Insight into cross-talk between intra-amoebal pathogens

Abstract

Background: Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to different bacterial phyla and often show a larger genome size than human-infecting pathogens. This characteristic is proposed to be the result of frequent gene exchanges with other bacteria that share a sympatric lifestyle and contrasts with the genome reduction observed among strict human pathogens.

Results: We sequenced the genome of a new amoebal pathogen, Legionella drancourtii, and compared its gene content to that of a Chlamydia-related bacterium, Parachlamydia acanthamoebae. Phylogenetic reconstructions identified seven potential horizontal gene transfers (HGTs) between the two amoeba-resistant bacteria, including a complete operon of four genes that encodes an ABC-type transporter. These comparisons pinpointed potential cases of gene exchange between P. acanthamoebae and Legionella pneumophila, as well as gene exchanges between other members of the Legionellales and Chlamydiales orders. Moreover, nine cases represent possible HGTs between representatives from the Legionellales or Chlamydiales and members of the Rickettsiales order.

Conclusions: This study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle.

Figure 1

Definition of orthologous proteins. Representation of the identity (%) and coverage (%) of the query alignment that results from a BLASTP search of P. acanthamoebae versus L. drancourtii. Of the 1023 proteins showing reciprocal best blast hits, 508 exhibited a similarity greater than 30% and an alignment coverage longer than 60% of the query (black) and were defined as orthologues. Of the remaining 515 proteins (gray), 53 did not fulfill the same criteria in the reciprocal analysis and, therefore were discarded, although they appear on this figure as passing the cutoffs. The correlation coefficient between both of the reciprocal BLAST analyses was 0.97 and 0.80 for the percentage identity and the percentage coverage, respectively.

Figure 2

Gene clusters. Orthologous genes were subjected to BLASTP against seven other organisms, colored in gray and black when using Parachlamydia and Legionella proteins as queries, respectively. Genes were clustered according to their presence (gray) or absence (black) in the six related bacteria and the amoebal species, D. discoideum. The genes form 8 major groups at a height of 3 (A to H).

Figure 3

The ABC transporter operon. (A) An operon encoding the ABC transporter was present in both P. acanthamoebae and L. drancourtii. (B, C, D and E) A bayesian tree of each orthologous protein (ID 127, 128, 129, and 130) encoded in the operon and their 10 best BLAST hits, restricted to one hit per bacterial genus. Sequences retrieved using L. drancourtii or P. acanthamoebae as the query in a BLAST homology search are tagged with an LLAP or PAH prefix, respectively. Sequences belonging to the best BLAST hit for both orthologues harbor both prefixes. All of the proteins encoded for in the operon exhibit a similar phylogenetic tree, which shows a clustering of P. acanthamoebae and L. drancourtii, thereby supporting the hypothesis of a single transfer event for all four genes.

Figure 4

dpsA phylogeny. The bayesian tree for dpsA (ID 263), a protein involved in protection against oxidative stress, and the 20 best BLAST hits shows the clustering of proteins from Rickettsia with Legionella species and, to a lesser extent, with Parachlamydiaceae and Synechococcus, a cyanobacterium. Sequences retrieved using L. drancourtii or P. acanthamoebae as the query in a BLAST homology search are tagged with an LLAP or PAH prefix, respectively. Sequences belonging to the best BLAST hits for both orthologues harbor both prefixes.

Figure 5

Potential gene transfers with members of the Rickettsiales order. The bayesian trees for each orthologous gene (ID 387, 388, 390, and 134) and their 10 best BLAST hits show the clustering of Chlamydiales and Legionellales with members of the Rickettsiales order. The retrieval of BLAST hits was restricted to one per bacterial genus for (A), (B), and (D) but not for (C). Sequences retrieved using L. drancourtii or P. acanthamoebae as the query in a BLAST homology search are tagged with an LLAP or PAH prefix, respectively. Sequences belonging to the best BLAST hits for both orthologues harbor both prefixes.