The Role of Elongator Complex in Saccharomyces Cerevisiae and Caenorhabditis Elegans

The role of Elongator complex in Saccharomyces cerevisiae and Caenorhabditis elegans

Changchun Chen

Department of Molecular Biology Umeå University Umeå 2011

Table of Contents Table of Contents 3 Abstract 4 Sammanfattning på svenska 5 Introduction 1. Translation process 7 1.1 Translation initiation 7 1.2 Translation elongation, termination and ribosome recycling 8 2. Translational control 8 2.1 Translational control at initiation 8 2.2 Translational control at elongation 9 2.3 Translational control at termination 10 3. Transfer RNA 11 3.1 Modified nucleosides and modification enzymes in S. cerecisiae 12 3.2 The role of modified nucleosides in S. cerecisiae 13 3.2.1 Modifications and tRNA surveillance 13 3.2.2 Modifications and translation decoding 14 4. Elongator complex 15 4.1 Elongator complex in S. cerecisiae 16 4.2 Elongator complex in multicellular organisms 16 4.3 Elongator complex and diseases 18 Results and discussion 19 Conclusions 27 Acknowledgements 28 References 30 Papers I-IV

Abstract

Elongator is a conserved protein complex in eukaryotes. The primary function of this complex in yeast is in formation of mcm5 and ncm5 side chains at wobble uridines (U34) of tRNAs. The aim of this thesis is to investigate why Saccharomyces cerevisiae Elongator mutants show defects in many different cellular processes, and to investigate the physiological role of Elongator complex in Caenorhabditis elegans. We show that the defects in transcription silencing and DNA damage response in yeast Elongator mutants are caused by a translational dysfunction due to 5 Lys Gln lack of mcm side chains at U , primarily in tRNA and tRNA 25 . In 34 25 UUUsmcm UUGsmcm order to identify gene products whose expression levels are decreased in Elongator mutants, we performed a genome wide analysis to search for open reading frames Lys Gln enriched in AAA or CAA codons, decoded by tRNA or tRNA 25 smcm 25 UUU smcm UUG respectively. This analysis led to the identification of IXR1, an ORF highly enriched in CAA codons, and we subsequently demonstrated that the presence of mcm5 side Gln chain in tRNA 25 UUGsmcm is important for efficient expression of Ixr1. Ixr1 protein is required for Rnr1 induction in response to DNA damage and the decreased Ixr1 levels in Elongator-deficient cells result in a defective Rnr1 induction upon DNA damage. Collectively, these observations suggest that Elongator complex influences the DNA damage response by its role in wobble uridine tRNA modification. To answer the question whether the Elongator complex is also required for wobble uridine tRNA modifications in multicellular organisms, we investigated the modification status of tRNAs isolated from Elongator mutants in C. elegans. The 5 5 mcm and ncm side chains at U34 of tRNA were abolished in worm Elongator mutants, which in turn caused an inefficient translation. Elongator mutant worms have defects in salt-associated learning, and a reduced efficiency in synaptic exocytosis due to a low production of neurotransmitters. We also showed that lack 5 5 of modifications at position 2 (2-thio) or at position 5 (mcm and ncm ) at U34 results in the context dependent readthrough of opal stop codon in lin-1(R175Opal) and suppress the multi-vulva phenotype caused by lin-1(R175Opal). Interestingly, mutations found in genes encoding Elongator subunits in humans have been linked to several neurodevelopmental disorders including familial dysautonomia (FD), amyotrophic lateral sclerosis (ALS) and epilepsy. We believe our results will provide important implications in understanding the etiology of these neurological diseases.

Sammanfattning på svenska

Elongator är ett protein komplex som är konserverat i eukaryoter. Den primära funktionen av detta komplex i jäst är bildandet av mcm5 och ncm5 sidokedjor på uridiner i wobble position (U34) i tRNA. Syftet med denna avhandling är att undersöka varför avsaknad av Elongator komplexet i jäst ger upphov till så många olika fenotyper samt att undersöka den fysiologiska roll som Elongator komplexet har i Caenorhabditis elegans. Vi har visat att bristerna i transkription repression och respons till DNA- skador i jäst Elongator mutanter orsakas av en translations defekt på grund av avsaknad av mcm5 och ncm5 sidokedjorna i främst tRNALys and 25 UUUsmcm Gln tRNA 25 UUGsmcm . För att finna kandidatgener vars uttryck minskar i Elongator mutanter, identifierade vi de mRNA i S. cerevisiae som är anrikade i AAA eller Lys Gln CAA kodoner, dvs. de kodoner som avkodas av tRNA and tRNA 5 2 . 25 UUUsmcm smcm UUG Denna analys ledde till identifieringen av genen IXR1 vars kodande region är 5 Gln anrikad i CAA kodoner ochvi fann att avsaknaden av mcm gruppen i tRNAmcm5 2UUGs orsakar en dramatisk minskning av Ixr1 protein nivån. Ixr1 proteinet krävs för induktion av Rnr1 som svar på DNA-skador och den minskade Ixr1 nivån i Elongator mutanter leder till en försämrad förmåga att inducera Rnr1 när cellerna utsätts för DNA skada. Dessa resultat visar att Elongator komplexets roll i tRNA modifiering påverkar cellens respons mot DNA skador. För att besvara frågan om Elongator komplexet också krävs för bildandet av mcm5 och ncm5 sidokedjor i tRNA från flercelliga organismer undersökte vi modifierings status av tRNA isolerad från Elongator mutanter i rundmasken C. elegans. Sidokedjorna mcm5 och ncm5 saknades, som i sin tur orsakade en ineffektiv translation. Elongator muterade maskar uppvisar defekter i salt-associerad inlärning och en minskad effektivitet i synaptisk exocytos på grund av låg produktion av neurotransmittorer. I den sista artikeln, visade vi att avsaknad av tRNA modifiering i position 2 (2-thio) eller position 5 (mcm och ncm sidokedjor) på U34 resulterar i genomläsning av ett opal stopp kodon i lin-1 (R175Opal) mutanten och undertrycker vulva fenotypen som orsakas av lin-1 (R175Opal). Mutationer i gener som kodar Elongator subenheter i människa är kopplade till flera störningar i nervsystemets utveckling, inklusive familjär dysautonomia (FD), amyotrofisk lateralskleros (ALS) och rolandisk epilepsi (RE). Vi tror att våra resultat kommer att öka vår förståelse för etiologin av dessa neurologiska sjukdomar.

Papers in this thesis

This thesis is based on the following papers and manuscripts labeled with Roman numerals (I-IV).

Paper I Elongator complex influences the transcriptional silencing and DNA damage response by its role in wobble uridine tRNA modification Changchun Chen, Bo Huang, and Anders S. Byström Manuscript

Paper II

Elongator complex enhances Rnr1 induction in response to DNA damage by promoting Ixr1 expression Changchun Chen, Olga Tsaponina, Mattias Eliasson, Patrik Rydén, Andrei Chabes, and Anders S. Byström Manuscript

Paper III

CHEN, C., S. TUCK and A. S. BYSTRÖM, 2009 Defects in tRNA modification associated with neurological and developmental dysfunctions in Caenorhabditis elegans elongator mutants. PLoS Genet 5: e1000561.

Paper IV

KIM, S., W. JOHNSON, C. CHEN, A. K. SEWELL, A. S. BYSTRÖM, M. HAN, 2010 Allele-specific suppressors of lin-1(R175Opal) identify functions of MOC-3 and DPH-3 in tRNA modification complexes in Caenorhabditis elegans. Genetics 185: 1235-1247.

Introduction

1. Translation process

Gene expression can be regulated at multiple levels with a crucial step in controlling the translation of mRNA into protein. The translation process is normally divided into four phases: initiation, elongation, termination and ribosome recycling (Kapp and Lorsch, 2004). Here a brief picture of the translation process in eukaryotes is described (Figure 1).

