Evidence for symmetric chromosomal inversions around the replication origin in bacteria

Abstract

Background: Whole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species.

Results: By comparing the recently completed genome sequences of Vibrio cholerae, Streptococcus pneumoniae and Mycobacterium tuberculosis to those of closely related species - Escherichia coli, Streptococcus pyogenes and Mycobacterium leprae, respectively - we have identified an unusual and previously unobserved feature of bacterial genome structure. Scatterplots of the conserved sequences (both DNA and protein) between each pair of species produce a distinct X-shaped pattern, which we call an X-alignment. The key feature of these alignments is that they have symmetry around the replication origin and terminus; that is, the distance of a particular conserved feature (DNA or protein) from the replication origin (or terminus) is conserved between closely related pairs of species. Statistically significant X-alignments are also found within some genomes, indicating that there is symmetry about the replication origin for paralogous features as well.

Conclusions: The most likely mechanism of generation of X-alignments involves large chromosomal inversions that reverse the genomic sequence symmetrically around the origin of replication. The finding of these X-alignments between many pairs of species suggests that chromosomal inversions around the origin are a common feature of bacterial genome evolution.

Figure 1

Between-species whole-genome DNA alignments. Plots of maximally unique matching subsequences (MUMs) between genomes as identified by the MUMmer program. (a)V. cholerae chrI forward strand versus E. coli forward strand. (b)E. coli forward versus V. cholerae chrI reverse. (c)V. cholerae chrI versus E. coli, forward and reverse overlaid. (d)S. pneumoniae forward versus S. pyogenes forward and reverse overlaid. (e)M. tuberculosis forward versus M. leprae forward and reverse overlaid. A point (x, y) indicates a DNA sequence that occurs once within each genome, at location x in one genome and at location y in the other genome. The matching sequences may occur on either the forward or the reverse strand; in either case, the locations indicate the 5' end of the sequences. The point (0,0) corresponds to the origin of replication for each genome.

Figure 2

Whole-genome proteome alignments. Plots show the chromosome locations of pairs of predicted proteins that have significant similarity (on the basis of fasta3 comparisons). (a)V. cholerae chrI versus E. coli. All significant matches for each V. cholerae ORF are shown. (b)V. cholerae chrI versus E. coli, top matches. Only the best match for each V. cholerae ORF is shown. The filtering for top matches for each ORF removes noise due to the presence of many large multigene families. This X-alignment is highly statistically significant (Table 2). (c)Chlamydia trachomatis versus C. pneumoniae, top matches. Only the best match for each C. trachomatis ORF is shown. The position of the origins (R) and termini (T) of replication are slightly shifted to see the inversions better. This pattern is consistent with the occurrence a small number of inversions around the origin and terminus in the two lineages since their divergence from a common ancestor (see Figure 4). (d)V. cholerae chrI versus V. cholerae chrI, self-alignment. Only recently duplicated pairs of genes are shown. Recent duplications were operationally defined as those genes that were more similar to another gene in V. cholerae than to any gene in any other complete genome sequence. The faint X-alignment is statistically significant (Table 2). No significant X-alignment was detected when all pairs of paralogs were included.

Figure 3

Within-genome DNA alignments. Plots of exactly matching sequences within four genomes as identified by the MUMmer program: (a)V. cholerae; (b)E. coli; (c)S. pyogenes; (d)S. pneumoniae. A point (x,y) indicates a DNA sequence that is repeated within the genome, occurring once at location x and again at location y. Points near the diagonal (y = x) correspond to tandem repeats. Points near the anti-diagonal (y = L - x, where L is genome length) correspond to repeats that occur at symmetric locations about the origin of location. The point (0,0) corresponds to the origin of replication in each plot. Statistically significant X-alignments occur in all four species (Table 1).

Figure 4

Schematic model of genome inversions. The model shows an initial speciation event, followed by a series of inversions in the different lineages (A and B). Inversions occur between the asterisks (^*). Numbers on the chromosome refer to hypothetical genes 1-32. At time point 1, the genomes of the two species are still co-linear (as indicated in the scatterplot of A1 versus B1). Between time point 1 and time point 2, each species (A and B) undergoes a large inversion about the terminus (as indicated in the scatterplots of A1 versus A2 and B1 versus B2). This results in the between-species scatterplot looking as if there have been two nested inversions (A2 versus B2), similar to that seen for C. trachomatis versus C. pneumoniae (see Figure 2). Between time point 2 and time point 3 each species undergoes an additional inversion (as indicated in the scatterplots of B2 versus B3 and A2 versus A3). This results in the between-species scatterplots beginning to resemble an X-alignment, similar to that seen in M. tuberculosis versus M. leprae (see Figure 2).