Immuno-précipitation des protéines

Préparation des cellules et préparation des extraits protéiques

Les souches sont ensemencées dans 50 ml de milieu YPD et incubées toute la nuit. A partir de cette préculture, 2 litres de YPD sont ensemencés pour arriver à une DO600 de 0,6.

Les cellules sont transvasées dans deux flacons de 500 ml puis récoltées par centrifugation pendant 5 minutes à 6000 rpm à 4° (rotor JA-10, Beckman). A partir de cette étape, les cellules sont toujours maintenues à 4°C. Les culots sont ensuite repris dans 4 ml de tampon IP + NP40 0,05% + PMSF 2,5 mM + anti-protéases CompleteTM (Roche ; une pastille pour 10 ml de tampon). Les cellules ensuite transférées dans une « chambre » pour presse Eaton refroidie la nuit à -80°C. Les chambres sont placées toute la nuit à -80°C. Les cellules sont ensuite lysées à la presse Eaton en appliquant 6 tonnes/cm2. Le lysat est transféré dans un tube pour rotor 50Ti puis centrifugé à 4000 rpm, pendant une heure, à 4°C (rotor 50Ti, Beckman Optima LE-80K Ultracentrifuge). Le surnageant contenant les protéines est transvasé dans des tubes Eppendorfs de 2 ml et ensuite stocké à -80°C.

Préparation des billes

8. 106 billes magnétiques Dynabeads® M450 couvertes d’IgG rat anti-IgG de souris (20 μl à 4.108 _{billes/ml) sont prélevées pour chaque échantillon. Ces billes sont lavées 2 fois}

avec 500 μl de PSB/BSA 0,1% puis sont repris dans 100 μl. 1,2 μg d’anticorps 12CA5 purifié (souris anti HA) sont ajoutés à chaque tube. Ces échantillons sont ensuite incubés 30 minutes à 4°C sous agitation de 1300 rpm, puis sont lavés 3 fois dans 500 μl de PBS/BSA 0,1 %, puis deux lavages dans du tampon IP+ NP40 0,05%.

Immuno-précipitation

1,5 mg d’extraits protéiques sont ajoutés à chaque échantillon de billes, puis les mélanges sont incubés 3 heures dans l’agitateur Eppendorf (4°C à 1000 rpm).

Les billes sont reprises dans 500 μl de tampon IP + NP40 0,05% + PMSF 2,5 mM + anti-protéases CompleteTM puis sont transférées dans des tubes propres. Quatre lavages dans du tampon IP sont ensuite réalisés. A la suite du dernier lavage, les billes sont reprises dans 16 μl de tampon IP auxquels ajoutés sont 4 μl de tampon de charge concentré 5X (Glycérol 50%, β-mercapto-éthanol 25%, SDS 10%, Tris-HCL 312,5 mM pH 6,8, bleu de bromophénol 0,005%). Les protéines immunoprécipitées sont éluées par chauffage à 95°C pendant 10 minutes. En parallèle, les extraits bruts sont décongelés, puis sont également dénaturés 10

minutes à 95° dans du tampon de chargement. Les éluats sont récupérés et sont conservés à - 20°C .

Marta KWAPISZ Frédéric BECKOUËT

Pierre THURIAUX *

Rpb8, a missing link between archaeal, eukaryotic and viral DNA-dependent RNA polymerases

(LETTER)

CEA, IbiTecS, Service de Biologie Intégrative & Génétique Moléculaire. Gif/Yvette, F-91191. FRANCE. * Corresponding author Tel: +33 1 69 08 35 86 Fax: +33 1 69 08 47 12 E-mail: pierre.thuriaux@cea.fr KEYWORDS

Archaea / RNA polymerase / Rpb8/ RpoG / Transcription / Yeast

RUNNING HEAD

ABSTRACT

The three DNA-dependent RNA polymerases of Eukaryotes have a conserved twelve- subunit core known to be closely related to archaeal RNA polymerases, except for Rpb8. This polypeptide, one of the five common subunits identical in all three enzymes, was believed so far to be typically eukaryotic, with a related gene product found in at least one type of nucleo- cytoplasmic DNA virus. We show here that Rpb8 is homologous to RpoG, a polypeptide co- purifying with the RNA polymerase of Sulfolobus acidocaldarius. RpoG/Rpb8-like polypeptides are present in all Eukaryotes and Crenarchaeota sequenced so far, but are not found in other archaeal lineages or in Bacteria.