Figure 1. Schematic drawing of translation initiation, Elongation and termination. Limited numbers of translational factors are shown.

1.1 Translation initiation

As an early step in the cap-dependent translation initiation (Figure 1), a ternary Met complex containing eukaryotic initiation factor eIF2, tRNAi and GTP joins the 40S ribosomal subunit to form the 43S pre-initiation complex, which also contains other eukaryotic initiation factors eIF1, eIF1A and eIF3. The loading of pre- initiation complex to mRNA requires another important complex eIF4F including eIF4E, eIF4A and eIF4G. eIF4E binds to the cap structure of mRNA and serves to mediate the other factors in binding to the 5’ end of mRNA. eIF4A has an ATP- dependent helicase activity to unwind mRNA in scanning. eIF4G is a large modular protein in bridging mRNA with ribosome. The 43S pre-initiation complex is recruited to mRNA by the interaction between eIF3 and eIF4F. With the attachment of 43S pre-initiation complex to the cap-proximal region, it scans mRNAs downstream of the cap to the AUG initiation codon. Once the 43S complex is attached to the initiation codon, a stable 48S initiation complex is formed. This triggers the hydrolysis of GTP bound to eIF2, a reaction catalyzed by eIF5, and the Met release of tRNAi into the P-site of ribosome. After the dissociation of the other eIFs, 60S subunit is recruited. The initiation ends with the GTP hydrolysis on eIF5B

and its release from initiation complex (Gebauer and Hentze, 2004; Kapp and Lorsch, 2004; Pestova et al., 2007).

1.2 Translation elongation, termination and ribosome recycling

The elongation phase of translation is a process repeating the cycle of aminoacyl- tRNA delivery and peptide bond formation (Taylor et al., 2007) (Figure 1). The aminoacyl-tRNA forms a ternary complex with eEF1A and GTP, entering the A site of ribosome. The proper codon-anticodon interaction induces the conformational change of the small ribosomal subunit, resulting in GTP hydrolysis of the ternary complex. The GDP bound eEF1A subsequently releases the aminoacyl-tRNA into the A site followed by the formation of a peptide bond between peptidyl-tRNA and the incoming amino acid. eEF2 catalyzes the translocation of the peptidyl-tRNA on the ribosome by hydrolyzing GTP. In fungi such as Saccharomyces cerevisiae, a third Elongation factor, eEF3, is required. The eEF3 has ribosome-dependent ATPase and GTPase activities, important for E site tRNA release and binding of the ternary complex to the A site (Kapp and Lorsch, 2004; Taylor et al., 2007). The elongation cycle is repeated until a stop codon is translocated into the A site of ribosome. In eukaryotes, all three stop codons are read by the class I release factor eRF1. eRF1, a functional and structural mimic of tRNA, binds directly to the A site of ribosome and activates the hydrolysis of peptidyl-tRNA (von der Haar and Tuite, 2007). Another release factor, eRF3, is a GTP binding protein. Its physical interaction with eRF1 and its GTP hydrolysis are important for the termination reaction (von der Haar and Tuite, 2007). After the termination of protein synthesis, ribosomal subunits are recycled that is catalyzed by eEF3 and ATP in yeast (Kurata et al., 2010).

2. Translational control

Key advantages of regulating gene expression at the translation level are the ability to synthesize the proteins locally in specific subregions of the cytoplasm and to control protein synthesis rapidly. Recently, it was shown that the translational machinery can associate with transmembrane receptors to rapidly regulate protein synthesis upon environmental stimulus (Tcherkezian et al., 2010). Translation can be regulated at different stages. It can also be regulated at a global level or specifically to certain mRNAs. Here, several important cases of translational control in eukaryotes are discussed.

2.1 Translational control at initiation

It is generally accepted that protein synthesis is primarily regulated at the initiation stage of translation. One important mechanism in the control of translation initiation is the phosphorylation of the initiation factors or their regulators. A key

phosphorylation target is eIF2α, a subunit of eIF2 (Dever et al., 2007). Phosphorylation of eIF2α at Ser51 inhibits the eIF2B-catalyzed GDP-GTP exchange reaction, which blocks the reconstitution of a functional ternary complex and inhibits translation initiation globally. A variety of conditions can activate different kinases to phosphorylate eIF2α at Ser51 (Ron and Harding, 2007). For example, under amino-acid starvation, Gcn2 is activated and phosphorylates eIF2α, decreasing translation globally (Dever et al., 2007). Another important and well characterized target for phosphorylation at translation initiation phase is 4E-BP (Raught and Gingras, 2007). The 4E-BP inhibits translation initiation by blocking the formation of eIF4F complex. It competes with eIF4G to bind an overlapping site on eIF4E. In the absence of nutrient, hypo-phosphorylated 4E-BP inhibits cap- dependent translation by binding tightly to eIF4E and blocking the access of eIF4G. In the presence of nutrients, external stimuli trigger a signaling cascade to promote 4E-BP phosphorylation, resulting in the release of 4E-BP from eIF4E and stimulation of cap-dependent translation initiation.

In addition to the regulation by phosphorylation at its early stage, translation initiation can also be controlled at post 43S-recruitment steps. For example, cis- acting elements in the 5’UTR of an mRNA such as upstream open reading frame (uORF) may play a significant role in modulating translation initiation (Hentze et al., 2007). Up to 50% of mammalian genes and around 13% yeast genes encode transcripts containing at least one uORF (Calvo et al., 2009; Lawless et al., 2009; Resch et al., 2009). The best characterized example of the uORF in translation regulation is the yeast GCN4 mRNA (Hinnebusch, 1997; Hinnebusch and Natarajan, 2002). GCN4 contains four uORFs upstream of AUG start codon. After translation of the first uORF, the 60S ribosomal subunit dissociates and 40S subunit resumes scanning. When nutrients are abundant, 40S can quickly bind with the active eIF2- Met tRNAi -GTP ternary complex and translate the downstream inhibitory uORFs, which promotes the ribosome dissociation and release. As a result, only low levels of Gcn4 are synthesized. Under amino acid deprivation, the amount of the active ternary complex is limited. The frequency of reinitiation from uORF2 to uORF4 is low, resulting in the translation of the main GCN4 ORF. In mammals, a similar regulation mechanism is used to translate ATF4 mRNA (Lu et al., 2004; Vattem and Wek, 2004).

2.2 Translational control at elongation

Even though translation is primarily regulated at the stage of initiation, accumulating evidence shows that translation can also be controlled at the elongation phase (Herbert and Proud, 2007). Similar to initiation factors, eukaryotic elongation components such as Elongation factor 2 (eEF2) undergo posttranscriptional modification and regulation. eEF2, which mediates the

translocation of peptidyl-tRNA on the ribosome, can be modified to diphthamide at a conserved histidine residue (Van Ness et al., 1978). The diphthamide modification is a substrate for ADP ribosylation by diphtheria toxin (DT) produced in Corynebacterium diphtheria (Dunlop and Bodley, 1983). ADP ribosylation of diphthamide by DT inhibits eEF2 function and blocks protein synthesis (Oppenheimer and Bodley, 1981). Strains lacking the diphthamide modification show increased rates of frameshifting indicating the importance of diphthamide modification in translation. In mammals, eEF2 can also be phosphorylated. The phosphorylation of eEF2 at Thr-56 can be altered under different circumstances. It has been reported that decreased eEF2 phosphorylation correlates with increased rates of translation elongation (Diggle et al., 1998; Hovland et al., 1999; McLeod et al., 2001; Redpath et al., 1996; Scheetz et al., 2000; Yan et al., 2003). The p38 MAP kinase and mTOR pathways have been shown to play a role in the regulation of eEF2 phosphorylation (Herbert and Proud, 2007).

