospholipid species and an overall increased abundance of unsaturated fatty acid species. Importantly, we found that A. baumannii relies largely upon fatty acid acquisition in all but one of the studied niches, the blood, where the pathogen biosynthesizes its own fatty acids. This work is the first to reveal the significance of balancing the making and taking of fatty acids in a Gram-negative bacterium during infection, which provides new insights into the validity of targeting fatty acid synthesis as a treatment strategy.Felise G. Adams, Claudia Trappetti, Jack K. Waters, Maoge Zang, Erin B. Brazel, James C. Paton, Marten F. Snel, Bart A. Eijkelkam
Uncovering the link between the SpnIII restriction modification system and LuxS in Streptococcus pneumoniae meningitis isolates
Streptococcus pneumoniae is capable of randomly switching their genomic DNA methylation pattern between six distinct bacterial subpopulations (A-F) via recombination of a type 1 restriction-modification locus, spnIII. These pneumococcal subpopulations exhibit phenotypic changes which favor carriage or invasive disease. In particular, the spnIIIB allele has been associated with increased nasopharyngeal carriage and the downregulation of the luxS gene. The LuxS/AI-2 QS system represent a universal language for bacteria and has been linked to virulence and biofilm formation in S. pneumoniae. In this work, we have explored the link between spnIII alleles, the luxS gene and virulence in two clinical pneumococcal isolates from the blood and cerebrospinal fluid (CSF) of one pediatric meningitis patient. The blood and CSF strains showed different virulence profiles in mice. Analysis of the spnIII system of these strains recovered from the murine nasopharynx showed that the system switched to different alleles commensurate with the initial source of the isolate. Of note, the blood strain showed high expression of spnIIIB allele, previously linked with less LuxS protein production. Importantly, strains with deleted luxS displayed different phenotypic profiles compared to the wildtype, but similar to the strains recovered from the nasopharynx of infected mice. This study used clinically relevant S. pneumoniae strains to demonstrate that the regulatory network between luxS and the type 1 restriction-modification system play a key role in infections and may support different adaptation to specific host niches.Hannah N. Agnew, John M. Atack, Ann R.D. Fernando, Sophie N. Waters, Mark van der Linden, Erin Smith, Andrew D. Abell, Erin B. Brazel, James C. Paton, and Claudia Trappett
Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic:Length of HIV sequence data and phylogeny reconstruction
HIV molecular epidemiology studies analyse viral pol gene sequences due to their availability, but whole genome sequencing allows to use other genes. We aimed to determine what gene(s) provide(s) the best approximation to the real phylogeny by analysing a simulated epidemic (created as part of the PANGEA_HIV project) with a known transmission tree. We sub-sampled a simulated dataset of 4662 sequences into different combinations of genes (gag-pol-env, gag-pol, gag, pol, env and partial pol) and sampling depths (100%, 60%, 20% and 5%), generating 100 replicates for each case. We built maximum-likelihood trees for each combination using RAxML (GTR + Γ), and compared their topologies to the corresponding true tree’s using CompareTree. The accuracy of the trees was significantly proportional to the length of the sequences used, with the gag-pol-env datasets showing the best performance and gag and partial pol sequences showing the worst. The lowest sampling depths (20% and 5%) greatly reduced the accuracy of tree reconstruction and showed high variability among replicates, especially when using the shortest gene datasets. In conclusion, using longer sequences derived from nearly whole genomes will improve the reliability of phylogenetic reconstruction. With low sample coverage, results can be highly variable, particularly when based on short sequences
The potential mRNA target sites for the ribosomal protein L10 found in Streptomyces griseus and S. coelicolor give evidence for the autogenous regulation of expression of the rplJL genes
On the basis of structural similarity between the m- and rRNA binding sites which underlies the molecular mechanism of the autogenous control of expression of the rplJL genes, mediated in prokaryotic organisms by ribosomal protein L10, we attempted to find the potential mRNA target sites in S. griseus and S. coelicolor. The potential targets found in both species of Streptomyces are of highly conserved structure and contain elements similar with the L10 binding domain of the 23S RNA. Compared to the L10, mRNA targets of Enterobacteria, Thermotoga maritima and Synechocystis, the target sites of Streptomyces contain a larger number of conserved and specific structural elements, similar in both analyzed species. Comparison of the structural organization of the "Streptomyces" and "Enterobacterial" types of the L10 mRNA targets with the structure of the L10 binding domain in the 23S RNA reveals that the elements, conserved in all the mentioned targets, are located in the ssA and dsA regions. The structure of the potential L10 mRNA target sites, which mimic the rRNA target of the regulatory ribosomal protein L10, gives evidence for the autogenous L1-0mediated control of expression of the rplJL genes in Streptomyces.Описано структурові особливості виявленого у представників Streptomyces постійного сайта зв'язування рибосомного білка L10, який розміщується в лідерній послідовності, що передує генам rplJL. Консервативність структурової організації сайта у двох видів Streptomyces і значна подібність структури до 23S мРНК свідчать про аутогенну регуляцію генів rplJL стрептоміцетів рибосомним білком L10.Описаны структурные особенности обнаруженного у представителей Streptomyces (Streptomyces griseus и Streptomyces coelicolor) потенциального сайта связывания рибосомного белка L10. расположенного в лидерной последовательности, предшествующей генам rplJL. Консервативность структурной организации сайта у двух видов Streptonmyces и высокое подобие структуры с 23S мРНК свидетельствуют об аутогенной регуляции экспрессии генов rplJL стриптомицетов рибосомным белком L10