Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development

Abstract

There is mounting evidence that the ribosome is not a static translation machinery, but a cell-specific, adaptive system. Ribosomal variations have mostly been studied at the protein level, even though the essential transcriptional functions are primarily performed by rRNAs. At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. Recently, we described for zebrafish a similar system in which the sole maternal-type 5S rRNA present in eggs is replaced completely during embryonic development by a somatic-type. Here, we report the discovery of an analogous system for the 45S rDNA elements: 5.8S, 18S, and 28S. The maternal-type 5.8S, 18S, and 28S rRNA sequences differ substantially from those of the somatic-type, plus the maternal-type rRNAs are also replaced by the somatic-type rRNAs during embryogenesis. We discuss the structural and functional implications of the observed sequence differences with respect to the translational functions of the 5.8S, 18S, and 28S rRNA elements. Finally, in silico evidence suggests that expansion segments (ES) in 18S rRNA, previously implicated in ribosome-mRNA interaction, may have a preference for interacting with specific mRNA genes. Taken together, our findings indicate that two distinct types of ribosomes exist in zebrafish during development, each likely conducting the translation machinery in a unique way.

Keywords: embryogenesis; maternal rRNA; ribosomal RNA; ribosomes; zebrafish.

FIGURE 1.

Expression of the maternal- and somatic-type rRNA types in zebrafish development. (A) Alignments of the maternal-type (M) and somatic-type (S) rRNAs. In the 5.8S rRNA alignment, identical nucleotides are indicated as dots, gaps as dashes. In the 18S and 28S rRNA alignments, the black vertical lines indicate the locations where maternal- and somatic-type differ (due to the scale, not all differences are visible; for a complete alignment check Supplemental File S1). The probes used for Northern blotting (panel C) are indicated with colored lines (green: -C, specific to a region common to both types; blue: -M, specific for maternal-type; red: -S, specific for somatic-type). The dark gray horizontal lines show the position of the regions used to discriminate between the three types of rRNA (cf. main text and Supplemental Table S1). (B) Expression of the maternal-type (blue) and somatic-type (red) rRNAs indicated by percentage of total 5.8S, 18S, and 28S rRNA sequencing reads, respectively. Prot-mouth, protruding-mouth; Adult FT, adult-female tail; Adult MWB, adult-male whole-body. (C) Northern blot analyses with total RNA from zebrafish eggs and adult-male whole-body tissue (Adult MWB) and probes as indicated in A. Each panel contains lanes from the same gel, but with adjusted brightness and contrast for visual clarity.

FIGURE 2.

Differences between zebrafish maternal- and somatic-type 5.8S and 28S rRNA. (A) Plot with the differences between maternal- and somatic-type 28S rRNA in relation to the structural domains (“D”: Domain), expansion segments (ES, green lines [Anger et al. 2013]) and functional domains (GAC, GTPase-associated center; PTC, peptidyl transferase center; SRD, sarcin–ricin domain). The black vertical lines indicates the spots where the maternal- and somatic-type differ (due to the scale, not all differences are visible). Asterisks indicate the 28S rRNA regions that interact with 5.8S rRNA. (B) The putative secondary structures for maternal- and somatic-type 5.8S rRNA and their interactions with the equivalent 28S rRNAs are shown (Petrov et al. 2014). The region that undergoes the conformational switch and interacts with ribosome-dissociating factors is highlighted in light green (Graifer et al. 2005). The nucleotides that differ between the two types are marked (yellow). (C) Putative secondary structures for maternal- and somatic-type GTPase-associated center (GAC). The nucleotides that differ between the two types are marked (yellow). (D) Putative secondary structures for maternal- and somatic-type sarcin–ricin domain (SRD). The nucleotides that differ between the two types are marked (yellow).

FIGURE 3.

Differences between zebrafish maternal- and somatic-type 18S rRNA. (A) Schematic representation of the differences between maternal- and somatic-type 18S rRNA in correlation with the structural domains (A, Domain A; 5′, Domain 5′; Central, Central Domain; 3′ M, 3′ Major domain; 3′ m, 3′ minor domain), expansion segments (ES, green lines [Anger et al. 2013]) and sticky regions (red boxes [Pánek et al. 2013]). The black vertical lines indicates the spots where the maternal- and somatic-type 18S rRNA sequences differ (due to the scale, not all differences are visible). (B) Putative secondary structures for maternal- and somatic-type sticky regions corresponding to ES3S. The nucleotides that differ between the two types are marked (yellow). Thick black lines indicate the regions (“range 3-I,” nucleotides: maternal-type 188–207; somatic-type 187–206) analyzed in panel D. (C) Putative secondary structures for maternal- and somatic-type sticky regions corresponding to ES6Ss. The nucleotides that differ between the two types are marked (yellow). Thick black lines indicate the regions (“range 6-I,” nucleotides: maternal-type 776–797; somatic-type 738–756) analyzed in panel D. (D) Table presenting the overrepresentation of maternal genes versus nonmaternal genes with respect to the binding of each gene transcript to 18S-ES3S and 18S-ES6S. The mentioned ranges correspond with the ranges indicated in panels B and C. (E) Graphical representation of the binding of maternal (blue line) and somatic (red line) mRNA transcripts to the indicated sticky regions of the SSU types. The + and − indicate the translation stimulating and repressing interactions, respectively, at the indicated ES sites.