Retortamonads from vertebrate hosts share features of anaerobic metabolism and pre-adaptations to parasitism with diplomonads

Abstract

Although the mitochondria of extant eukaryotes share a single origin, functionally these organelles diversified to a great extent, reflecting lifestyles of the organisms that host them. In anaerobic protists of the group Metamonada, mitochondria are present in reduced forms (also termed hydrogenosomes or mitosomes) and a complete loss of mitochondrion in Monocercomonoides exilis (Metamonada:Preaxostyla) has also been reported. Within metamonads, retortamonads from the gastrointestinal tract of vertebrates form a sister group to parasitic diplomonads (e.g. Giardia and Spironucleus ) and have also been hypothesized to completely lack mitochondria. We obtained transcriptomic data from Retortamonas dobelli and R. caviae and searched for enzymes of the core metabolism as well as mitochondrion- and parasitism-related proteins. Our results indicate that retortamonads have a streamlined metabolism lacking pathways for metabolites they are probably capable of obtaining from prey bacteria or their environment, reminiscent of the biochemical arrangement in other metamonads. Retortamonads were surprisingly found do encode homologs of components of Giardia ‘s remarkable ventral disk, as well as homologs of regulatory NEK kinases and secreted lytic enzymes known for involvement in host colonization by Giardia . These can be considered pre-adaptations of these intestinal microorganisms to parasitism. Furthermore, we found traces of the mitochondrial metabolism represented by iron‑sulfur cluster assembly subunits, subunits of mitochondrial translocation and chaperone machinery and, importantly, [FeFe]‑hydrogenases and hydrogenase maturases (HydE, HydF and HydG). Altogether, our results strongly suggest that a remnant mitochondrion is still present.

Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Fornicata

“…Given that the role for clathrin assemblies in Giardia has not been elucidated and that the nature of Gl CLC ( Gl 4259) as a clathrin light chain orthologue is dubious, we sought to shed light on the significance of this correlation by investigating the distribution of both CHC and CLC orthologues in selected eukaryotic lineages. To do this, we employed protein homology searches based on Hidden-Markov Models (HMM) (Eddy 2011) using as query an alignment of canonical and documented CHC or CLC sequences from several protozoa and metazoan species (Supplementary Tables 2 and 5) (Morgan et al 2001; Kaksonen et al 2005; Adung’a et al 2013; Kirchhausen et al 2014; Karnkowska et al 2016; Karnkowska et al 2019, Füssy et al, 2021). In our search we considered assembled read data from RNA-seq experiments (transcriptomics) as reliable as genomic sequence data (Cheon et al 2020).…”

“…In stark contrast to CHC, the search for bona fide CLC sequences did not retrieve any reliable predictions in available genomes and transcriptomes from species of the Fornicata lineage, including the lineages Hexamitidae, Retortamonas and Carpediemonas-like organisms (Xu et al 2014;Leger et al 2017;Tanifuji et al 2018;Füssy et al 2021;Salas-Leiva et al 2021). Importantly, this search did not return the putative, highly diverged GlCLC (Zumthor et al 2016).…”

Evidence for an Independent Hydrogenosome-to-Mitosome Transition in the CL3 Lineage of Fornicates

“…We denote the grouping comprised of diplomonads and their relatives up to Chilomastix spp. as the ACS1 group, since these fornicates are characterized by the shared possession of the ACS1 form of acetyl-CoA synthase that presumably replaced the ACS2 form ancestral for fornicates ( Leger et al, 2017 ; Füssy et al, 2021 ). Interestingly, previous analyses recovered A. paluster (CL2) and E. cyprinoides (CL5) as independent lineages, with A. paluster branching sister to the ACS1 group (bootstrap value of 88%) and E. cyprinoides sister to both these taxa combined ( Leger et al, 2017 ).…”

“…Other taxa, such as the preaxostylan Paratrimastix pyriformis , the fornicate Dysnectes brevis , and the single barthelonid investigated in this regard, exhibit MROs that may produce H 2 without a link to ATP generation. Such a MRO type has most recently been hypothesized to also occur in the so-called vertebrate retortamonads, a sister group of diplomonads within Fornicata ( Füssy et al, 2021 ; Stairs et al, 2021 ), and seems to have been preserved in some diplomonads (e.g., the free-living Trepomonas ; Leger et al, 2017 ). However, other diplomonads exhibit typical hydrogenosomes that are thought to have evolved by secondarily acquiring MRO-localized ATP production via horizontal gene transfer (e.g., the endobiotic Spironucleus salmonicida ) or, as is the case of the Giardia lineage, have further reduced the MRO into a mitosome lacking both H 2 and ATP production.…”

Inheritance of the reduced mitochondria of Giardia intestinalis is coupled to the flagellar maturation cycle

“…They all are genomeless and lack many mitochondrial functions including the respiratory chain and the coupled ATP synthesis. Due to their variability, these organelles are often referred to as mitochondria-related organelles (MROs) [ 71 – 74 ]. Interestingly, MROs are always present in large numbers (in tens to hundreds), and concerning their dynamics, they are very stable during the cell cycle [ 7 ].…”