The Rnase MRP and Rnase P Complexes, Will Be Summarised

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The human The human RNase MRP complex RNase MRP complex Composition, assembly and role in human disease Hans van Eenennaam Hans van Eenennaam The human RNase MRP complex Composition, assembly and role in human disease Hans van Eenennaam, 2002 The human RNase MRP complex Composition, assembly and role in human disease een wetenschappelijke proeve op het gebied van de Natuurwetenschappen, Wiskunde en Informatica PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Katholieke Universiteit Nijmegen, volgens besluit van het College van Decanen in het openbaar te verdedigen op vrijdag 14 juni 2002 des namiddags om 1:30 uur precies door Hans van Eenennaam Cover illustration Statue of the Dwarf Seneb and his family, painted limestone, height 34 cm, width 22.5 cm, geboren op 3 november 1973 Giza, Tomb of Seneb, Late Fifth - Early Sixth te Middelburg Dynasty. From: The Cairo museum Masterpieces of Egyptian Art, Francesco Tiradritti, Thames & Hudson Ltd, London, 1998 Promotor Prof. Dr. W.J. van Venrooij Co-promotor Dr. G.J.M. Pruijn voor mijn ouders Manuscriptcommissie Prof. Dr. L.B.A. van de Putte Prof. Dr. F.P.J.T. Rutjes Prof. Dr. H.F. Tabak (Universiteit van Amsterdam) ISBN 90-9015696-8 © 2002 by Hans van Eenennaam The research described in this thesis was performed at the Department of Biochemistry, Faculty of Science, University of Nijmegen, the Netherlands. This work was supported in part by the Netherlands Foundation for Scientific Research (NWO-CW). Table of contents hoe Chapter 1 General introduction .................................................................................. 9 als je je Part I met zorgeloosheid Chapter 2 hPop4: a new protein subunit of the human RNase MRP............................ 25 and RNase P ribonucleoprotein complexes kon omringen Chapter 3 hPop5, a protein subunit of the human RNase MRP................................... 39 and RNase P endoribonucleases en dat dat Part II je ruimte Chapter 4 Basic domains target protein subunits of the RNase MRP ........................... 55 complex to the nucleolus independently of complex association was Chapter 5 RNA-protein interactions in the human RNase MRP .................................. 71 ribonucleoprotein complex Chapter 6 Identity of the RNase MRP and RNase P associated.................................... 91 Th/To-autoantigen. Part III (Bert Schierbeek) Chapter 7 Autoantibodies against small nucleolar ribonucleoprotein ........................ 107 complexes and their clinical associations. Chapter 8 Mutations in the RNA component of the RNase MRP cause a ................... 121 pleiotropic human disease, cartilage-hair hypoplasia. Part IV Chapter 9 General discussion.................................................................................. 137 Samenvatting/Summary.......................................................................... 151 References.............................................................................................. 155 List of publications................................................................................. 162 Dankwoord en acknowledgements .......................................................... 163 Curriculum vitae .................................................................................... 167 Chapter 1 General introduction Adapted from IUBMB Life (2000) 49: 265-272 owadays, it is generally assumed that the ‘RNA world’ was one of the early phases in the evolution of life. At that stage of evolu- Ntion ribonucleic acids (RNAs) were thought to play a key role in the catalysis of chemical reactions and its own replication. In the current 1 phase of evolution, one of the major functions of RNA is the transfer of information stored in genes, from DNA (deoxyribonucleic acid) to proteins. During this process, a copy of the DNA is made in the form of messenger RNA (mRNA). This messenger RNA is subsequently transported to the site of protein synthesis, where the message is translated and the encoded protein is synthesised. In the latter process, two other classes of RNA are involved. The transfer RNAs (tRNA) delivers the amino acids to the ribosome. This synthesising machinery binds the incoming amino acids to the growing polypeptide chain. The ribosome itself contains numerous proteins and four RNAs, called ribosomal RNAs (rRNA). Before these different RNAs (mRNA, tRNA and rRNA) can function in the above-described processes, they undergo a maturation process directly after their synthesis. In eukaryotes all these RNAs are cleaved and/or undergo modifications such as ribose-methylation and