Recently, computational analysis yielded new insights into codon sequence and tRNA pools in controlling translation elongation, and a universally conserved translation efficiency profile has been identified (Cannarozzi et al., 2010; Tuller et al., 2010). First, the predicted translation speed differs in different regions over a single mRNA. In general, the first 30-50 codons are translated with a low efficiency (Translational ramp) followed by an increase of translation efficiency to a plateau level in the rest of the transcript (Tuller et al., 2010). This model is supported by ribosome profiles showing that ribosome density decreases with the increased distance from initiation codon (Ingolia et al., 2009). The translational ramp might increase translation efficiency by reducing the traffic jam during elongation phase and promoting the proper folding of nascent polypeptide (Fredrick and Ibba, 2010; Tuller et al., 2010). Second, the amount of tRNAs adapted to the codons in the mRNA is another critical determinant of translational speed in elongation (Akashi, 2003; Man and Pilpel, 2007; Tuller et al., 2010). Increased expression of a rare tRNA could improve the translational speed of the corresponding codons, and codon substitutions to adapt the availability of tRNA pools could significantly enhance the protein expression (Arava et al., 2003; DeRisi et al., 1997; Fredrick and Ibba, 2010; Percudani et al., 1997; Tuller et al., 2010). Finally, codon composition in an mRNA is well organized rather than randomly chosen from synonymous codons (Cannarozzi et al., 2010). When the synonymous codons appear in a coding sequence, the codon decoded by the same tRNA is preferred (Cannarozzi et al., 2010). Reuse of codons could significantly increase the speed of translation (Cannarozzi et al., 2010).

2.3 Translational control at termination

The efficiency of translation termination can be regulated by changing the activities of eRF1 and/ or eRF3 (von der Haar and Tuite, 2007). It has been shown that yeast

eRF1 is subjected to two post-translational modifications, methylation of a glutamine residue in a conserved domain of eRF1, and phosphorylation at two serine residues (Heurgue-Hamard et al., 2005; Kallmeyer et al., 2006; Polevoda et al., 2006). The methyltransferase reaction is catalyzed by Mtq2, which requires the interaction with Trm112 to be functional. A MTQ2 deletion mutant has a severe growth defect indicating the importance of methylation for eRF1 function. At least, non-methylated mitochondrial release factor 1 (mRF1) leads to an increased stop codon readthrough (Polevoda et al., 2006). The role of eRF1 phosphorylation in the regulation of termination is less clear (von der Haar and Tuite, 2007). Even though the post-translational modifications of eRF3 have not been described so far, the activity of this termination factor can be regulated by forming prion-like polymers in certain strains, [PSI+]. Formation of the [PSI+] prion decreases the translation termination efficiency detected with increased suppression of nonsense mutations (Tuite and Cox, 2006).

3. Transfer RNA

Transfer RNAs are small RNA molecules that play a central role in decoding mRNA into protein. tRNAs are often presented in a secondary cloverleaf structure consisting of 4 base-paired stems and 3 non-base-paired loops: D-loop, anticodon loop and TΨC loop (Figure 2A). In the three dimensional structure, tRNAs fold into an L-shaped configuration (Figure 2B). At one end, the anticodon sticks out to interact with mRNA codons, and at the other end an amino acid is attached to its acceptor stem. tRNA genes are transcribed by RNA polymerase III (PolIII) and the newly transcribed precursor tRNA undergoes a number of processing and modification steps before it is utilized in translation (Phizicky and Hopper, 2011).

Figure 2. Schematic drawing of the tRNA secodary (A) and tertiary (B) structures. The colors in (A) match with those in (B).

3.1 Modified nucleosides and modification enzymes in S. cerevisiae

Transfer RNAs are always posttranscriptionally modified. In total, 92 different tRNA modifications have been described in the three domains of life. On average, 8 different positions of each tRNA are modified (Phizicky and Alfonzo, 2010; Phizicky and Hopper, 2011). Of the total 50 different modified nucleosides identified in eukaryotic tRNAs, 25 of them can be found in S. cerevisiae cytosolic tRNAs (Johansson and Byström, 2005; Phizicky and Hopper, 2011). These 25 modified nucleosides are located at 36 different positions (Phizicky and Alfonzo, 2010). Two positions at the anticodon loop, positions 34 (wobble position) and 37, are frequently modified.

Figure 3. Schematic structures of uridine and uridine derivatives at wobble position. Wobble uridine can be modified to 5-carbamoylmethyluridine (ncm5U), 5- methoxycarbonylmethyl (mcm5U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U).

The formation of modified nucleosides in tRNA can be either very simple or extremely complicated. In most cases, only one or two gene products have been identified to be required for the synthesis of a modified nucleoside such as the formation of a methylated nucleoside (Johansson and Byström, 2005; Phizicky and Hopper, 2011). Most methylation reactions can be reconstituted in vitro in the presence of the methyltransferase, the methyl donor and the tRNA substrate. However, the formation of some modified nucleosides is a very complex process. For example, a common step in the synthesis of 5-carbamoylmethyluridine (ncm5) and 5-methoxycarbonyluridine (mcm5) side chains at wobble uridines requires at least 13 gene products probably to generate a cm5 group (Huang et al., 2005; Huang et al., 2008) (Figure 3). To form the mcm5 side chain, two extra proteins, Trm9 and Trm112, are required for the methyl ester formation (Kalhor et al., 2005; Mazauric et al., 2010; Songe-Moller et al., 2010). The gene products required for the amidation of ncm5 side chain have not been identified. In addition to the mcm5 side chain, U of three tRNA species, tRNA Lys , tRNAGln and tRNAGlu , 34 25 UUUsmcm 25 UUGsmcm 25 UUCsmcm is further modified at position 2 with a thio group to form mcm5s2U. So far, 11 gene 2 products have been described that are required for s formation at U34 (Björk et al.,

2007; Dewez et al., 2008; Esberg et al., 2006; Huang et al., 2005; Huang et al., 2008; Leidel et al., 2009; Nakai et al., 2008; Nakai et al., 2007; Nakai et al., 2004; Noma et al., 2009; Schlieker et al., 2008). Thus, formation of the mcm5s2U nucleoside is a complicated process involving multiple gene products.

3.2 The role of modified nucleosides in S. cerevisiae

Most gene products required for formation of modified nucleosides in tRNA have been identified in yeast (Johansson and Byström, 2005; Phizicky and Hopper, 2011). By investigating the phenotypes displayed by mutants defective in modification formation, modified nucleosides of tRNA have been shown to play critical roles in multiple processes. Here the importance of modifications for tRNA integrity and translational decoding in yeast S. cerevisiae is discussed.

3.2.1 Modifications and tRNA surveillance

Many genes encoding enzymes that catalyze tRNA modifications outside the anticodon region are not required for growth in a wild type background. For example, null alleles of PUS4, TRM1, TRM2 or TRM3, encoding enzymes for Ψ55, 2 5 m2 G26, m U54 and Gm18 respectively, do not show any obvious growth reduction (Becker et al., 1997; Cavaille et al., 1999; Ellis et al., 1986; Hopper et al., 1982; Ser Nordlund et al., 2000). However, introduction of a second site mutation in tRNA CGA , which carries these modifications, leads to a synergistic phenotype with deletion of PUS4, TRM1, TRM2 or TRM3 (Johansson and Byström, 2002). The synergistic Ser growth reduction is caused by instability of tRNA CGA , suggesting that these tRNA modifications and their enzymes are important for maintaining tRNA integrity (Johansson and Byström, 2002).

