Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction

Abstract

We have reconstructed the gene content and order of the last common ancestor of the human pathogens Mycobacterium leprae and Mycobacterium tuberculosis. During the reductive evolution of M. leprae, 1537 of 2977 ancestral genes were lost, among which we found 177 previously unnoticed pseudogenes. We find evidence that a massive gene inactivation took place very recently in the M. leprae lineage, leading to the loss of hundreds of ancestral genes. A large proportion of their nucleotide content ( approximately 89%) still remains in the genome, which allowed us to characterize and date them. The age of the pseudogenes was computed using a new methodology based on the rates and patterns of substitution in the pseudogenes and functional orthologous genes of closely related genomes. The position of the genes that were lost in the ancestor's genome revealed that the process of function loss and degradation mainly took place through a gene-to-gene inactivation process, followed by the gradual loss of their DNA. This suggests a scenario of massive genome reduction through many nearly simultaneous pseudogenization events, leading to a highly specialized pathogen.

Figure 1.

Phylogenetic relationships among mycobacterial species. See Methods for abbreviations. The numbers to the left of each node are bootstrap values. A line of length 0.1 amino acid substitutions per site is shown.

Figure 2.

Chromosomal rearrangements between Mav, Mtu(I), Mle, and the ancestor’s genome. (A) Number of breakpoints from the ancestor’s genome to each species used. The position of the ancestor’s genome is marked with a shaded circle. (B) Graphic representation of the genome rearrangements. From the outside: ancestor, Mav, Mtu(I), and Mle. White spaces represent absent genes in the corresponding genome. The black line in the ancestral genome and in the genomes of Mav and Mtu(I) (top, marked by the arrow) corresponds to two genes of unknown order in the ancestor. Each change of color from dark to light gray indicates a breakpoint.

Figure 3.

Phylogenetic tree of Mav (a), Mle (l) and the M. tuberculosis group (t). The common ancestor to t and l is designed as i. Two periods are considered in the branch of Mle: a first period as an active gene (g) and a second period as a pseudogene (ps). Parameters y and z are the numbers of nonsynonymous substitutions per nucleotide site in the Mle branch, in the event that the active gene had reached the present time or it had evolved as a pseudogene from i until the present, respectively. dN_it is the number of nonsynonymous substitutions from the ancestor to Mtu.

Figure 4.

Frequency distribution for the age of Mle pseudogenes (n = 611).

Figure 5.

Distribution of genes with the status of absent genes in Mle. The chromosomal position of these genes in the ancestor’s genome has been analyzed. Absent genes may be isolated (block size = 1, although they are not blocks, we called them blocks of a single gene with the aim of simplifying the figure) or in blocks of several contiguous absent genes (size range 2–37).

Figure 6.

Percentage of lost DNA in Mle pseudogenes or absent genes. (A) Proportion of lost DNA in pseudogenes. (B) Proportion of lost DNA in absent genes.