Ribosomal RNA expansion segments and their role in ribosome biology

Abstract

Ribosomes are universally conserved cellular machines that catalyze protein biosynthesis. The active sites underly immense evolutionary conservation resulting in virtually identical core structures of ribosomes in all domains of life including organellar ribosomes. However, more peripheral structures of cytosolic ribosomes changed during evolution accommodating new functions and regulatory options. The expansion occurred at the riboprotein level, including more and larger ribosomal proteins and at the RNA level increasing the length of ribosomal RNA. Expansions within the ribosomal RNA occur as clusters at conserved sites that face toward the periphery of the cytosolic ribosome. Recent biochemical and structural work has shed light on how rRNA-specific expansion segments (ESs) recruit factors during translation and how they modulate translation dynamics in the cytosol. Here we focus on recent work on yeast, human and trypanosomal cytosolic ribosomes that explores the role of two specific rRNA ESs within the small and large subunit respectively. While no single regulatory strategy exists, the absence of ESs has consequences for proteomic stability and cellular fitness, rendering them fascinating evolutionary tools for tailored protein biosynthesis.

Keywords: cotranslational factor recruitment; nascent peptide chain maturation; rRNA expansion segments; translation elongation; translation regulation.

Figure 1.. LSU rRNA expansion and the evolutionary growth of helix 63 into expansion segment 27L.

(A) E. coli, S. cerevisiae and H. sapiens LSU rRNA structures were aligned and displayed to proportion based on structures (8cgv, 4v88 and 5aj0) to illustrate the expansion. The expansions are highlighted in cyan for yeast or hot pink for human ribosomes. The extent to which expansion occurred is underestimated in these figures since many of the large ES cannot be resolved. ES27L is one of the segments displaying high flexibility and which can only be visualized upon capture with interaction partners. (B) The rRNA backbone found in the bacterium E. coli is displayed as a bar and yeast cyan) and human (hot pink) expansion segments are indicated. White bars show the location of the peptidyl-transferase center. (C) The expansion of bacterial helix 63 into ES27L is illustrated based on secondary structures from RNA central [5]. The arrow indicates the position of the original helix 63 in E. coli that expanded in S. cerevisiae and H. sapiens. The colored part of the helix indicates the specific expansion of helix 63 in yeast (cyan) and human (hot pink).

Figure 2.. SSU rRNA expansion and the evolutionary growth of helix 26 into expansion segment 7S.

(A) E. coli, S. cerevisiae, H. sapiens and T. cruzi SSU rRNA structures were aligned and displayed to proportion based on structures (8cgv, 4v88, 5aj0 and 7ase) to illustrate the rRNA expansion. The expansions are highlighted in cyan for yeast, hot pink for human and green for trypanosomal ribosomes. The extent to which expansion occurred is underestimated in these figures since many of the large ES cannot be resolved. (B) The bars illustrate the bacterial SSU rRNA backbone with yeast (cyan), human (hot pink) and Trypanosoma-specific (green) expansions. White bars indicate the position of the decoding residues A1494 and A1495 in E. coli or their conserved counterparts in the other species. The absolute length is given for each species. (C) Illustration of the expansion of ES7S from bacterial helix 26 based on secondary structures from RNA central [5]. The arrow indicates the position of the original helix 26 in E. coli that expanded in S. cerevisiae, H. sapiens and especially in T. cruzi.

Figure 3.. ES27L recruits peptide channel interactors cotranslationally and during ribosome biogenesis.

ES27L recruits Ebp1 (first column, pdb: 6sxo), Arx1 (second column, pdb: 7z34), NatA (third column, pdb: 6hd7) and NatB (fourth column, pdb: 8bip). The top row displays the ES27L (grey) interaction with various protein partners (colored). ES7L as part of the interaction surface is indicated. The second and third row displays the charge distributions of protein partners at the ES27L binding site. Structures are rotated 180° vertically and 90° horizontally with respect to the first row. The ribbon and grey surface indicate ES27L, the red surface indicates negative charge and the blue surface indicates positive charge. The third row is rotated vertically by 90° with respect to row 2. Figures were prepared using ChimeraX software.