Several in vivo studies have clearly shown that the effect on tRNA stability resulting from lack of tRNA modifications was highly specific, and is limited to a subset of tRNA species which contain these modifications (Phizicky and Alfonzo, 1 2010). Strains defective in formation of m A58 have a decreased level of Met hypomodified pre- tRNAi (Anderson et al., 1998; Calvo et al., 1999; Kadaba et al., 2004). A nuclear surveillance pathway including Trf4 poly(A) polymerase and Rrp6 Met containing nuclear exosome specifically degrades aberrant pre- tRNAi (Kadaba et al., 2004). However, no other tRNA species were found to be the substrate of this nuclear surveillence pathway (Anderson et al., 1998; Schneider et al., 2007). Later, Phizicky and co-workers identified a distinct pathway in degrading pre-existing Val tRNA when hypomodified. In the trm8Δ trm4Δ double mutant, tRNA AAC , lacking both m7G and m5C, undergoes a rapid degradation (Alexandrov et al., 2006). This rapid tRNA degradation pathway (RTD) is mediated by Met22 and the 5’-3’ exonucleases Rat1 and Xrn1 (Chernyakov et al., 2008). The degradation is very

Val 7 specific to unmodified tRNA AAC since other tRNA species that have both m G and m5C are not degraded in the trm8Δ trm4Δ double mutant (Alexandrov et al., 2006; Chernyakov et al., 2008; Phizicky and Alfonzo, 2010). It has also been shown that Ser Ser hypomodified tRNACGA and tRNA UGA were selectively degraded by this RTD pathway in the tan1Δ trm44Δ double mutant (Kotelawala et al., 2008; Chernyakov et al., 2008). These observations indicate that cartain tRNA modifications are important for the stability of particular tRNA species, but not for the others even though they carry the same modifications.

3.2.2 Modifications and translation decoding

The genetic code consists of 64 triplets including 61 sense codons. In fact, the number of tRNA species is always fewer than 61 as certain tRNAs have the capacity to read more than one codon. The first base of anticodon (Position 34, wobble position) can pair with more than one base in the third position of the codon (Crick, 1966). The wobble position in tRNAs is frequently modified. Modifications at this position primarily influence the decoding properties of tRNA. In S. cerevisiae, 13 tRNA species contain a uridine at the wobble position, 11 of which have either ncm5 or mcm5 side chains. In addition to modifications at position 5, uridines of tRNALys , tRNAGln and tRNAGlu are also thiolated at position 2 25 UUUsmcm 25 UUGsmcm 25 UUCsmcm (Figure 3). Based on in vitro translational expriments, these modifications at wobble uridines in eukaryotes were suggested to facilitate the reading of A-ending codons but prohibit the recognition of G-ending codons (Takai and Yokoyama, 2003) (Weissenbach and Dirheimer, 1978) (Yokoyama et al., 1985). More recently, based on a study of the crystal structure of modified anticodon stem loop, it has been suggested that tRNAs containing a mcm5s2U modified nucleoside might read both A- and G- ending codons (Murphy et al., 2004).

With the identification of gene products required for formation of these wobble uridine modifications, the in vivo roles of mcm5, ncm5 and s2 in decoding have been systematically investigated (Johansson et al., 2008). The mcm5 side chain Arg Gly in tRNA and tRNA 5 was shown to promote reading of G-ending 5UCUmcm UCCmcm codons (Johansson et al., 2008). For the tRNA species having both mcm5 and s2 groups, an mcm5s2U nucleoside promotes the reading of both A- and G- ending codons at least for tRNAGln (Johansson et al., 2008). The esterified methyl 25 UUGsmcm group of mcm5 side chain only has a minor contribution on decoding compared to the entire mcm5 side chain (Johansson et al., 2008). By using a similar strategy, the ncm5U residue in tRNAVal , tRNASer and tRNAThr was shown to 34 5UACncm 5UGAncm 5UGUncm facilitate the recognition of G-ending codons (Johansson et al., 2008). In the case of Pro 5 tRNAUGG , both ncm modified and unmodified forms can efficiently read G-ending

codons and pyrimidine-ending codons, suggesting that the presence of the ncm5 side Pro chain in tRNAUGG does not prevent pairing with all these codons (Johansson et al., 2008). In summary, the modified nucleosides mcm5U, ncm5U and mcm5s2U promote the decoding of G-ending codons, and the primary role of mcm5s2U nucleoside might be to improve the decoding of A-ending codons.

4. Elongator complex

Elongator complex was initially identified in yeast by virtue of its apparent association with hyperphosphorylated elongation form of RNA polymerase II (PolII) (Otero et al., 1999). It consists of a core complex, Elp1-Elp3, and a sub-complex, Elp4-Elp6 (Krogan and Greenblatt, 2001; Otero et al., 1999; Winkler et al., 2001). This complex is highly conserved in eukaryotes. Studies in yeast, worm and plant have shown that Elongator is required for the formation of tRNA modifications at wobble uridines (Huang et al., 2005; Mehlgarten et al., 2010) (Paper III) (Figure 4). Interestingly, mutations found in genes encoding Elongator subunits in humans have been linked to several neurodevelopmental disorders including familial dysautonomia (FD), amyotrophic lateral sclerosis (ALS) and epilepsy (Anderson et al., 2001; Simpson et al., 2009; Slaugenhaupt et al., 2001; Strug et al., 2009).

Figure 4. The role of Elongator complex in S. cerevisiae. Elongator complex is required for formation of mcm5 side chain at wobble uridine in tRNA. The mcm5 side chain formation is important for the expression of gene products crucial for PolII transcription, exocytossis and DNA damage response.

4.1 Elongator complex in yeast S. cerevisiae

Elongator complex has been reported to have many cellular functions in diverse processes including elongation of PolII transcription, exocytosis, DNA damage response and wobble uridine tRNA modification (Huang et al., 2005; Li et al., 2009; Otero et al., 1999; Rahl et al., 2005; Winkler et al., 2002; Winkler et al., 2001; Wittschieben et al., 1999) (Figure 4). Evidence suggesting a role for the Elongator complex in transcription include its association with PolII holoenzyme, its ability to bind to nascent pre-mRNA and its requirement for histone acetylation (Gilbert et al., 2004; Otero et al., 1999; Winkler et al., 2002). Indeed, delayed transcription activation of certain genes and decreased histone acetylation levels were observed in Elongator mutants (Otero et al., 1999; Winkler et al., 2002; Wittschieben et al., 1999). However, several lines of evidence did not support a direct role for the Elongator complex in transcription. First, the complex is localized in the cytosol (Huh et al., 2003; Pokholok et al., 2002; Rahl et al., 2005). Second, an association between Elongator and PolII subunits was not detected by tandem affinity purification (Krogan and Greenblatt, 2001). Third, Elongator complex was not found on actively transcribed genes (Pokholok et al., 2002). Last, its participation in exocytosis did not require its nucleus localization (Rahl et al., 2005).

A crucial step in understanding the roles of yeast Elongator complex is the discovery of its requirement in formation of mcm5 and ncm5 side chains at wobble uridine (Huang et al., 2005). This observation raised the possibility that the pleiotropic phenotypes observed in Elongator mutants might be caused by an inefficient translation due to a tRNA modification defect. In a genetic screen searching for genes that in high dosage could suppress the temperature-sensitive (Ts) phenotype of an elp3Δ mutant, plasmids encoding tRNALys were obtained 25 UUUsmcm Lys Gln (Esberg et al., 2006). Elevated levels of tRNA together with tRNA 2 , which 2UUUs UUGs are modified by mcm5 side chain in wild type, could suppress the defects of Elongator mutants in transcription, exocytosis and DNA damage response without restoring tRNA modification (Esberg et al., 2006) (Paper I). In addition to the mcm5 Lys Gln side chain, U34 of tRNA UUU and tRNA UUG also contains a 2-thio group. Tuc2 in yeast is required for s2 formation. In a tuc2Δ strain, a similar phenotypic pattern as Elongator mutants was observed (Esberg et al., 2006) (Paper I). The phenotypes of the tuc2Δ mutant can also be suppressed by increased expression hypomodified Lys Gln tRNA and tRNA 5 (Esberg et al., 2006) (Paper I). These observations 5 UUUmcm mcm UUG indicate that the mcm5 and s2 side chains are critical for efficient expression of gene products which play important roles in transcription, exocytosis and DNA damage response processes (Figure 4).

