Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae

Abstract

In Chlamydiaceae, the nucleotide sequence between the 5S rRNA gene and the gene for subunit F of the Na(+)-translocating NADH-quinone reductase (nqrF or dmpP) has varied lengths and gene contents. We analyzed this site in 45 Chlamydiaceae strains having diverse geographical and pathological origins and including members of all nine species.

FIG. 1.

Genetic diversity at the 5S rrn-nqrF site. The schematic diagram presents the genetic organization of the rrn-nqrF intergenic segment. Chlamydia species are separated into four groups based on genetic relatedness at the site. Vertical bars indicate mutations that cause frameshifts or translation stops. Homologous ORFs are indicated graphically as shaded arrows. The diagram is drawn approximately to scale. seq., sequence(s).

FIG. 2.

Multiple alignment of the poly(C) and poly(T) tracts and flanking sequences at the rrn-nqrF sites in three Chlamydia species. Base numbering is from the 3′ end of rrn.

FIG. 3.

Multiple repeats at the rrn-nqrF site of C. pecorum. (A) Gel electrophoresis of amplicons generated with primers 5S rRNA F and nqrF R (data available upon request) for 10 C. pecorum isolates (Table 1). The numbers of octamer repeats are indicated above the lanes. Numbers at the left are molecular sizes. (B) Nucleotide sequence of the rrn-nqrF site of C. pecorum strain 1710S, which contains 35 octamer repeats.