Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

Abstract

Background: The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results: We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions: The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.

Repurposing of Synaptonemal Complex Proteins for Kinetochores in Kinetoplastida

“…The paralogues KKT2,3 and 20, and KKT10,19 have arisen through gene duplications, and this also appears to be the case for KKT17 and KKT18 [16]. Although KKT17,18 are conserved even in divergent kinetoplastids [39], previous studies did not reveal any recognisable domains in these proteins [16].…”

“…To identify potential homologues of the KKT16 complex proteins and to detect proteins or protein complexes with similar domain architectures, we used Hidden Markov Modelling methods (Data & Methods). We generated multiple sequence alignments (MSAs) of previously detected homologues of KKT16-18 found among divergent kinetoplastids [16,39]. We then constructed profile Hidden Markov Models (HMM) based on these MSAs and performed secondary structure-aware profile-versus-profile HMM searches against databases of known conserved domains and structures (Data & Methods, Figure 2a, Figure 3a) using HHsearch [42].…”

Unconventional kinetochore kinases KKT2 and KKT3 have unique centromere localization domains

“…Protein sequences and accession numbers for KKT2 and KKT3 homologs were retrieved from TriTryp database (Aslett et al, 2010), Wellcome Sanger Institute (https://www.sanger.ac.uk/), UniProt (UniProt Consortium, 2019), or a published study (Butenko et al, 2020). Searches for KKT2/3 homologs in Prokinetoplastina and Bodonida were done using hmmsearch on its predicted proteome using manually prepared KKT2/3 hmm profiles (HMMER version 3.0 (Eddy, 1998)).…”

Catalase and Ascorbate Peroxidase in Euglenozoan Protists

“…While euglenids, studied so far, do not encode CAT [11,31], we wondered whether the same pattern applies to diplonemids, which constitute a sister clade to kinetoplastids [32,33]. For this purpose, we took advantage of the transcriptomic data derived from the axenic cultures of several diplonemid species [26]. As supported by maximum likelihood, the CAT sequences of Diplonema japonicum, N. karyoxenos, Rhynchopus humris, A. motanka, and S. specki are nested within eukaryotes with maximum support, consistent with the ancestral origin of their CAT ( Figure 2B).…”

“…In addition, trypanosomatids also lack the whole thioredoxin/thioredoxin reductase pathway, and it was proposed that trypanothione actually substitutes it. However, in the absence of CAT, trypanothione and thioredoxin systems co-exist in Euglena gracilis, indicating that these systems are not entirely redundant [24][25][26].…”