biomolecules Review Turning Uridines around: Role of rRNA Pseudouridylation in Ribosome Biogenesis and Ribosomal Function Marianna Penzo * and Lorenzo Montanaro * ID Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy * Correspondence: [email protected] (M.P.); [email protected] (L.M.); Tel.: +39-051-214-4520 (M.P.), Tel.: +39-051-214-4524 (L.M.) Received: 30 April 2018; Accepted: 31 May 2018; Published: 5 June 2018 Abstract: Ribosomal RNA (rRNA) is extensively edited through base methylation and acetylation, 20-O-ribose methylation and uridine isomerization. In human rRNA, 95 uridines are predicted to by modified to pseudouridine by ribonucleoprotein complexes sharing four core proteins and differing for a RNA sequence guiding the complex to specific residues to be modified. Most pseudouridylation sites are placed within functionally important ribosomal domains and can influence ribosomal functional features. Information obtained so far only partially explained the degree of regulation and the consequences of pseudouridylation on ribosomal structure and function in different physiological and pathological conditions. This short review focuses on the available evidence in this topic, highlighting open questions in the field and perspectives that the development of emerging techniques is offering. Keywords: pseudouridylation; rRNA; ribosome biogenesis; X-linked dyskeratosis congenita; cancer; mRNA translation; ribosome diversity; translational control; internal ribosome entry site-mediated translation 1. RNA Pseudouridylation and Its Roles in Ribosome Biogenesis Pseudouridine (Y) is the 5-ribosyl isomer of uridine (Figure1). It derives from the uracil base rotation of 180◦, which makes the uracil attached to the 10 carbon (C1´) of the ribose via a carbon-carbon instead of a nitrogen-carbon glycosidic bond (see [1,2] for a broader review). Pseudouridine (Y) is the most prevalent within more than 100 different modified nucleosides found in RNA, with about 9500 Y residues identified in mammals and yeast and deposited in the RMBase database [3]. Pseudouridine (Y) is found in all species and in many classes of RNA, including ribosomal RNA (rRNA), transfer RNA (tRNA), mitochondrial tRNAs (Mt-tRNAs), small Cajal Body-specific RNAs (scaRNAs), small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs), messenger RNAs (mRNAs), and other miscellaneous RNAs (misc_RNAs) [4]. Uridine isomerization to Y is carried out by either RNA-driven enzymatic complexes or stand-alone enzymes, depending on the class of the RNA harboring the target residue. In rRNA, Ys are generated by RNA-guided enzymatic complexes, and they account for about the 1.4% of all bases, with a total of 95 predicted Ys in human 28S, 18S, 5.8S, and 5S rRNAs [5–7]. In bacteria and yeast rRNAs, the number of Ys is significantly lower (36 in E. coli, 46 in S. cerevisiae [8]), mirroring the complexity level of these organisms. Biomolecules 2018, 8, 38; doi:10.3390/biom8020038 www.mdpi.com/journal/biomolecules BiomoleculesBiomolecules2018 2018, 8,, 388, x FOR PEER REVIEW 2 of 210 of 10 FigureFigure 1. 1.Structure Structure formulae formulae of uridine and and pseudouridine. pseudouridine. TheThe presence presence of of an an extra extra hydrogen hydrogen bondbond donor at at its its non non-Watson-Crick‐Watson‐Crick edge edge endows endows Ψ withY with biochemicalbiochemical and and biophysical biophysical properties properties distinct distinct from from those those of uridine of uridine and all otherand all known other nucleotides. known nucleotides. In particular, the presence of Ψ is able to provide: (i) greater rigidity to the In particular, the presence of Y is able to provide: (i) greater rigidity to the phosphodiester backbone phosphodiester backbone of the RNA; (ii) stabilization of Ψ‐A base pairs (compared to that of U‐A of the RNA; (ii) stabilization of Y-A base pairs (compared to that of U-A base pairs) through some base pairs) through some effects on base stacking and water coordination, thus affecting RNA effects on base stacking and water coordination, thus affecting RNA structure, spatial conformation structure, spatial conformation and, ultimately, its functional properties; and (iii) increased thermal and, ultimately, its functional properties; and (iii) increased thermal stability (reviewed in [9]). stability (reviewed in [9]). TheThe site-specific site‐specific modification modification of targetof target uridines uridines in rRNA, in rRNA, as for as other for modificationother modification types occurring types in thisoccurring class of in RNA, this class represents of RNA, an represents extremely an important extremely passage important of ribosome passage of synthesis. ribosome Many