4.2 Elongator complex in multicellular organisms

In higher eukaryotes, a complicated picture about the role of Elongator complex has been painted with lots of controversial data. IKAP/ hElp1, the largest subunit of Elongator complex in mammalian cells, was first identified as a scaffold protein in the IκB kinase pathway to assemble NIK and IKKs into an active kinase complex involved in pro-inflammatory cytokine signaling (Cohen et al., 1998). However, the role of IKAP in the IκB pathway was questioned by the failure to detect IKAP in the IκB complex (Krappmann et al., 2000). Subsequently in a two hybrid screen, overexpressed IKAP was found to interact with c-Jun N-terminal kinase (JNK) participating in the regulation and activation of the mammalian stress response (Holmberg et al., 2002). IKAP depleted cells showed the cell motility defects due to reduced transcription of actin cytoskeleton modulators gelsolin, paxillin and caveolin-1 as well as reduced transcription of beclin involved in autophagy (Close et al., 2006). Later, these observations were questioned by the failure to repeat those results (Johansen et al., 2008).

Recently, two reports described a possible function of Elongator complex in acetylation of α-tubulin (Creppe et al., 2009; Solinger et al., 2010). In mouse, depletion of Elongator subunits delayed the radical migration of projection neurons and decreased the level of α-tubulin acetylation (Creppe et al., 2009). An Elp3- enriched fraction was able to acetylate α-tubulin in vitro with a reaction efficiency far lower than expected (Creppe et al., 2009; Wynshaw-Boris, 2009). In C. elegans, the α-tubulin acetylation was nearly normal in the adult worms but reduced levels were observed in the early development stage (Solinger et al., 2010), indicating that Elongator is not absolutely required for α-tubulin acetylation. Furthermore, the physiological importance of α-tubulin acetylation at Lys-40 in worms was challenged by the observation that the mec-12(e1607) mutant defective in Lys-40 acetylation of α-tubulin did not display Elongator mutant associated phenotype (Paper III). In a recent report, MEC-17 was shown to be the α-tubulin acetyltransferase in Tetrahymena cells, C. elegans, zebrafish and mammalian cells (Akella et al., 2010), suggesting that Elongator mutants might indirectly affect α- tubulin acetylation levels by modulating the expression of α-tubulin acetylase.

The involvement of Elongator complex in tRNA modification has also been reported in C. elegans and A. thaliana (Mehlgarten et al., 2010) (Paper III). In C. elegans, total tRNAs isolated from Elongator mutants abolished the formation of mcm5 and ncm5 side chains at wobble uridines (Paper III). Lack of mcm5 and ncm5 modifications causes a clear reduction in the translation efficiency in worms. Similarly, AtELP3 mutants in A. thaliana also eliminate the formation of ncm5 and 5 mcm side chains at U34 (Mehlgarten et al., 2010). All these data indicate that Elongator complex has a conserved role in formation of wobble uridine tRNA modifications. In future, it is of importance to clarify the relevance between the inefficient translation in Elongator mutants and the defects observed in the other cellular processes in higher eukaryotes.

4.3 Elongator complex and diseases

Several neurological diseases have been linked to mutations of human Elongator subunits. The neurodegenerative disease familial dysautonomia (FD) is caused by mutations in the hELP1/ IKBKAP gene (Anderson et al., 2001; Slaugenhaupt et al., 2001). Mutations, located in intron 20 of IKBKAP, lead to a splicing defect of IKBKAP mRNA, resulting in a C-terminal truncation of its product, the IKAP protein (Slaugenhaupt et al., 2001). FD patients have a tissue-dependent splicing defect of IKBKAP mRNA causing a low IKAP production in brain tissues but normal in lymphoblasts (Cuajungco et al., 2003; Slaugenhaupt et al., 2001). Additionally, allelic variants of hELP3 have been associated with amyotrophic lateral sclerosis (ALS), which is a deadly motor neuron disease in humans (Simpson et al., 2009). Furthermore, variants in hELP4 were linked to rolandic epilepsy, a neurodevelopmental disorder with classical focal seizures preceded by several developmental defects (Strug et al., 2009). It is still unclear why alterations of Elongator activities in humans lead to these neurological disorders. Based on a conserved requirement of Elongator in tRNA modification, it is tempting to speculate that the neurological diseases associated with alterations of Elongator complex might involve impaired translation.

Results and discussion

Paper I: Elongator complex modulates the transcriptional silencing and DNA damage response via its role in wobble uridine tRNA modification

Elongator complex in Sacchromyces cerevisiae consists of six subunits, Elp1-Elp6. The main function of this complex in yeast is in formation of mcm5 and ncm5 side chain at wobble uridines in tRNAs (Esberg et al., 2006). The mcm5 side chain Lys Gln present in tRNA and tRNA 25 is crucial for the efficient translation of 25 UUUsmcm UUGsmcm gene products important for PolII transcription and exocytosis. In a recent report, Elongator complex was proposed to participate in transcriptional silencing and DNA damage response by its physical interaction with Proliferating Cell Nuclear Antigen (PCNA) and its requirement for histone acetylation (Li et al., 2009).

To explore the possibility that the defects observed in transcriptional silencing and DNA damage response were also the consequences of a translational dysfunction caused by the absence of tRNA modifications, we investigated whether Lys Gln Glu increased expression of tRNA , tRNA 2 and tRNA 2 could suppress these 2UUUs UUGs UUCs defects. Elevated levels of these three tRNA species overcame the telomeric gene silencing defect and hydroxyurea sensitivity of Elongator mutants. In addition, the synergistic growth reduction and hydroxyurea sensitivity generated by histone chaperone mutant asf1Δ or histone acetyltransferase mutant rtt109Δ with the elp3Δ mutant (asf1Δ elp3Δ and rtt109Δ elp3Δ) were also suppressed by increased Lys Gln expression of three tRNA species. In tRNA , tRNA 25 and 25 UUUsmcm UUGsmcm Glu 5 tRNA 25 UUCsmcm , U34 contains a 2-thio group in addition to the mcm side chain. Tuc2 in yeast is required for 2-thio formation at wobble uridines (Esberg et al., 2006). In a tuc2Δ strain, the formation of s2 group is abolished. Similar to Elongator mutants, defects in telomeric gene silencing and DNA damage response were also observed Lys Gln in the tuc2Δ strain. Increased levels of tRNA 5 , tRNA 5 and UUUcmm UUGcmm Glu tRNA 5UUCcmm could completely suppress those defects of the tuc2Δ mutant. All these 5 2 observations suggest that both mcm side chain and s group at U34 are important for the expression of gene products in telomeric gene silencing and DNA damage response.