conversion of a uridine to a pseudouridine. The cleavage generating the mature 5’-end of tRNAs and the cleavages and modifications needed for the complete maturation of rRNAs are mediated by other RNAs that are primarily found in the nucleolus and therefore designated as small nucleolar RNAs or snoRNAs. In this chapter our knowledge on the structure and function of these small nucleolar RNAs, with emphasis on the RNase MRP and RNase P complexes, will be summarised. Small nucleolar (1,2). These processing and modification events ribonucleoprotein particles are mediated by small nucleolar RNAs and their associated proteins (the so-called small nucleo- In eukaryotes the 5.8S, 18S and 25/28S lar ribonucleoproteins or snoRNPs). Although rRNAs are transcribed by RNA polymerase I snoRNAs are heterogeneous in size, snoRNAs as one long precursor. The processing of this can be classified in three distinct groups based precursor not only involves endo- and exonu- on conserved sequence elements: box C/D cleolytic cleavages, but also ribose methylation snoRNAs, box H/ACA snoRNAs and RNase and conversion of uridines to pseudouridines MRP/RNase P RNAs ((3), reviewed in ref. (4,5)). General introduction 11 Box C/D snoRNPs A small group of box C/D snoRNAs lack “rRNA recognition motifs” present in the The box C/D snoRNAs contain the con- sequence complementarity to rRNA and these snoRNA are able to base pair with rRNA RNase MRP and RNase P served C (consensus sequence: RUGAUGA) and snoRNAs have been demonstrated to function sequences flanking the uridine to be converted ribonucleoprotein D (consensus sequence: CUGA) boxes, which in endonucleolytic processing of pre-rRNA. into pseudouridine (Figure 1B) (3,17). particles 1 are frequently followed or preceded by a stem This group includes U3, U8, U13 and U22 At present, 42 of the 91-93 pseudouri- structure (see Figure 1A). Imperfect copies snoRNA (reviewed in ref. (4,5,12)) dines present in mammalian rRNAs can be Function and subcellular localisation of of box C/D sequences (referred to as box C’ Three proteins have been shown to be explained by the identification of 40 box RNase MRP and D’) have been described and are located specifically associated with all box C/D H/ACA snoRNAs, e.g. U64-U72 ((2,11) and refe- The RNase MRP (for Mitochondrial RNA between box C and box D (6-8). Most of the snoRNAs: fibrillarin, Nop56 and Nop5/58 rences therein). Processing) was originally identified in mouse box C/D snoRNAs, e.g. U24-U63, harbour an (13-15). Although no clear function has been Four proteins have been shown to be spe- cells by virtue of its ability to cleave the mito- extended region (10-21 nucleotides) of base demonstrated for these proteins, sequence and cifically associated with box H/ACA snoRNAs: chondrial RNA that functions as a primer for complementarity to rRNA, thereby positioning structure homology between known methyl- hGar1, NAP57/dyskerin, hNHP2 and hNOP10 mitochondrial DNA replication in vitro (22). box D and/or D’ exactly 5 nucleotides from the transferases and fibrillarin strongly suggest (18-20). The homology between NAP57/ Initiation of mitochondrial DNA replication nucleotide that has to be modified via 2’-O- that fibrillarin is the 2’-O-methyltransferase dyskerin and pseudouridine synthases involved occurs at two origins of replication (OH and ribose methylation (Figure 1A) (6,9). enzyme (16). in tRNA and bacterial rRNA modifications OL). OH initiates the replication of the heavy At present 51 of the 55 ribose methylation strongly suggests that NAP57/dyskerin repre- strand of mtDNA, whereas OL is involved in the sites in yeast ribosomal RNA have been assigned Box H/ACA snoRNPs sents the pseudouridine synthase associated replication of the complementary light strand. to 41 different guide snoRNAs (10). In mam- The box H/ACA snoRNAs possess 5’ and with the box H/ACA snoRNPs (21). Initiation of the replication of the heavy strand mals 105-107 ribose methylation sites have 3’ hairpin domains, connected and followed is a two step process (reviewed in ref. (23)). been mapped and at present only 14 ribose by single-stranded hinge and tail regions that RNase MRP/RNase P methylations remain without identified cog- carry the conserved H (AnAnnA) and ACA The RNase MRP and RNase P complexes A nate guide snoRNA (2,11). boxes, respectively (Figure 1B). Two short are the only known representatives of the third H-strand class of small nucleolar RNPs. Both ribonucleo- 3' A B protein particles function as endonucleases and mtTFA mtRPOL 5' have been shown to be involved in the process- L-strand LSP ing of pre-rRNA and pre-tRNA, respectively. A transcription

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