synthesis. aspects of uridineMany aspects modification of uridine process modification are now process quite are clear,now quite including clear, including the players the players involved, involved, the timing the andtiming the cellular and the localization cellular localization of the processes, of the processes, and the position and the onposition rRNAs on in rRNAs the three-dimensional in the three‐ structuredimensional of the structure ribosome of (even the ribosome though (even all of though this information all of this information might not bemight available not be available for each singlefor modification)each single modification) [10]. Still, to [10]. understand Still, to understand the function the (or function functions) (or functions) of many of of many these ofY sthese remains Ψs a demandingremains a challenge demanding for challenge investigators for investigators in the field. in the field. Pseudouridylation,Pseudouridylation, together together with with other other rRNArRNA modifications, modifications, is is only only one one aspect aspect of ofthe the process process of of preparationpreparation of of rRNAs rRNAs for for ribosome ribosome biogenesis. biogenesis. As As discussed discussed later later on, some on, some of these of these modifications modifications are areconsidered considered important important for for ribosome ribosome production production to tooccur, occur, since since this this process process is characterized is characterized by bythe the presencepresence of of multiple multiple control control steps, steps, which, which, in in thethe end, ensure the the production production of of competent competent ribosomes. ribosomes. RibosomalRibosomal RNA RNA is synthesized is synthesized by two by differenttwo different RNA polymerases.RNA polymerases. While 5SWhile rRNA 5S is rRNA transcribed is transcribed by RNA PolIII in the nucleoplasm, mature 5.8S, 18S, and 28S rRNAs are derived from a by RNA PolIII in the nucleoplasm, mature 5.8S, 18S, and 28S rRNAs are derived from a unique unique precursor, termed 47S, also harboring two external transcribed spacers (5′ and 3′ external precursor, termed 47S, also harboring two external transcribed spacers (50 and 30 external transcribed transcribed spacer (ETS)) and two internal transcribed spacers (ITS1 and 2) transcribed in the spacer (ETS)) and two internal transcribed spacers (ITS1 and 2) transcribed in the nucleolus by nucleolus by RNA PolI. ETS and ITS sequences are sequentially removed by exo‐ and endo‐ RNAnucleolytic PolI. ETS cleavages, and ITS sequences in coordinated are sequentially series of processing removed by events exo- andthat endo-nucleolytic may present variations cleavages, in coordinateddepending on series cellular of type processing or status events (for a broader that may review present of the variations topic please depending refer to [11]). on cellular In rRNA, type orpseudouridylation status (for a broader is carried review out of by the ribonucleoprotein topic please refer (RNP) to [complexes11]). In rRNA, called pseudouridylationH/ACA box RNPs, is carriedeach outconsisting by ribonucleoprotein of one H/ACA snoRNA (RNP) complexes and four core called proteins, H/ACA namely box RNPs, GAR1, each NHP2, consisting NOP10 and of one H/ACAdyskerin snoRNA (DKC1). and H/ACA four core snoRNAs proteins, contain namely a GAR1,conserved NHP2, ANANNA NOP10 sequence and dyskerin called (DKC1). “hinge H/ACAbox” snoRNAs(indicated contain with H) a conservedand a sequence ANANNA of three sequence nucleotides called (ACA) “hinge present box” at their (indicated 3′ end with(called H) ACA and a sequencebox). Structurally of three nucleotides H/ACA snoRNAs (ACA) present are characterized at their 30 endby the (called presence ACA of box). a double Structurally hairpin, H/ACA each snoRNAsharboring are a characterized pseudouridylation by the pocket, presence which of a is double specific hairpin, to a particular each harboring target sequence, a pseudouridylation based on pocket,sequence which‐specific is specific base pairing. to a particular The interaction target between sequence, the based guide snoRNA on sequence-specific and the substrate base guides pairing. Thethe interaction enzymatic between complex the on guidethe target snoRNA uridine. and A the further substrate stabilization guides theoccurs enzymatic thanks complexto additional on the targetinteractions uridine. of A furtherthe substrate stabilization RNA with occurs protein thanks component to additional of small interactions nucleolar ofribonucleoproteins the substrate RNA with(snoRNPs) protein component and in particular of small with nucleolar DKC1, which ribonucleoproteins carries out the (snoRNPs)isomerization