Whole-genome organization and functional properties of miniature DNA insertion sequences conserved in pathogenic Neisseriae

The chromosome of pathogenic Neisseriae is peppered by members of an abunda nt family of small DNA sequences known as Correia elements. These DNA repea ts, that we call nemis (for neisseria miniature insertion sequences) can be sorted into two major size classes. Both unit-length (154-158 bp) and inte rnally rearranged (104-108 bp) elements feature long terminal inverted repe ats (TIRs), and can potentially fold into robust stem-loop structures. Nemi s are (or have been) mobile DNA sequences which generate a specific 2-by ta rget site duplication upon insertion, and strictly recall RUP, a repeated D NA element found in Streptococcus pneumoniae. The subfamilies of 26L/26R, 2 6L/27R, 27L/27R and 27L/26R elements, found by wide-genome computer surveys in both the Neisseria meningitidis and the Neisseria gonorrhoeae genomes, originate from the combination of TIRs which vary in length (26-27 bp) as i n sequence content (L and R types). In both species, the predominant subfam ily is made by the 26L/26R elements. The number of nemis is comparable in t he N. meningitidis Z2491 (A serogroup) and the MC58 (B serogroup) strains, but is sharply reduced in the N. gonorrhoeae strain F1090. Consequently, se veral genes which are conserved in the two pathogens are flanked by nemis D NA in the meningococcus genome only. More than 2/3 of nemis are intersperse d with single-copy DNA, and are found at close distance from cellular genes . Both primer extension and RNase protection data lend support to the notio n that nemis are cotranscribed with cellular genes and subsequently process ed, at either one or both TIRs, by a specific endoribonuclease, which plaus ibly corresponds to RNase III. (C) 2001 Elsevier Science B.V. All rights re served.