Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome

Abstract

Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo-EM structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are universally highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which acts as an architectural co-factor to stabilize a protein-protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation.

'Lose-to-gain' adaptation to genome decay in the structure of the smallest eukaryotic ribosomes

“…We then used the cryo-EM maps to build the model of rRNA and ribosomal proteins. We found that, compared to the previously determined structures of V. necatrix and P. locustae ribosomes (both structures represent the same family of Nosematidae microsporidians and are very similar to each other) 31,32 , E. cuniculi ribosomes underwent further degeneration of numerous rRNA and proteins segments (Figs. S3-S6).…”

“…3B). Notably, we found that most of these bulges are also lost in the previously determined structures of V. necatrix and P. locustae ribosomes, which was overlooked by previous structural analyses 31,32 .…”

“…In species ranging from E. coli to humans, the base of this rRNA helix contains 24-32 nucleotides that form a slightly irregular helical structure. In the previously determined structures of ribosomes from V. necatrix and P. locustae 31,32 the base of helix H18 is partially unwound yet the base-pairing of nucleotides is preserved. In E. cuniculi, however, this rRNA segment is turned into the minimal-length linkers 228 UUUGU 232 and 301 UUUUUUU 307 .…”

“…E. cuniculi is a fungi-like organism which belongs to the group of parasites microsporidia, which possess anomalously small eukaryotic genomes and are therefore used as model organisms to study genome decay [25][26][27][28][29][30] . Recently, cryo-EM structures of ribosomes were determined for microsporidians with moderately reduced genomes, Paranosema locustae and Vairimorpha necatrix 31,32 (~3.2 Mb genomes). These structures showed that the loss of some rRNA expansions is compensated by evolving new contacts between adjacent ribosomal proteins or by acquisition of a new ribosomal protein, msL1 31,32 .…”

“…Recently, cryo-EM structures of ribosomes were determined for microsporidians with moderately reduced genomes, Paranosema locustae and Vairimorpha necatrix 31,32 (~3.2 Mb genomes). These structures showed that the loss of some rRNA expansions is compensated by evolving new contacts between adjacent ribosomal proteins or by acquisition of a new ribosomal protein, msL1 31,32 . Encephalitozoon species (~2.5 Mb genomes), along with their closest relatives Ordospora, show the ultimate degree of genome reduction in eukaryotes -they have less than 2,000 protein-coding genes and their ribosomes were predicted to lack not only rRNA expansion segments (rRNA segments that distinguish eukaryotic ribosomes from bacterial ribosomes) but also four ribosomal proteins due to the absence of their homologs in the E. cuniculi genome [26][27][28] .…”