Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome

Abstract

Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance 1-3 , and are significant opportunistic parasites of humans 4. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle 5 , rudimentary mitochondria and the smallest known eukaryotic genomes 5-7. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome 8-10. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites. Reprints and permissions information is available at www.nature.com/reprints.

Evolution of microsporidia: An extremely successful group of eukaryotic intracellular parasites

“…Microsporidia also have reduced noncoding RNAs, including the 18s RNA, which is only approximately 2/3 as large as in other eukaryotes and results in the smallest eukaryotic ribosomes [13]. Although this reduction has led to several binding sites being eliminated, structural and mass spectrometry analysis of ribosomes from Vairimorpha necatrix demonstrated that most conserved ribosomal proteins can still bind [14]. Microsporidia also have reduced organelles, including mitochondrial remnants known as mitosomes [15].…”

“…The use of ancestral gene reconstruction has revealed how nucleotide transporter genes evolved [16]. Proteomic technologies such as mass spectrometry have been used to study the localization of microsporidia proteins as well as their translational fidelity [12,14,19]. Cryoelectron microscopy has been used to determine the structures of microsporidia ribosomes.…”

“…Cryoelectron microscopy has been used to determine the structures of microsporidia ribosomes. This work allowed the identification of a conserved, microsporidia-specific ribosomal protein (msL1) and also identified two conserved microsporidia dormancy factors, one that is conserved throughout eukaryotes (MDF1) and the other that was only found in several species of microsporidia (MDF2) [14]. Although it is currently not possible to genetically modify microsporidia, using RNAi to knockdown genes provides a powerful approach to directly study microsporidia protein function in the context of infection [44,49].…”

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

“…An important example of divergence among eukaryotes is the kinetoplastid family, which has been the object of several structural studies [ 21 , 22 , 23 , 24 ], showing ribosomes with fragmented rRNA’s that are comparable in size to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. Similarly, during their evolution into organisms with highly compacted genomes, microsporidia have removed essentially all eukaryotic expansion segments and repurposed several ribosomal proteins to compensate for the extensive rRNA reduction [ 25 ]. On the prokaryotic side, bacteria with short genomes also commonly show a reduction of rRNA variation with loss of specific ribosomal proteins [ 26 ], suggesting some future work to visualize and confirm these changes through 3D structures.…”

LSTrAP-Crowd: Prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data

“…While the structure of the ribosomes is well conserved, structural features of ribosomes may vary significantly between different species, suggesting species-specific adaptations of protein synthesis (Ahmed et al ., 2016; Ahmed et al ., 2017; Barandun et al ., 2019; Bieri et al ., 2017; Kushwaha and Bhushan, 2020; Eyal et al ., 2015; Greber and Ban, 2016; Melnikov et al ., 2012; Melnikov et al ., 2018). For example, structural analysis of mycobacterial ribosome revealed that the 30S ribosomal subunit lacks the protein bS21 that is found in Escherichia coli .…”