Three DNA-dependent RNA polymerases, hereafter called Pol I, II and III, transcribe the nuclear genomes of Eukaryotes. Studies in the budding yeast Saccharomyces cerevisiae have established that these transcriptionally specialized enzymes share a conserved set of twelve polypeptide. As shown in Table 1, the two largest subunits (Rpb1 and Rpb2) and three small polypeptides (Rpb4, Rpb7, Rpb9) of Pol II are encoded by related but distinct genes in the other two enzymes. However, five small subunits are identical in the three yeast polymerases (Rpb5, Rpb6, Rpb8, Rpb10 and Rpb12), and two other (Rpc19, Rpc40) are common to Pol I and III, with Pol II paralogues (Rpb3, Rpb11). This pattern is widely conserved among Eukaryotes, with only minor exceptions known so far (Proshkina et al. 2006).

Bacterial polymerases have a β’βα2ω core structure homologous to five of the eukaryotic

core subunits (Table 1), but archaeal polymerases are much more close to the eukaryotic ones, with significant homology to eleven of the twelve core Pol I, II and III subunits (Langer et al. 1995; Werner and Weinzierl 2002; Goede et al. 2006). However, no archaeal gene product related to Rpb8 has been identified so far (Briand et al. 2001; Werner and Weinzierl 2002; Goede et al. 2006). Rpb8 is a common component of the three yeast polymerases (Woychik et

al. 1990; Voutsina et al. 1999; Briand et al. 2001). It is strongly conserved among Eukaryotes and an homologous protein is also encoded by the Emiliana huxleyi Virus 86, an algal DNA virus endowed with its own RNA polymerase (Wilson et al. 2005). Using iterative sequence alignments based on the PSI-Blast algorithm (Schaffer et al. 2001), we confirmed the presence of an Rpb8-like protein in all Eukaryotes sequenced so far (http://www.ncbi.nlm.nih.gov/), with no significant homology to any non-eukaryotic genome.

Turning to Archaea, we noticed that a purified RNA polymerase of Sulfolobus

acidocaldarius, a Crenarchaeon, contains a 121 amino acid polypeptide called RpoG (D.

Langer, Ph. D. Thesis 1991, quoted in Langer et al., 1995). However, there is no RpoG-like component in the well-defined euryarchaeal enzymes of Methanocaldococcus jannaschii (Werner and Weinzierl 2002) and Pyrococcus furiosus (Goede et al. 2006), and it was therefore possible that RpoG may not be a bona fide polymerase subunit. PSI-Blast readily identified RpoG-like polypeptides in all crenarchaeal genomes sequenced so far. Intriguingly, this homology search also yielded several gene products that, although well above the threshold value of 0.05, happened to be fungal Rpb8-like polypeptides and included the well-defined Rpb8 subunit of the fission yeast Schizosaccharomyces pombe (Voutsina et al. 1999; Shpakovski et al. 2000). Further homology search eventually merged all Rpb8- and RpoG-like gene products into a single protein family, as illustrated by the sequence alignments provided in the Supplementary Material. As indicated in Figure 1, the Rpb8/RpoG protein exists in all Eukaryotes and in all Crenarchaeota sequenced so far (13 genomes), but were not found in Euryarchaeota (47 genomes) or in Nanoarchaeota (1 genome). They were also absent from Bacteria and were only represented in the one viral genome already mentioned.

Some fifteen amino acids are (nearly) invariant in Eukaryotes (Rpb8) and Archaea (RpoG), and their spatial distribution in the yeast Pol II enzyme underscores the similarity of these two proteins. As shown in Figure 2, the ten β sheets of yeast Rpb8 form a compact barrel fold

(Cramer, Bushnell, and Kornberg 2001) where the amino acids shared with RpoG are all closely packed on four β strands (β4, β6, β9 and β10). Moreover, Rpb8-β6 and Rpb1-β18 form a strong β addition motif binding Rpb8 to Rpb1, the largest Pol II subunit. Rpb1-β18 corresponds to a 563PAIIKP568 motif conserved in the largest subunit of Pol I (Rpa190) and Pol

III (Rpc160) of Eukaryotes. Remarkably, this conservation extends to the corresponding RpoA’ subunit of Crenarchaeota and to the EHV86 virus, to the exclusion of all other archaeal or viral RNA polymerases, indicating that the Rpb8-β6/Rpb1-β18 addition exists in all organism endowed with an Rpb8/RpoG-like polypeptide (the corresponding alignments are shown as Supplementary Material).

