Abundant 5S rRNA-Like Transcripts Encoded by the Mitochondrial Genome in Amoebozoa

Abstract

5S rRNAs are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. Nevertheless, a clearly identifiable, mitochondrion-encoded 5S rRNA is present in Acanthamoeba castellanii, a member of Amoebozoa. During a search for additional mitochondrial 5S rRNAs, we detected small abundant RNAs in other members of Amoebozoa, namely, in the lobose amoeba Hartmannella vermiformis and in the myxomycete slime mold Physarum polycephalum. These RNAs are encoded by mitochondrial DNA (mtDNA), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5S rRNAs. Further, in the mtDNA of another slime mold, Didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the Physarum small RNA. A mtDNA-encoded small RNA previously identified in Dictyostelium discoideum is here shown to share several characteristics with known 5S rRNAs. Again, we detected genes encoding potential homologs of this RNA in the mtDNA of three other species of the genus Dictyostelium as well as in a related genus, Polysphondylium. Taken together, our results indicate a widespread occurrence of small, abundant, mtDNA-encoded RNAs with 5S rRNA-like structures that are associated with the mitoribosome in various amoebozoan taxa. Our working hypothesis is that these novel small abundant RNAs represent radically divergent mitochondrial 5S rRNA homologs. We posit that currently unrecognized 5S-like RNAs may exist in other mitochondrial systems in which a conventional 5S rRNA cannot be identified.

Mitochondrial Genome of Vannella croatica (Amoebozoa, Discosea, Vannellida)

“…), and Vermamoeba (Bullerwell et al. ). It is noticeable that the universal code is used in all so far studied members of Conosa clade ( sensu Cavalier‐Smith et al.…”

“…However, the majority of studied amoebozoans are suggested to apply modified genetic code, where the codon TGA specifies tryptophan (GenBank translation table 4). Those are Acanthamoeba (Burger et al 1995); Balamuthia (Greninger et al 2015), Korotnevella (Zlatogursky et al 2016); Vannella (Nassonova et al 2010); Neoparamoeba (labeled as Paramoeba) (Tanifuji et al 2017), and Vermamoeba (Bullerwell et al 2010). It is noticeable that the universal code is used in all so far studied members of Conosa clade (sensu Cavalier-Smith et al 2004), while sequenced to the moment members of Tubulinea and Discosea use modified one (Table S1).…”

Eukaryotic Sequences in the 16SrRNA Metagenomic Dataset of Algal–bacterial Consortia of the White Sea Coastal Zone

“…The sequences related to Vermamoeba (formerly Hartmanella , 100% homology with from Bullerwell et al. ) were presented in all the samples.…”

RNA Secondary Structure Analysis Using Abstract Shapes

“…Bullerwell et al [6] used consensus shapes and shape probabilities to characterize 5S rRNA-like transcripts encoded in the mitochondrial genomes of Amoebozoa. The consensus shape, termed rabbit shape, was found to be similar to the one known for conventional 5S rRNAs.…”