Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation

Abstract

Background: The Correia Repeat Enclosed Element (CREE) of the Neisseria spp., with its inverted repeat and conserved core structure, can generate a promoter sequence at either or both ends, can bind IHF, and can bind RNase III and either be cleaved by it or protected by it. As such, the presence of this element can directly control the expression of adjacent genes. Previous work has shown differences in regulation of gene expression between neisserial strains and species due to the presence of a CREE. These interruptions perhaps remove the expression of CREE-associated genes from ancestral neisserial regulatory networks.

Results: Analysis of the chromosomal locations of the CREE in Neisseria gonorrhoeae strain FA1090 and N. gonorrhoeae strain NCCP11945 has revealed that most of the over 120 copies of the element are conserved in location between these genome sequences. However, there are some notable exceptions, including differences in the presence and sequence of CREE 5' of copies of the opacity protein gene opa, differences in the potential to bind IHF, and differences in the potential to be cleaved by RNase III.

Conclusion: The presence of CREE insertions in one strain relative to the other, CREE within a prophage region, and CREE disrupting coding sequences, provide strong evidence of mobility of this element in N. gonorrhoeae. Due to the previously demonstrated role of these elements in altering transcriptional control and the findings from comparing the two gonococcal genome sequences, it is suggested that regulatory differences orchestrated by CREE contribute to the differences between strains and also between the closely related yet clinically distinct species N. gonorrhoeae, Neisseria meningitidis, and Neisseria lactamica.

Figure 1

CREE sequence structures. Comparative illustration of the sequence structures of different lengths of CREE. Sequences in the key are based on consensus sequences of all aligned N. gonorrhoeae CREE. Three different length types of CREE are present in the gonococcal genome sequences, however the shortest (69–73 bp) have two different structure types. An IHF binding site is only possible in the longest of the CREE (153–157 bp).

Figure 2

CREE sequence features. For illustration purposes a consensus sequence of the longer CREE is shown, here 156 bp. The ways in which the two different CREE associated promoters are generated from native sequence (blue line) and CREE sequence (red line) are shown for the Snyder promoter (left) [11] and the Black promoter (right) [10]. Both of these would drive transcription from left to right. Given favourable native sequence it might be possible to generate both promoters on the opposite strand as well, transcribing right to left. The IHF-binding site within the CREE is shown (orange), as are the inverted repeats that potentially form mRNA hairpin substrates for RNase III (green).

Figure 3

CREE distribution in the chromosomes. Distribution of the CREE (x-axis) and their lengths (y-axis) in the genome sequences of N. gonorrhoeae strain FA1090 (A) and N. gonorrhoeae strain NCCP11945 (B). Length variants are shown with larger spots and are colour coded: green – 97 bp CREE due to a 9 bp deletion; purple – 110 bp CREE due to a 5 bp duplication; blue – 143 bp CREE due to an 11 bp deletion; red – 169 bp CREE due to a 64 bp duplication in a 105 bp CREE.

Figure 4

CREE and chromosomal rearrangement. Alignment of the N. gonorrhoeae strain FA1090 (top) and strain NCCP11945 (bottom) genome sequences using progressive Mauve [43]. Several chromosomal rearrangements and inversions of large regions of sequence can be seen represented here by coloured blocks. Those below the mid-line in strain NCCP11945 are inverted relative to the strain FA1090 sequence. The arrows indicate the left and right ends of a single CREE in strain FA1090 and their alignment with two separate CREE at a chromosomal rearrangement point relative to strain NCCP11945.