The Genome of the Amoeba Symbiont “CandidatusAmoebophilus asiaticus” Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

Abstract

Protozoa play host for many intracellular bacteria and are important for the adaptation of pathogenic bacteria to eukaryotic cells. We analyzed the genome sequence of "Candidatus Amoebophilus asiaticus," an obligate intracellular amoeba symbiont belonging to the Bacteroidetes. The genome has a size of 1.89 Mbp, encodes 1,557 proteins, and shows massive proliferation of IS elements (24% of all genes), although the genome seems to be evolutionarily relatively stable. The genome does not encode pathways for de novo biosynthesis of cofactors, nucleotides, and almost all amino acids. "Ca. Amoebophilus asiaticus" encodes a variety of proteins with predicted importance for host cell interaction; in particular, an arsenal of proteins with eukaryotic domains, including ankyrin-, TPR/SEL1-, and leucine-rich repeats, which is hitherto unmatched among prokaryotes, is remarkable. Unexpectedly, 26 proteins that can interfere with the host ubiquitin system were identified in the genome. These proteins include F-and U-box domain proteins and two ubiquitin-specific proteases of the CA clan C19 family, representing the first prokaryotic members of this protein family. Consequently, interference with the host ubiquitin system is an important host cell interaction mechanism of "Ca. Amoebophilus asiaticus". More generally, we show that the eukaryotic domains identified in "Ca. Amoebophilus asiaticus" are also significantly enriched in the genomes of other amoeba-associated bacteria (including chlamydiae, Legionella pneumophila, Rickettsia bellii, Francisella tularensis, and Mycobacterium avium). This indicates that phylogenetically and ecologically diverse bacteria which thrive inside amoebae exploit common mechanisms for interaction with their hosts, and it provides further evidence for the role of amoebae as training grounds for bacterial pathogens of humans.Free-living amoebae, such as Acanthamoeba spp., are ubiquitous protozoa which can be found in such diverse habitats as soil, marine water, and freshwater and in many engineered environments (62, 100). They are important predators of prokaryotic and eukaryotic microorganisms, thereby having great influence on microbial community composition, soil mineralization, plant growth, and nutrient cycles (14, 100). Interestingly, many well-known pathogens of humans are able to infect, survive, and multiply within amoebae (39, 51). These protozoa can thus serve as reservoirs and vectors for the transmission of pathogenic bacteria to humans, as demonstrated for L. pneumophila and Mycobacterium avium (2, 115). It is also increasingly being recognized that protozoa are important for the adaptation of (pathogenic) bacteria to higher eukaryotic cells as a niche for growth (2,24,42,78,89).In addition to the many recognized transient associations between amoeba and pathogens, stable and obligate relationships between bacteria and amoebae also were described for members of the Alphaproteobacteria (11, 34, 48), the Betaproteobacteria (49), the Bacteroidetes (50), and the Chlamydiae (4, 12, 35, 52...

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

“…These features include reduced genome size, AT bias, and loss of biosynthetic pathways (64,65). In particular, amino acid biosynthetic genes are often lost in obligate symbiotic bacterial genomes (obligate host pathogens and obligate endosymbionts) (64,66,67), where amino acids are obtained from the host environment.…”

Genome Dynamics in Legionella: The Basis of Versatility and Adaptation to Intracellular Replication

“…A similar observation has been made when the genome sequence of the amoeba symbiont "Candidatus Amoebophilus asiaticus" has been analyzed. Interestingly, many of the eukaryotic motifs identified in Legionella are also present in this bacterium (Schmitz-Esser et al 2010). Most interestingly, an enrichment analysis comparing the fraction of all functional protein domains among 514 bacterial proteomes revealed that all genomes of bacteria replicating in amoeba were enriched in protein domains that are predominantly found in eukaryotic proteins (Schmitz-Esser et al 2010).…”

“…Interestingly, many of the eukaryotic motifs identified in Legionella are also present in this bacterium (Schmitz-Esser et al 2010). Most interestingly, an enrichment analysis comparing the fraction of all functional protein domains among 514 bacterial proteomes revealed that all genomes of bacteria replicating in amoeba were enriched in protein domains that are predominantly found in eukaryotic proteins (Schmitz-Esser et al 2010). The most highly enriched domains were ANK repeats, LRR, SEL1 repeats, and Fand U-box domains, all of which are also present in L. pneumophila and L. longbeachae.…”

“…The interaction between both organisms provides bacteria with the capacity to infect human cells and to become human pathogens. Furthermore, genome analyses and comparative genomics of amoeba-associated bacteria revealed that common virulence factors are present in bacteria living with amoebae (Schmitz-Esser et al 2010). This finding suggested that the genes coding for these virulence factors may be interchanged and that they may thus be part of mobile genetic elements.…”

Free living amoebae in water environment: health implications

“…Per la capacità di sostenerne la sopravvivenza e la crescita e attivare la virulenza dei microrganismi veicolati, è altamente plausibile che le amebe a vita libera rivestano un ruolo preponderante nella proliferazione dei microrganismi nelle reti idriche. La potenzialità ad acquisire una maggiore infettività (46,48,52) dopo la crescita all'interno delle amebe, unitamente alla possibilità che abbiano luogo fenomeni di scambio di materiale genetico (44), conferiscono ai microrganismi a diffusione idrica un notevole vantaggio biologico che è di fondamentale importanza nella loro evoluzione a patogeni umani. È emerso che le amebe a vita libera presenti nelle reti idriche ospiterebbero microrganismi più frequentemente di quanto accada per quelle isolate da sorgenti idriche naturali.…”