Elp3, one subunit of Elongator complex, contains a radical S- adenosylmethionine (SAM) domain in the N-terminal region and a sequence similar to histone acetyltransferase (HAT) in its C-terminal end. Amino-acid substitutions have been made in these two regions that disrupt the FeS cluster formation (elp3- C103A, elp3-C108A, elp3-C118A and elp3-C121A), eliminate the radical SAM

binding (elp3-G168R and elp3-G180R G181R) and inactive the HAT activity (elp3- Y540A and elp3-Y541A) (Greenwood et al., 2009; Li et al., 2009) (Wittschieben et al., 2000). Interestingly, strains carrying these elp3 mutant alleles have different phenotypes in telomeric gene silencing and DNA damage response (Li et al., 2009). We demonstrated in this article that phenotypic differences among those mutants in telomeric gene silencing and DNA damage response correlate with different levels 5 2 of mcm s side chain at U34 in tRNA. The elp3-C103A and elp3-G168R mutants have the same phenotypes in telomeric silencing and DNA damage response as wild type. Total tRNAs islolated from the elp3-C103A and elp3-G168R mutants have 96% and 51% mcm5s2U left, respectively. The HAT mutants, elp3-Y540A and elp3- Y541A displaying a medium level of reduction in telomeric gene silencing and HU sensitivity, have 3 or 4% mcm5s2U left compared to the wild type. Total tRNAs from the mutant strains, which exhibit the same phenotypes as an elp3 null mutant, completely lack the formation of the mcm5 side chain. By using a dual luciferease reporter system (Keeling et al., 2004) to investigate the ochre stop codon 5 readthrough by the SUP4-encoded suppressor tRNA, containing mcm U34, the readthrough level in the elp3Δ strain is reduced to 46% of wild type due to lack of mcm5 side chain in the suppressor tRNA. In elp3-Y540A and elp3-Y541A mutants, the presence of 3-4% modified nucleoside significantly improves the ochre stop codon readthrough by the suppressor tRNA compared to the elp3 null mutant.

Based on the observations in this article, we conclude that Elongator complex does not directly participate in transcriptional gene silencing and DNA damage response and that the wobble uridine tRNA modifications are important for efficient translation of gene products for telomeric gene silencing and DNA damage response.

Paper II: Elongator complex modulates Rnr1 induction by promoting Ixr1 expression

Elongator mutants in yeast display pleiotropic phenotypes. All phenotypes of Elongator mutants, except for the tRNA modification defect, could be bypassed by Lys Gln increased expression of hypomodified tRNA and tRNA 2 . We hypothesized 2UUUs UUGs that Elongator mutant phenotypes may be caused by inefficient translation of mRNAs enriched in AAA and CAA codons, which are decoded by tRNA Lys 25 UUUsmcm Gln and tRNA 25 UUGsmcm respectively. To identify open reading frames (ORFs) highly enriched in AAA or CAA codons, we analyzed 6718 DNA sequences encoding ORFs in the yeast genome database (SGD) by using R software. To investigate whether mRNAs highly enriched in AAA or CAA codons were poorly translated in Elongator mutants, we used the TAP-fusion strain collection (Open Biosystems) and compared the recombinant protein levels between wild type and the elp3Δ mutant. This analysis led to the identification of IXR1, an ORF highly enriched in CAA

codons. Ixr1 expression was decreased in an elp3Δ background. The decreased expression of Ixr1 in an elp3Δ background was suppressed by increased expression Gln of tRNA 2UUGs indicating that reduced Ixr1 expression was caused by inefficient Gln 5 decoding of CAA codons by tRNA 2UUGs caused by the lack of the mcm side chain in the elp3Δ mutant.

Ixr1 is required for the Rnr1 induction in response to DNA damage. Based on our observations, we assumed that Elongator mutants might have defects in Rnr1 induction in response to DNA damage due to decreased expression of Ixr1. We observed that Rnr1 levels were decreased in the elp3Δ strain under the normal growth conditions. Similar to the ixr1Δ strain, the elp3Δ mutant was defective in Rnr1 induction after exposure to MMS for 1 hour. Increased expression of Lys Gln Glu tRNA , tRNA 2 and tRNA 2 could suppress the Rnr1 induction defect in 2UUUs UUGs UUCs the elp3Δ mutant but not in the elp3Δ ixr1Δ double mutant. In addition, the ixr1Δ or elp3Δ did not affect the induction of the other ribonucleotide reductase (RNR) subunits in response to DNA damage. All these observations suggest that Elongator complex affects the DNA damage response by promoting Ixr1 expression.

In yeast, there are no deoxyribonucleoside kinase activities and dNTP synthesis is entirely dependent on RNR activities. Decreased RNR levels and activities correlate with reduction in dNTP levels. Since the elp3Δ strain has a decreased Rnr1 expression and is defective in Rnr1 induction in response to DNA damage, the dNTP levels were expected to be reduced in this strain. However, the dNTP levels in asynchronized Elongator-deficient cells are 2-3 fold higher than those in wild type. In theory, increased dNTP levels are associated with enhanced tolerance to DNA damage agents. Even though increased dNTP pools were observed, the elp3Δ strain was hyper-sensitive to HU. So, Elongator mutants must affect other components in the DNA damage response pathway, which results in its HU sensitivity phenotype. HU is a potent inhibitor of RNR enzyme activities. It slows down DNA replication by inhibiting dNTP production. When RNR levels were monitored at different time points after HU treatment, we observed that Rnr3 is less efficiently induced in the elp3Δ mutant compared to the wild type indicating an inefficient DNA replication checkpoint activation. An early and sensitive marker of checkpoint activation is the serine phosphorylation of histone H2A at 129 in yeast. Consistent with the reduced Rnr3 induction observed, no increased H2A-S129 phosphorylation was observed in the elp3Δ mutant. The defect in H2A-S129 Lys Gln phosphorylation was suppressed by increased expression of tRNA , tRNA 2 2UUUs UUGs Glu and tRNA 2UUCs . These observations indicate that HU sensitivity phenotype of the elp3Δ strain might be caused by inefficient activation of DNA replication checkpoint.

Since HU sensitivity phenotype of the elp3Δ mutant could be suppressed by Lys Gln Glu elevated levels tRNA , tRNA 2 and tRNA 2 , certain mRNAs, encoding 2UUUs UUGs UUCs protein products important for HU response, must be poorly translated when the 5 mcm side chain at U34 is lacking. To identify those genes, we performed a screen for genes that in high dosage could overcome the HU sensitivity of the elp3Δ strain. In total, we obtained 8 plasmids carrying the wild type Elp3 gene and 18 plasmids carrying genes encoding tRNALys . This result suggests that the HU sensitivity 25 UUUsmcm phenotype of the elp3Δ strain is due to decreased expression of proteins encoded by ORFs enriched in AAA codons. Since no other plasmids were obtained in the screen, it indicated that increased dosage of more than one gene was required to suppress the HU sensitivity of the elp3Δ strain.

In summary, we have demonstrated that the presence of mcm5 side chain in Gln tRNA 25 UUGsmcm is important for efficient expression of Ixr1. We have also shown that Rnr1 induction defect in the elp3Δ strain is due to decreased expression of Ixr1. The HU sensitivity phenotype of the elp3Δ strain might be caused by inefficient activation of the DNA checkpoint. However, several questions remain to be answered. First, why does the elp3Δ strain have increased dNTP levels even though it has defects in Rnr1 expression and induction. Second, could Ixr1 expression be Gln restored in the elp3Δ strain by replacing all CAA codons decoded by tRNA 25 UUGsmcm Gln to CAG codons decoded by tRNACUG . Third, the HU sensitivity phenotype is caused by an inefficient translation of ORFs enriched in AAA codons. One interesting candidate is MRC1, in which AAA codons are over-represented. Mrc1 is required for DNA replication checkpoint activation, and the mrc1Δ strain is hyper-sensitive to HU as the elp3Δ strain. We are currently investigating whether the level of Mrc1 is reduced in the elp3Δ mutant and whether such a reduction can explain the HU sensitivity phenotype of the elp3Δ mutant.

Paper III: Defects in tRNA modification associated with neurological and developmental dysfunctions in Caenorhabditis elegans elongator mutants

Although a requirement of Elongator complex for the addition of mcm5 and ncm5 side chains to wobble uridines in yeast tRNAs is well established (Esberg et al., 2006; Huang et al., 2005), prior to this work, studies on the functions of this complex in tRNA modification in metazoans had not been reported. To investigate whether Elongator complex was also required for tRNA modifications in multicellular organisms, we analyzed the role of Elongator complex in C. elegans.

