Dataset Information

Dialects of the DNA uptake sequence in Neisseriaceae.

ABSTRACT: In all sexual organisms, adaptations exist that secure the safe reassortment of homologous alleles and prevent the intrusion of potentially hazardous alien DNA. Some bacteria engage in a simple form of sex known as transformation. In the human pathogen Neisseria meningitidis and in related bacterial species, transformation by exogenous DNA is regulated by the presence of a specific DNA Uptake Sequence (DUS), which is present in thousands of copies in the respective genomes. DUS affects transformation by limiting DNA uptake and recombination in favour of homologous DNA. The specific mechanisms of DUS-dependent genetic transformation have remained elusive. Bioinformatic analyses of family Neisseriaceae genomes reveal eight distinct variants of DUS. These variants are here termed DUS dialects, and their effect on interspecies commutation is demonstrated. Each of the DUS dialects is remarkably conserved within each species and is distributed consistent with a robust Neisseriaceae phylogeny based on core genome sequences. The impact of individual single nucleotide transversions in DUS on meningococcal transformation and on DNA binding and uptake is analysed. The results show that a DUS core 5'-CTG-3' is required for transformation and that transversions in this core reduce DNA uptake more than two orders of magnitude although the level of DNA binding remains less affected. Distinct DUS dialects are efficient barriers to interspecies recombination in N. meningitidis, N. elongata, Kingella denitrificans, and Eikenella corrodens, despite the presence of the core sequence. The degree of similarity between the DUS dialect of the recipient species and the donor DNA directly correlates with the level of transformation and DNA binding and uptake. Finally, DUS-dependent transformation is documented in the genera Eikenella and Kingella for the first time. The results presented here advance our understanding of the function and evolution of DUS and genetic transformation in bacteria, and define the phylogenetic relationships within the Neisseriaceae family.

SUBMITTER: Frye SA

PROVIDER: S-EPMC3630211 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Dialects of the DNA uptake sequence in Neisseriaceae.

Frye Stephan A SA Nilsen Mariann M Tønjum Tone T Ambur Ole Herman OH

PLoS genetics 20130418 4

In all sexual organisms, adaptations exist that secure the safe reassortment of homologous alleles and prevent the intrusion of potentially hazardous alien DNA. Some bacteria engage in a simple form of sex known as transformation. In the human pathogen Neisseria meningitidis and in related bacterial species, transformation by exogenous DNA is regulated by the presence of a specific DNA Uptake Sequence (DUS), which is present in thousands of copies in the respective genomes. DUS affects transform ...[more]

PMID: 23637627

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Project description:All results in this paper are based upon a new dataset consisting in 60 Swadesh lists of 207 items, overall 12,420 terms collected during 2018-2019. Each list corresponds to a different variety of Malagasy, which is not simply identified by the name of the ethnicity but also by the precise location where the variety was collected. This is very important since some traditional ethnic groups are a heritage of historical events rather than representing communities with similar habits and dialects. This new dataset is by far the best available, both for dimension and completeness. The varieties are classified both by standard tools, as the trees generated by UPGMA and NJ which privilege genealogy by detecting vertical transmissions, and by a new method which privileges horizontal exchanges. The new method results in a two-dimensional chart of Madagascar which realistically reproduces geography despite being generated only by comparison of words. The landing date of the ancestors of Malagasy is determined about 650 CE. This result is obtained by a straightforward approach based on the comparison of the UPGMA Malagasy family tree with the analogous tree of Romance family of languages for which all dates are well historically attested. We also propose an improved definition of Diversity computed for every locus in Madagascar and not only in places where the dialects were collected. Moreover, Diversity becomes a locally determined quantity as it is usually in biology. Diversity differences point to the South-East coast as the location where the first colonizers landed or, at least, where Malagasy variants started their dispersion. Finally, we find that the dialect spoken by the Mikea, a hunter-gatherer people in the South-West of Madagascar, is not very different from the variants of their neighbours Vezo and Masikoro. Therefore, Mikea unlikely can be linked to eventual aboriginal populations living in Madagascar prior to the main colonization event in 650 CE.

Project description:Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the Neisseriaceae and Moraxellaceae. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera Acinetobacter, Moraxella, and Neisseria, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to Escherichia coli positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600). Neisseria macacae and Neisseria mucosa subsp. mucosa (ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of Acinetobacter lwoffii, Moraxella lacunata, and N. mucosa. Neisseria meningitidis isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of Neisseriaceae and Moraxellaceae and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (http://www.ridom.hygiene.uni-wuerzburg.de/). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes.

Dataset Information

Dialects of the DNA uptake sequence in Neisseriaceae.

Publications

Dialects of the DNA uptake sequence in Neisseriaceae.

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