title: The transposon-like Correia elements encode numerous strong promoters and provide a potential new mechanism for phase variation in the meningococcus.
abstract: Neisseria meningitidis is the primary causative agent of bacterial meningitis. The genome is rich in repetitive DNA and almost 2% is occupied by a diminutive transposon called the Correia element. Here we report a bioinformatic analysis defining eight subtypes of the element with four distinct types of ends. Transcriptional analysis, using PCR and a lacZ reporter system, revealed that two ends in particular encode strong promoters. The activity of the strongest promoter is dictated by a recurrent polymorphism (Y128) at the right end of the element. We highlight examples of elements that appear to drive transcription of adjacent genes and others that may express small non-coding RNAs. Pair-wise comparisons between three meningococcal genomes revealed that no more than two-thirds of Correia elements maintain their subtype at any particular locus. This is due to recombinational class switching between elements in a single strain. Upon switching subtype, a new allele is available to spread through the population by natural transformation. This process may represent a hitherto unrecognized mechanism for phase variation in the meningococcus. We conclude that the strain-to-strain variability of the Correia elements, and the large number of strong promoters encoded by them, allows for potentially widespread effects within the population as a whole. By defining the strength of the promoters encoded by the eight subtypes of Correia ends, we provide a resource that allows the transcriptional effects of a particular subtype at a given locus to be predicted.
authors.affiliation: School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom.
authors.forename: Azeem
authors.initials: A
authors.lastname: Siddique
authors.forename: Nicolas
authors.initials: N
authors.lastname: Buisine
authors.forename: Ronald
authors.initials: R
authors.lastname: Chalmers
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D008585:Meningitis, Meningococcal / Q000382:microbiology*; D008969:Molecular Sequence Data; D009344:Neisseria gonorrhoeae / Q000235:genetics; D009345:Neisseria meningitidis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D058727:RNA, Small Untranslated / Q000235:genetics; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D004251:DNA Transposable Elements; D058727:RNA, Small Untranslated