Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication

Abstract

Mycobacterium tuberculosis is a high GC Gram-positive member of the actinobacteria. The mycobacterial cell wall is composed of a complex assortment of lipids and is the interface between the bacterium and its environment. The biosynthesis of fatty acids plays an essential role in the formation of cell wall components, in particular mycolic acids, which have been targeted by many of the drugs used to treat M. tuberculosis infection. M. tuberculosis has approximately 250 genes involved in fatty acid metabolism, a much higher proportion than in any other organism. In silico methods have been used to compare the genome of M. tuberculosis CDC1551 to a database of 58 complete bacterial genomes. The resulting alignments were scanned for genes specifically involved in fatty acid biosynthetic pathway I. Phylogenetic analysis of these alignments was used to investigate horizontal gene transfer, gene duplication, and adaptive evolution. It was found that of the eight gene families examined, five of the phylogenies reconstructed suggest that the actinobacteria have a closer relationship with the alpha-proteobacteria than expected. This is either due to either an ancient transfer of genes or deep paralogy and subsequent retention of the genes in unrelated lineages. Additionally, adaptive evolution and gene duplication have been an influence in the evolution of the pathway. This study provides a key insight into how M. tuberculosis has developed its unique fatty acid synthetic abilities.

Fig. 1.

Simplified diagram of the Kyoto Encyclopedia of Genes and Genomes fatty acid biosynthetic pathway I indicating the EC numbers of the enzymes involved and the number of sequences in each alignment. The colored boxes indicate that an alignment has been analyzed for this step of the pathway, and the letters of the alphabet (A-G) in order correspond to the tree diagram constructed for that alignment (see Figs. 2, 3, 4, 5 and 7-9).

Fig. 2.

Phylogenetic tree of the acetyl-CoA carboxylase, carboxyl transferase β-subunit, corresponding to Fig. 1 A. The numbers on the branches are Bayesian clade probabilities. The arrow indicates the branch that was analyzed for signatures indicative of adaptive evolution.

Fig. 3.

Phylogenetic tree inferred from the 3-oxoacyl-(acp) synthase III genes. This tree corresponds to Fig. 1C. Numbers on internal branches indicate clade credibility values for those internal branches where the values were <100. All unlabeled branches correspond to credibility values of 100. The arrow indicates the branch that was analyzed for signatures indicative of adaptive evolution.

Fig. 4.

Phylogenetic tree inferred from 3-oxoacyl (acp) reductase genes. This tree corresponds to Fig. 1F. The numbers on the internal branches are Bayesian clade credibility values. The arrow indicates the branch that was analyzed for signatures indicative of adaptive evolution.

Fig. 5.

Phylogenetic tree inferred from enoyl (acp) reductase genes. This tree corresponds to Fig. 1G. The numbers on the internal branches are Bayesian clade credibility values. The arrow indicates the branch that was analyzed for signatures indicative of adaptive evolution.