Multicomponent Machines in RNA Modification: H/ACA Ribonucleoproteins

Pseudouridylation, the isomerization of uridine to pseudouridine, is the most frequent post‐ transcriptional modification of RNA, such that pseudouridine has even been termed the fifth nucleotide. Whereas eubacteria employ single protein enzymes to identify and modify target uridines, archaebacteria and eukaryotes additionally evolved more complex modification machines, H/ACA ribonucleoproteins (RNPs). Each H/ACA RNP consists of a short RNA and the same four core proteins, one of which is the pseudouridine synthase related to the bacterial single protein enzymes. In this chapter, we will give an overview of these multicomponent machines with emphasis on the eukaryal systems that have acquired additional functions and that are the subject of the inherited bone marrow failure syndrome dyskeratosis congenita. Introduction Nuclei of metazoans harbor several hundred individual small nucleolar ribonucleoproteins (snoRNPs) that predominantly function in RNA modification. They are divided into two major classes according to their function‐defining snoRNAs, box H/ACA and box C/D snoRNPs, which pseudouridylate and 2′‐O‐methylate their target RNAs, respectively. SnoRNAs guide the modification by site‐specific base pairing while an enzyme (which is one of four core proteins of each RNP) catalyzes the reaction. Collectively, the snoRNAs account for one of the largest families of noncoding RNAs. In this overview, we will focus on the H/ACA class of RNPs (see chapter by Gagnon et al for C/D RNPs). H/ACA RNAs H/ACA RNAs are generally 60‐150 ribonucleotides in length, noncoding, trans‐acting mol‐ ecules, for reviews see.1,2‐9 Defining features of H/ACA RNAs are two hairpins separated by a short single stranded sequence (hinge), which includes an ANANNA consensus hexanucleotide, and an ACA triplet exactly three nucleotides from their 3′‐end (Fig. 1A).10,11 Although the num‐ ber of hairpins can vary, H/ACA RNAs are conserved from archaea to mammals. The hairpins contain internal bulges and can differ in size and organization of stems and loops (Fig. 1A). The vast majority of H/ACA RNAs contain in their bulges two 3‐10 ribonucleotide long stretches (3′ and 5′ of the upper stem) that are complementary to the sequences flanking their target uridines (Fig. 1A, arrows).12,13 Hence, these internal loops are also known as pseudouridylation pockets. So © 20 08 C op yr ig ht L an de s B io sc ie nc e. N ot fo r D ist rib ut io n