Based on bioinformatics prediction, homologues of human Elongator subunits hElp1 to hElp4 exist in C. elegans, namely ELPC-1 to ELPC-4. We used two deletion mutants, elpc-1(tm2149) and elpc-3(tm3120) kindly provided by S.

Mitani in Japan, to study the Elongator function in C.elegans. The formation of mcm5 and ncm5 side chains was abolished in total tRNAs extracted from the elpc- 1(tm2149) or elpc-3(tm3120) mutant worms. The defect in formation of wobble uridine tRNA modification in elpc-1(tm2149) was rescued by expressing elpc-1::gfp on an extrachromosomal array. These results indicate that the requirement of the Elongator complex in tRNA modification is conserved in C. elegans. By using a lacZ reporter construct driven by a heat shock-responsive element from the hsp16-1 gene, we observed a significant reduction (~14-18%) in β-galactosidase activity in elpc mutants compared to wild type. No reduction in the induction of lacZ mRNA was observed in elpc-1(tm2149) and elpc-3(tm3120). To monitor the rate of protein synthesis in particular cell compartments, we performed an assay called fluorescence recovery after photobleaching with GFP reporters expressed in specific cells or tissues. In all the constructs examined, we observed significant recovery of fluorescence after photobleaching in wild type animals, but not in elpc-1(tm2149) and elpc-3(tm3120) mutant worms, indicating that lack of mcm5 and ncm5 side chains leads to a reduction in translation efficiency in C. elegans.

To investigate the localization of ELPC-1 in C. elegans, we generated a worm strain with a transgene encoding a functional, full-length ELPC-1 protein fused with GFP at its C-terminus. The fusion protein encoded by the transgene was predominantly expressed in sensory neurons in the head, particularly high in the ASE, ADF and ASK pairs of neurons. Expression was also observed in several other tissues including the pharynx and the intestine. This expression pattern promoted us to investigate the possible role of Elongator complex in nervous system. In elpc- 1(tm2149) and elpc-3(tm3120) mutants, the neuronal development was not affected and the mutant worms chemotaxed normally to both water soluble and volatile attractants. However, elpc-1 or elpc-3 mutants were defective in the salt associated learning. Modulation of synaptic transmission has been shown to be associated with learning pattern of behavior in C. elegans (Voglis and Tavernarakis, 2006, 2008). Since Elongator complex in yeast is required for exocytosis, we assumed that Elongator mutants in C. elegans might be defective in salt learning by affecting synaptic exocytosis.

Neurotransmitters are secreted by exocytosis in two types of vesicles. The classical transmitters such as acetylcholine are packaged in small clear synaptic vesicles. Neuropeptides and monoamines are secreted from dense core vesicles. Synaptic release of acetylcholine can be examined by exposing worms to aldicarb, an inhibitor of acetylcholinesterase. Aldicarb exposure results in worm hypercontraction and death due to accumulation of acetylcholine in the synaptic cleft. Mutants with decreased synaptic transmission are resistant to aldicarb because of a slow accumulation of acetylcholine. Mutations which alter the post-synaptic receptors could also lead to the resistance to aldicarb. The elpc-1 and elpc-3 mutants are much more resistant to aldicarb compared to wild type, but show normal

response to levamisole, which is an agonist of the acetylcholine receptor. These data suggest Elongator mutants affect the presynaptic processes due to either less production or less secretion of acetylcholine. To investigate the exocytosis of dense core vesicles, we examined the synthesis and secretion of ANF::GFP expressed exclusively in the nervous system. ANF::GFP secretion from neurons could be evaluated by its accumulation in coelomocytes located in pseudocoelomic space. Less accumulation of ANF::GFP in coelomocytes was observed in both elpc-1 and elpc-3 mutants. If the production of ANF::GFP is the same in wild type and Elongator mutant worms, less secretion of ANF::GFP in mutant worms would result in the more accumulation of ANF::GFP in the nervous system. However, less GFP signals were observed in Elongator mutant worms, which was confirmed by western blot, indicating that reduced accumulation of ANF::GFP in coelomocytes was most likely caused by an inefficient production of ANF::GFP in the neurons of Elongator mutants.

Elongator complex in mouse has been shown to be important for acetylation of α-tubulin (Creppe et al., 2009). To exclude the possibility that the phenotypes observed in Elongator mutant worms were caused by decreased acetylation of α- tubulin, we analyzed the α-tubulin acetylation levels in Elongator mutants. We did not detect any obvious reduction of α-tubulin acetylation in elpc-1 and elpc-3 mutants. In C. elegans, mec-12 encodes the single α-tubulin which can be acetylated at a lysine residue at position 40. The mec-12(e1607) mutant, which completely eliminates the acetylation of α-tubulin, is not resistant to aldicarb. Based on these observations, we concluded that phenotypes observed in Elongator mutant worms were not caused by a defect in α-tubulin acetylation.

In C. elegans, formation of the 2-thio group in mcm5s2U requires tuc-1. In elpc-1; tuc-1 double mutant, both mcm5 and s2 side chains were abolished and a synergistic reduction in translation efficiency was observed. Neither elpc-1 nor tuc-1 single mutant became sterile at 25ºC, but the elpc-1; tuc-1 double mutant strain was completely sterile at this temperature. In a temperature shift experiment, the elpc-1; tuc-1 double mutant hermaphrodites were shifted to 25°C after grown at 15°C to different developmental stages. When double mutant worms raised at 15°C to L1 or L2 larvae stage were shifted to 25°C, they developed to small sterile adults with defects in vulva development, maturation of oocytes and spermatogenesis. When worms were raised at 15°C to L4 stage, and shifted to 25°C, they were able to develop to fertile adults. The eggs they produced were arrested at different stages in embryogenesis at 25°C. The temperature shift experiment indicates that Elongator complex and TUC-1 promote efficient synthesis of gene products required for different stages during development.

In summary, we demonstrated for the first time that Elongator complex is required for mcm5 and ncm5 side chains formation at wobble uridines in a

multicellular organism. Reduced translation efficiency due to lack of modifications at U34 in Elongator mutant worms results in low production of neurotransmitters and causes developmental disorders. In humans, mutations in hELP1 cause a severe neurodegenerative disease familial dysautonomia (FD). Our results in C. elegans provide implications that a translational dysfunction might play a role in the etiology of FD.

Paper IV: Allele-specific suppressors of lin-1(R175Opal) identify functions of MOC-3 and DPH-3 in tRNA modification complexes in Caenorhabditis elegans

Vulval development in C. elegans is a multiple-step process including generation of vulval precursor cells (VPCs), patterning of VPCs, generation of the adult cells, anchor cell invasion and vulva morphogenesis (Sternberg, 2005). The RAS and Notch signaling pathways play important roles in vulval development of C. elegans (Sternberg and Han, 1998; Sundaram, 2005). LIN-1 is a transcriptional factor which acts downstream of RAS signaling. In lin-1 mutants, an ectopic vulval induction, the multivulva (Muv) phenotype, was observed indicating that LIN-1 plays a negative role in vulval induction (Beitel et al., 1995). In a partial loss-function (lf) allele of lin-1, lin(e1275), around 80% of worms have Muv phenotype when raised at 20°C.

