WhollyRickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells

Abstract

Reductive genome evolution has purged many metabolic pathways from obligate intracellular Rickettsia (Alphaproteobacteria; Rickettsiaceae). While some aspects of host-dependent rickettsial metabolism have been characterized, the array of host-acquired metabolites and their cognate transporters remains unknown. This dearth of information has thwarted efforts to obtain an axenic Rickettsia culture, a major impediment to conventional genetic approaches. Using phylogenomics and computational pathway analysis, we reconstructed the Rickettsia metabolic and transport network, identifying 51 host-acquired metabolites (only 21 previously characterized) needed to compensate for degraded biosynthesis pathways. In the absence of glycolysis and the pentose phosphate pathway, cell envelope glycoconjugates are synthesized from three imported host sugars, with a range of additional host-acquired metabolites fueling the tricarboxylic acid cycle. Fatty acid and glycerophospholipid pathways also initiate from host precursors, and import of both isoprenes and terpenoids is required for the synthesis of ubiquinone and the lipid carrier of lipid I and O-antigen. Unlike metabolite-provisioning bacterial symbionts of arthropods, rickettsiae cannot synthesize B vitamins or most other cofactors, accentuating their parasitic nature. Six biosynthesis pathways contain holes (missing enzymes); similar patterns in taxonomically diverse bacteria suggest alternative enzymes that await discovery. A paucity of characterized and predicted transporters emphasizes the knowledge gap concerning how rickettsiae import host metabolites, some of which are large and not known to be transported by bacteria. Collectively, our reconstructed metabolic network offers clues to how rickettsiae hijack host metabolic pathways. This blueprint for growth determinants is an important step toward the design of axenic media to rescue rickettsiae from the eukaryotic cell.

The extracellular association of the bacterium “CandidatusDeianiraea vastatrix” with the ciliateParameciumsuggests an alternative scenario for the evolution ofRickettsiales

“…In details, in terms of metabolic capabilities, it could have been equipped with the core biosynthetic pathways, in particular for amino acids (present work), but also for cofactors and nucleotides (as in multiple current Anaplasmataceae, Dunning Hotopp et al 2006), and was possibly capable to survive in low-oxygen conditions (Sassera et al 2011). From the morpho-functional side, it could have been provided with a robust structure made by functional peptidoglycan and LPS (Driscoll et al 2017;Sassera et al 2011;Schulz et al 2016, present study), could synthesize capsule (Schulz et al 2016), possessed flagella (Sassera et al 2011;Vannini et al 2014;Schulz et al 2016;Kwan and Schmidt 2013;Martijn et al 2015) and pili (present work; Schulz et al 2016), and was able to perform chemotaxis (Martijn et al 2015). During the course of evolution, the association of its descendants to eukaryotic cells would have then become tighter and tighter, with a reduction in genome size and complexity, finally leading to the parallel depletion of most metabolic and functional features, including, in most known lineages, the capability to reproduce extracellularly, and a consequent adaptation to the obligate intracellular state.…”

A newly recorded Rickettsia of the Torix group is a recent intruder and an endosymbiont in the whitefly Bemisia tabaci

“…Similar to an uncultured pathogenic endosymbiont ‘ Candidatus Liberibacter asiaticus' in psyllid (Jain et al ., ), glycolysis and the pentose phosphate pathways are both absent in Rickettsia_ bellii_MEAM1, indicating that this Rickettsia could be an energy scavenger and thus import ATP from its host (Jain et al ., ). The absence of glycolysis and the pentose phosphate pathways in Rickettsia _bellii_MEAM1 could be complemented by the host (Driscoll et al ., ) or other microbial symbionts in the host. The above analyses suggest that RiTBt is more recently acquired than Rickettsia _bellii_MEAM1 by its host and is thus less co‐evolved but still shows signs of adaptation to endosymbiosis in its host strain distribution and gene family loss in comparison to the Orientia outgroup.…”

Controlled replication of ‘Candidatus Liberibacter asiaticus‘ DNA in citrus leaf discs

“…The ‘ Ca. L. asiaticus ’ genome encodes an apparently intact ATP/ADP transporter ( nttA ; Duan et al , ; Vahling et al , ; Jain et al , ), suggesting the pathogen acts like an ‘energy parasite’ by importing ATP directly from the host akin to the obligate intracellular bacteria Rickettsia prowazekii (Plano and Winkler, ; Driscoll et al , ) and Chlamydia trachomatis (Iliffe‐Lee and McClarty, ). It is possible that leaf tissue converts glucose to ATP and therefore that the increase in ‘ Ca.…”

“…L. asiaticus' (Duan et al, 2009). Similar to other bacterial obligate intracellular parasites including species of the genus Rickettsia (Driscoll et al, 2017) and phytoplasmas (Oshima et al, 2013), the 'Ca. L. asiaticus' genome has undergone genome reduction (Duan et al, 2009) suggesting that the bacterium relies on the host to obtain essential metabolites in order to replicate.…”