Ribosome heterogeneity inDrosophila melanogastergonads through paralog-switching

Abstract

13Ribosomes have long been thought of as homogeneous, macromolecular machines but 14 recent evidence suggests they are heterogeneous and their specialisation can regulate translation. 15Here, we have characterised ribosomal protein heterogeneity across 5 tissues of Drosophila 16 melanogaster. We find that testis and ovary contain the most heterogeneous ribosome populations, 17 and that specialisation in these tissues occurs through paralog-switching. For the first time, we have 18 solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in 19 precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid 20 composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-21 switching could alter the ribosome surface, enabling different proteins to regulate translation. One 22 testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of 23 ribosome specialisation. Overall, this work allows us to propose possible mechanisms by which 24 ribosome specialisation can regulate translation. 25 26 27 48 effects [1], whilst RpL38 mutants in D. melanogaster exhibit large wings, small bristles, delayed 49 development and disorganised wing hair polarity [14]. 50 2 Human cytoplasmic ribosomes usually comprise of 80 RPs and 4 rRNAs. This is similar across 51 the majority of multicellular eukaryotes including D. melanogaster with 80 RPs and 5 rRNAs. 52 However, annotated in FlyBase there are 93 cytoplasmic RP genes, including 39 small subunit 53 proteins and 54 large subunit proteins [15]. These additional genes code for 13 paralogs in D. 54 melanogaster. In fact, across eukaryotes many RP genes possess paralogs, for example human RpL3 55 and RpL3L [11] and Arabidopsis RpS8A and RpS8B [13]. In total, there are 19 pairs of paralogs in 56 humans [4] and all 80 RPs in Arabidopsis thaliana have paralogs [16].57 To dissect the function of ribosome heterogeneity it is necessary to understand biological 58 importance within context of whole organisms. Within the developmental biology field, a large 59 proportion of research focuses on the contribution of transcription to gene expression control.60 However, during development a variety of processes and key time points are highly dependent on 61 the regulation of mRNA translation (oogenesis in Xenopus [17], early embryo development in 62 Drosophila [18] and mammalian erythropoiesis [19]). The balance between self-renewal and 63 differentiation at the stem cell niche is highly dependent on translation in both the ovary and the 64 testis [20]. This is exemplified by disruptions to the stem cell niche in the testis when RPs are 65 knocked down e.g. RpL19 RNAi results in over-proliferation of early germ cells in D. melanogaster 66 [21]. During the meiotic phase of gametogenesis, transcription does not occur [22]; therefore 67 meiotic cells rely on post-transcriptional gene regulation [23]. The translational machinery has 68 evolved to become specialise...

Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis

“…Paralog rearrangements can characterize ribosome specialization in eukaryotes [13,116,117]. Similarly, as we have shown, several paralog-specific changes characterize cold-acclimated ribosomes in Arabidopsis.…”

“…Already in simpler eukaryotic ribosomal proteomes, as compared to that of plants, selective translation can be achieved by differential use of RPs or RP paralogs [12,13]. In fact, however, eukaryotes select transcripts for translation through several distinct mechanisms [14,15].…”

Functional diversity and evolution of the Drosophila sperm proteome

“…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).…”

Ribosomal heterogeneity – A new inroad for pharmacological innovation

“…Cryo-electron microscopy also offers promise to observe the composition of individual ribosomes. The technique has been used to visualise the structure of the human and Drosophila ribosome [42] but, until a very recent report (made available in pre-print form, pending validation by peer-review, in January 2020 [43]) had not been applied to observing ribosome heterogeneity. A challenge to overcome was to achieve adequate resolution of individual structural differences using a technique that averages data from many complexes into an individual structure.…”