Repeated extragenic sequences in prokaryotic genomes: a proposal for the origin and dynamics of the RUP element in Streptococcus pneumoniae

• Published in: Microbiology (Society for General Microbiology) Vol. 145; no. 10; pp. 2647 - 2653
• Main Authors: Oggioni, Marco R, Claverys, Jean-Pierre
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.10.1999; Society for General Microbiology
• Subjects: Bacteriology; Base Sequence; Biological and medical sciences; DNA Transposable Elements - genetics; DNA, Bacterial - genetics; Fundamental and applied biological sciences. Psychology; Genetics; Genome, Bacterial; insertion sequence IS630; Microbiology; Models, Genetic; Molecular Sequence Data; Recombination, Genetic; Repetitive Sequences, Nucleic Acid - genetics; RUP element; Sequence Homology, Nucleic Acid; Spn1 gene; Streptococcus pneumoniae; Streptococcus pneumoniae - genetics; Terminal Repeat Sequences; Streptococcaceae; Genetic variability; Repeated sequence; Gene rearrangement; Bacteria; Micrococcales; Spacer DNA; Transposable element; Genome; IS element; Streptococcus pneumoniae
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/00221287-145-10-2647

Microbiologia/Universita’ di Siena, Via Laterina 8, 53100 Siena, Italy 1 Laboratoire de Microbiologie et Génétique Moléculaire CNRS-UPR 9007, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France 2 Author for correspondence: Jean-Pierre Claverys. Tel: +33 561 33 59 11. Fax: +33 561 33 58 86. e-mail: claverys{at}ibcg.biotoul.fr A survey of all Streptococcus pneumoniae GenBank/EMBL DNA sequence entries and of the public domain sequence (representing more than 90% of the genome) of an S. pneumoniae type 4 strain allowed identification of 108 copies of a 107-bp-long highly repeated intergenic element called RUP (for r epeat u nit of p neumococcus). Several features of the element, revealed in this study, led to the proposal that RUP is an insertion sequence (IS)-derivative that could still be mobile. Among these features are: (1) a highly significant homology between the terminal inverted repeats (IRs) of RUPs and of IS 630 -Spn 1 , a new putative IS of S. pneumoniae ; and (2) insertion at a TA dinucleotide, a characteristic target of several members of the IS 630 family. Trans -mobilization of RUP is therefore proposed to be mediated by the transposase of IS 630 -Spn 1 . To account for the observation that RUPs are distributed among four subtypes which exhibit different degrees of sequence homogeneity, a scenario is invoked based on successive stages of RUP mobility and non-mobility, depending on whether an active transposase is present or absent. In the latter situation, an active transposase could be reintroduced into the species through natural transformation. Examination of sequences flanking RUP revealed a preferential association with ISs. It also provided evidence that RUPs promote sequence rearrangements, thereby contributing to genome flexibility. The possibility that RUP preferentially targets transforming DNA of foreign origin and subsequently favours disruption/rearrangement of exogenous sequences is discussed. Keywords: chromosome rearrangements, genetic flexibility, intergenic regions, repeated elements, Streptococcus pneumoniae Abbreviations: IS, insertion sequence; IR, inverted repeat; IRL, left IR; IRR, right IR The GenBank/EMBL accession numbers of the sequences determined in this work are AJ242695 –AJ242698