Intragenic Recombination Has a Critical Role on the Evolution of Legionella pneumophila Virulence-Related Effector sidJ

Abstract

SidJ is a Dot/Icm effector involved in the trafficking or retention of ER-derived vesicles to Legionella pneumophila vacuoles whose mutation causes an observable growth defect, both in macrophage and amoeba hosts. Given the crucial role of this effector in L. pneumophila virulence we investigated the mechanisms shaping its molecular evolution. The alignment of SidJ sequences revealed several alleles with amino acid variations that may influence the protein properties. The identification of HGT events and the detection of balancing selection operating on sidJ evolution emerge as a clear result. Evidence suggests that intragenic recombination is an important strategy in the evolutionary adaptive process playing an active role on sidJ genetic plasticity. This pattern of evolution is in accordance with the life style of L. pneumophila as a broad host-range pathogen by preventing host-specialization and contributing to the resilience of the species.

Genomic Analysis Reveals Novel Diversity among the 1976 Philadelphia Legionnaires’ Disease Outbreak Isolates and Additional ST36 Strains

“…Collectively, SNPs were accumulated within these VGRs at ~20-fold higher frequency compared to surrounding sequence, accounting for ~82% of the variation between strain CDC Philadelphia-1 and its sister strains, apart from pP36-Ph. Of the 1,663 single nucleotide variants within VGR-1 and -2 protein coding regions, ~69% were translationally silent or resulted in conservative amino acid substitutions, which is consistent with a previous study of one virulence-associated gene ( sidJ ) within VGR-1 [ 77 ]. Examination of VGR-1 flanking sequences revealed a remarkable concentration of potential and confirmed Dot/Icm secretion substrates both upstream ( legAU13 , lpg2144; legA6 , lpg2131; legK2 , lpg2137; mavC , lpg2147; hypothetical protein, lpg2148) and downstream ( sdeA/laiA , lpg2157; hypothetical protein, lpg2160; lem19 , lpg2166; and legS2 , lpg2176) [ 64 , 78 – 83 ].…”

“…Direct genetic evidence includes the conservation and distribution of VGR-1 and VGR-2 sub-types (“A” and “B”) among the current ST36 strains, confirming that most variation between strain CDC Philadelpia-1 and its sister genomes, apart from pP36-Ph, is due to HGT rather than single nucleotide substitution [ 85 ]. Additional VGR sub-types beyond those identified here certainly exist, as several alleles of dotA and sidJ have been previously reported within VGR-2 and -1, respectively [ 77 , 103 ]. Lastly, we documented 12 non-HGT-associated polymorphisms shared only among strains Philadelphia-2, -3, and -4 ( Table 4 ), which argues against the hypothesis that variation within the Philadelphia clade arose after clinical isolation, but strongly supports a prior split in this lineage.…”

A supervised statistical learning approach for accurateLegionella pneumophilasource attribution during outbreaks

“…Recombination is a driving force in the evolution of the Legionellae (5, 7, 28-31). Therefore, to further understand the structure and evolution of this Lpn-SG1 population we assessed the impact of DNA exchange.…”

The recombination dynamics of Staphylococcus aureus inferred from spA gene

“…Neighbor-net analysis was performed and converted to a splits graph by SplitsTree4 software – version 4.6 [ 48 , 49 ], as previously described [ 50 ]. Intragenic recombination was screened within the aligned sequences with GARD method [ 51 ] available in Datamonkey server [ 52 ] as previously described [ 53 ]. GARD results were confirmed [ 54 ] using a recombination cost “delta dirac” and mutation cost “Hamming” implemented in the Recco program [ 55 ].…”

“…RDP3 program [ 56 ] was performed to validate the obtained results [ 53 ] with the requirement that each potential event had to be detected simultaneously by three or more methods.…”