A genetic screen was performed for mutations which can suppress the Muv phenotype of lin(e1275). Two suppressors, ku300 and ku305, reduced the Muv phenotype of lin(e1275) from 81.9% to 1.6% and 1.2%, respectively. The ku300 allele was mapped to an uncharacterized ORF, F42G8.6. We named the gene moc-3 for MOCo synthesis pathway gene 3, encoding a conserved protein known as Uba4 in yeast. The ku305 allele is located in DPH3, a highly conserved gene in eukaryotes. Deletion mutants or RNAi of moc-3 and dph-3 also suppress the Muv phenotype of lin-1(e1275). However, the Muv phenotype caused by other lin-1 mutant alleles, lin-1(n176), lin-1(n1047) and lin-1(n303), was not suppressed by moc-3(lf) and dph-3(lf). Moreover, the moc-3(lf) and dph-3(lf) mutants did not suppress the Muv phenotype caused by other mutants in the RAS signaling pathway, indicating that the Muv suppression by moc-3(lf) and dph-3(lf) was specific to lin- 1(e1275) by alteration of its gene activity. RNAi depletion of lin-1 in lin-1(e1275); moc-3(ku300) and lin-1(e1275); dph-3(ku305) double mutants restored the Muv phenotype in both strains, suggesting a role of moc-3(lf) and dph-3(lf) in enhancement of lin-1 gene activity. Elevated lin-1 activity in lin-1(e1275); moc- 3(ku300) and lin-1(e1275); dph-3(ku305) double mutants was also supported by the observation that the expression of egl-17 , regulated by LIN-1 activity, was restored in the lin-1(e1275) mutant by introducing moc-3(ku300) or dph-3(ku305) mutations in vulval cells.

The orthologs of MOC-3 and DPH-3 in yeast are Uba4 and Dph3/Kti11, which are important for formation of wobble uridine tRNA modifications. Uba4 is

required for the formation of 2-thio group and Dph3/Kti11 is involved in formation of mcm5 and ncm5 side chains at wobble uridines. To investigate whether MOC-3 and DPH-3 in C.elegans also participate in wobble uridine tRNA modification, total tRNAs isolated from wild type and various mutant strains were analyzed by HPLC. Similar to their yeast counterparts, MOC-3 is essential for the formation of 2-thio group and DPH-3 is required for mcm5 side chain formation at wobble uridine in C.elegans. The elpc-3 deletion mutant or RNAi of Elongator subunits also suppressed the Muv phenotype of lin-1(e1275). Since Elongator complex, MOC-3 and DPH-3 are all involved in wobble uridine tRNA modifications, we assumed that the Muv phenotype of the lin-1(e1275) mutant worms was suppressed by readthrough of the opal stop codon due to hypomodified tRNA in moc-3, dph-3 and Elongator mutants. To investigate this possibility, transgenic worms containing a lin-1(e1275)::gfp under sur-5 promoter control were generated. The sur-5 drives almost ubiquitous expression of the transgene in C. elegans (Yochem et al., 1998). GFP expression was not observed in the wild type background. In moc-3 mutant, GFP signal was detected in a fraction of cells but not in all tissues. We also integrated a construct, sur-5p::gfp::lin-1(e1275)::flag, into the genome to generate a transgenic line kuIs76. We observed a high expression of GFP in all developmental stages and in most of tissues. kuIs76 suppressed the fully penetrant Muv phenotype of lin-1(n176) in moc-3 or dph-3 mutant background, indicating that the full length GFP-LIN-1-FLAG protein was produced. However, the readthrough protein product was not detected in moc-3(lf) or dph-3(lf) mutant background by western blot using anti-GFP or FLAG antibodies. This indicates that the readthrough of the opal stop codon is not efficient and that only a small amount of the full length protein is produced, which is not enough to be detected by western blot but is sufficient for its function.

In summary, we demonstrated that moc-3 and dph-3 in C. elegans are required for 2-thio and mcm5 side chain formation at wobble uridines. The moc-3 and dph-3 mutants suppressed the Muv phenotype of lin-1(e1275) by readthrough of the opal stop codon and synthesis of the full length LIN-1 protein.

Conclusions

1. The defects in transcriptional silencing and DNA damage response observed in Elongator mutants is caused by a translational dysfunction due to lack of wobble uridine tRNA modifications.

2. In Elongator mutants, Rnr1 induction in response to DNA damage was defective but the induction of other RNR subunits is normal. The defect of Rnr1 induction was caused by decreased expression of Ixr1 due to reduced decoding ability of Gln hypomodified tRNA 2UUGs in Elongator mutants.

3. Elongator complex in C. elegans is required for formation of wobble uridine 5 5 tRNA modifications. Elimination of mcm and ncm side chains at U34 in C. elegans Elongator mutants leads to a decreased efficiency of translation.

4. The neurological defects observed in Elongator mutant worms might be caused by reduced production of neurotransmitters.

5. In C. elegans, lack of modifications at position 5 or position 2 at U34 leads to a context-dependent readthrough of an opal stop codon resulting in the synthesis of the full length LIN-1 in the lin-1(R175Opal) mutant and the suppression of multivulva phenotype caused the lin-1(R175Opal).

Acknowledgements

Anders Byström (my boss), you are a great man (References needed). Thanks so much for your support and training in all these years (maybe longer). I really like the way that you give me a little pressure by showing your hungry for results just like for food. I must say Mona can always make really nice food, but I am not always cooking nice results for you. Special thanks to Prof. Simon Tuck for introducing me into the wonderful worm field. Thanks so much for your endless support, and for many nice talks about science and also football.

I am grateful to all members in ABYeast group: Marcus (now a collaborator)-Believe it or not, you showed me how to use pipette in my early days. I can always learn something (good or bad) from you every time we talk. Jian-Like a big brother. I cannot imagine what would happen without you. Thanks so much for your help and care both in the lab and in my life. Anders E-Lots of fun being together with you. And you influenced me a lot on the way I am doing lab work. Bo- I am still digging the gold (or something else) in the mine of Elongator. Thank you also for many wonderful dinners. Hao-for taking care of those unfinished projects. Tony-It is nice and fun to have you in the lab, and thanks for your contribution to one of dirtiest lab corners in Umeå. Hasan-Sometimes I feel so strong to move to your bench both in the lab and office. Gunilla-Thanks for your fantastic technical support. I also would like to thank those short-stayed members of GRPASB: Nikolas*2, Fredrick, Yue, Adrian and Anna.

All of you in the worm lab also deserve many thanks: Lars, for your organization of journal club and mini C. elegans course (I hope there will be more before I leave). Gautam, for so many valuable suggestions and so much fun as well. Morten, for lots of help in research and fun in football. Agnetha, for showing me how to put needles into worms. Eva, for the smile when listen to my Chinese accent Swedish. Ola and Bala, for sharing nice lab time together.

I would like to thank Jonas Nilsson for allowing me to do experiments in your lab. All the members in group JN are acknowledged for so much help you provide to me. I also would like to thank Andrei Chabes and Olga Tsaponina for enormous support in the DNA damage project.

I need to thank Glenn, Mikael, Tracy, Tord, and their group members for valuable scientific discussion.

Special thanks to Mikael for your organization of innebandy. You should know it is Wednesday, not Weekend, I am most looking forward to. Many thanks

for many people who have played on Wednesday in last 5 years (especially for those who played in black T-shirt). I also would like to thank all the people who played indoor and outdoor football together (too many names to be listed, but I do remember you). Sara Carlsson, we are always in the same team (football and innerbandy) and Team black (maybe it is only me) miss you so much.

I am very grateful to Johnny, dishwashing, media and secretaries for providing valuable services.

I really need to thank Mats and Helena. I do not remember how many times I have been to Skellefteå, but I do remember those fantastic holidays in your summer house and terrible experience of river swim in the early winter.

Big thanks to those close Chinese friends, Jian and his family, Bo, Gangwei, Daping and his family and Tangtang. It is so hard for me to say goodbye to all of you one by one. I also would like to thank Lixiao Wang and his family, Junfa Liu, Sa Chen, Peng Chen, Chang Chen and Congting Qi for talks now and then.

Special thanks to Jin. Huge hugs first. It is really tough for me to write this part. I hope you understand. Everything is beyond words. Many thanks to Gu for so many nice dinners.

My parents and Ming’s parents, I really appreciate your support, sacrifice and love in all these years. You are always there when needed. Ming, my lovely wife, you make my life full of laugh and love. You should be aware that this is just a start of a life-long journey with me.

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