A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist

The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss; therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrial-encoded RM system can function as a toxin-antitoxin selfish element and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.Peer reviewe

Chlamydial contribution to anaerobic metabolism during eukaryotic evolution

The origin of eukaryotes is a major open question in evolutionary biology. Multiple hypotheses posit that eukaryotes likely evolved from a syntrophic relationship between an archaeon and an alphaproteobacterium based on H-2 exchange. However, there are no strong indications that modern eukaryotic H-2 metabolism originated from archaea or alphaproteobacteria. Here, we present evidence for the origin of H-2 metabolism genes in eukaryotes from an ancestor of the Anoxychlamydiales-a group of anaerobic chlamydiae, newly described here, from marine sediments. Among Chlamydiae, these bacteria uniquely encode genes for H-2 metabolism and other anaerobiosis-associated pathways. Phylogenetic analyses of several components of H-2 metabolism reveal that Anoxychlamydiales homologs are the closest relatives to eukaryotic sequences. We propose that an ancestor of the Anoxychlamydiales contributed these key genes during the evolution of eukaryotes, supporting a mosaic evolutionary origin of eukaryotic metabolism

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors— members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis

Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%–61%median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize ?-glucans rather than ?-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease

RQUA tree datasets

File - Description ## Within MLanalysis ## *iqtree.log logfile from IQTREE analysis *IQtreefile.nex IQTREE output tree *seqs.fasta sequences unaligned *mafft.fasta sequences aligned with mafft *mafft.bmge_masked.fasta BMGE masked alignment ## Within TopologyTests ## *.log IQTREE logfile from site likelihood inference *.sitelh site likelihood file from IQTREE *_ContrainTrees_BootstrapTrees.tre ML cosntrain trees *_consel.catpv output from CONSEL ## FILES ## RQUA_full_datasets/MLanalysis rqua.iqtree.log rqua.IQtreefile.nex rqua.mafft.bmge_masked.fasta rqua.mafft.fasta rqua.seqs.fasta RQUA_full_datasets/TopologyTests RQUA_fulldataset_consel.catpv RQUA_fulldataset_ContrainTress_BootstrapTrees.tre RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.log RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.sitelh RQUA_GroupA_datasets/MLanalysis rqua.GroupA.IQtree.log rqua.GroupA.IQtree.treefile rqua.GroupA.mafft.bmge_masked.fasta rqua.GroupA.mafft.fasta rqua.GroupA.seqs.fasta RQUA_GroupA_datasets/TopologyTests RQUA_GroupA_consel.catpv RQUA_GroupA_ConstrainTrees.tre RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.log RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.sitelh RQUA_GroupB_datasets/MLanalysis rqua.GroupB.IQtree.log rqua.GroupB.IQtree.treefile rqua.GroupB.mafft.bmge_masked.fasta rqua.GroupB.mafft.fasta rqua.GroupB.seqs.fasta RQUA_GroupB_datasets/TopologyTests RQUA_GroupB_consel.catpv RQUA_GroupB_ConstrainTrees.tre RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.log RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.sitel

alphaprotebacteria_datasets

Alignment file and raw tree file for alphaproteobacteria phylogeny. See Figure 2 - figure supplement 2