These data strongly argue that RpoG and Rpb8 are homologous components of the eukaryotic and archaeal transcription systems, presumably sharing similar functions. The yeast subunit is essential in vivo but little is known of its transcriptional role (Woychik et al. 1990; Voutsina et al. 1999; Briand et al. 2001). The role of the archaeal subunit is also quite puzzling given that RpoG-like proteins only exist in Crenarchaeota. Equivalent but structurally unrelated subunits, if they exist in Euryarchaeota, could at best have an accessory role in vitro since they are not part of the fully reconstituted RNA polymerase of M. jannaschii (Werner and Weinzierl 2002). Crenarchaeota also differ from Euryarchaeota and Nanoarcheaota by usually lacking histones (Reeve 2003; Cubonova et al. 2005), which might call for an additional RNA polymerase subunit like RpoG. However, an histone-encoding gene was recently identified in

Cenarchaeum symbiosum, a psychrophilic Crenarchaeon (Reeve 2003; Cubonova et al. 2005),

and our own Psi-Blast search showed that archaeal histones and RpoG-like proteins co-exist in two other Crenarchaeota, Thermofilum pendens and Caldivirga maquilingensis (see Figure 1).

The Rpb8/RpoG homology implies that the entire twelve-subunit core structure of Pol I, II and III derives from some archaeal ancestor(s). Nevertheless, all currently sequenced eukaryotic genomes share a large N-terminal fold, present in their Rpb5 subunit but lacking in

its archaeal RpoH homolog. As discussed elsewhere (Zaros et al. 2007), this domain may directly contact the nucleosomes downstream of the elongating RNA polymerase, thus fulfilling a function needed in all three nuclear transcription systems.

We therefore speculate that the ancestor of eukaryotic polymerases existed before the separation of the two main archaeal lineages, and that it was endowed with histones and with an RpoG-like subunit as two contemporary Crenarchaeaota (T. pendens, C. maquilingensis). The N-terminal fold of Rpb5 then probably appeared in early forms of the nucleus, as an adaptation to nucleosomes, and was followed by the emergence of the three paralogous enzymes now found in all sequenced Eukaryotes (Proshkina et al. 2006).

Acknowledgments. P.T. dedicates this work to the memory of Wolfram Zillig, in remembrance of a great scientist and of a good friend. M.K. and F.B. were supported by the Fondation pour la Recherche Médicale and the Association pour la Recherche sur le Cancer.

FIGURES

Figure 1. Simplified three-domain phylogenetic tree. The only species indicated are those mentioned in the text. Stars denote the presence of an Rbp8/RpoG gene product. Dots indicate the presence of eukaryotic or archaeal histones. Based on Cubonova et al. 2005.

Figure 2. Spatial organization of Rpb8 and of the eukaryotic-specific domain of Rpb5 in the yeast RNA polymerase II crystal structure. Figure based on the 2NVZ PDB file (Wang et al. 2006) and prepared with the Pymol software (http://pymol.sourceforge.net/). Upper panel: whole RNA polymerase II structure, emphasizing the secondary structure of Rpb8 and Rpb5 (first 142 amino acids). Lower panel: secondary structures of Rpb8. Conserved positions are shown in blue (in Eukaryotes only) and red (in Eukaryotes and Archaea) and correspond to the alignments shown as Supplementary Material. The Rpb1-β18 sheet is shown in cyan, and corresponds to the conserved 563PAIIKP568 motif.

Table 1. Conservation of the core subunits of bacterial, archaeal, eukaryotic and viral RNA polymerases.

Archaea Eukaryotes DNA

viruses Bacteria

Chloroplasts Euryarchaeota

Nanorchaeota Crenarchaeota Pol II Pol I Pol III EHV86

β’ β α α ω RpoA’, RpoA’’ RpoB RpoD RpoL RpoK RpoF RpoH RpoE’ RpoM RpoN RpoP RpoA’, RpoA’’ RpoB’, RpoB’’ RpoD RpoL RpoK RpoF RpoH RpoE’ RpoM RpoN RpoP RpoG Rpb1 Rpb2 Rpb3 Rpb11 Rpb6 Rpb4 Rpb5 Rpb7 Rpb9 Rpb10 Rpb12 Rpb8 Rpa190 Rpa35 Rpc40 Rpc19 Rpb6 Rpa14 Rpb5 Rpa43 Rpa12 Rpb10 Rpb12 Rpb8 Rpc160 Rpc128 Rpc40 Rpc19 Rpb6 Rpc17 Rpb5 Rpc25 Rpc11 Rpb10 Rpb12 Rpb8 + + + + + + + +

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