Ribosome heterogeneity inDrosophila melanogastergonads through paralog-switching

Abstract

Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.

Functional diversity and evolution of the Drosophila sperm proteome

“…For the remaining paralogs we identified only one member of each pair: the most abundant paralog found in the testis for seven, and the less abundant paralog for two (Table S4). For RpL10Ab and RpS14b only one paralog was identified in both the current study and by Hopes et al (36), and we did not identify either paralog of RpS10 (RpS10a or RpS10b). Together, these results suggest a complex landscape of paralog switching in the gonad during spermatogenesis and highlight distinct differences between sperm-RP and testis-RP populations.…”

“…Significant differences were found between all four tissues as only three RP paralogs were observed in the DmSP3 (RpL22-like, RpS14b and RpS28b) whereas both RPs and paralog RPs were found in all tissues with the exception of two (Rp10Aa and RpS14a; Table S4). Notably, RpL22-like is more abundant in the testis (36), whereas RpL22 was more abundant in the DmSP3. For the remaining paralogs we identified only one member of each pair: the most abundant paralog found in the testis for seven, and the less abundant paralog for two (Table S4).…”

“…Although the significance of paralog heterogeneity for ribosome function is currently unknown, paralog switching of RPs has been observed in gonads and other tissues (36). We therefore compared RP paralogs in the DmSP3 to those previously described in four tissue types including the testis (36). Significant differences were found between all four tissues as only three RP paralogs were observed in the DmSP3 (RpL22-like, RpS14b and RpS28b) whereas both RPs and paralog RPs were found in all tissues with the exception of two (Rp10Aa and RpS14a; Table S4).…”

“…The canonical ribosome contains 80 RPs including 13 paralog pairs in Drosophila (FlyBase.org). Although the significance of paralog heterogeneity for ribosome function is currently unknown, paralog switching of RPs has been observed in gonads and other tissues (36). We therefore compared RP paralogs in the DmSP3 to those previously described in four tissue types including the testis (36).…”

Negative charge in the RACK1 loop broadens the translational capacity of the human ribosome

“…For example, celltype-specific expression of the large ribosomal subunit protein L38 (RPL38) (Kondrashov et al, 2011;Xue et al, 2015) and ribosomal expansion segments (Leppek et al, 2020) regulate homeobox (Hox) mRNA translation during cytoskeletal patterning. Ribosomal protein (RP) paralogs diversify ribosome activity during gonad development (Hopes et al, 2021), and intracellular heterogeneity in ribosomes regulates translation (Shi et al, 2017). However, the structural basis by which these subunit differences alter ribosome specificity remains unclear.…”