Sequence analysis

The alignment of the Sso10a2 amino acid sequence (Figure 4.1) with those of its paralogs Sso10a (Q97VX8), Sso10a3 (Q97UL8) and several similar sequences from crenarchaeal species shows that the first twenty- six residues are not present in any of the homologous proteins. Fur- thermore, aBLAST(Altschul et al. 1990) search with these twenty-six residues did not uncover any sequences with significant similarity and it is unclear whether the full-length Sso10a2 protein or transcript exists. A N-terminalα-helix predicted with thePSIPRED(Buchan and Ward

2010) server for secondary structure prediction server, is not essential for DNA binding or protein stability, as we have found that the Sso10a2 protein truncated to Met27 to Glu130 is stable in solution and binds DNA in both electrophoretic mobility shift assay (EMSA) and tethered particle motion (TPM) experiments (results not shown).

uctural anal ysis of DNA binding pr otein Sso10a2 ^o^o^o^o^o^o^o^o^ I ^o^o^o^o^o^o^o^ ^o^o^o^o^o^o^o^o^ 10_. 20_. 30_. 40_. 50_. 60_. 70_.

Q97V10_SULSO MTYGYNIFTVIKFSDNVYKLQLIYYSMQLERRKRGTMEIMFDILRNCEPK...CGITRVIYGAGINYVVAQKYLD 72

Q97VX8_SULSO ...MAKKRSKLEIIQAILEAC.KSG..SPKTRIMYGANLSYALTGRYIK 43 Q97UL8_SULSO ...MR..RTRDDIISDILEAIDSKI..NRISSIMKNVNLSASLAKKYIS 42

Q4J7Y2_SULAC ...MSEMPKHRSKIEIMYTILKVLRESETEVKKTHLMYLVGLNYDVFSKYIS 49 Q4JAD3_SULAC ...MMAEVTTGRKKRTRYEIIHDILAQC.ENG..AKKTWLMYKANLSYELTNNYIN 50 A4YG75_METS5 ...MTTKRRGKLEIYLDILSIC.AMG..GKKTEIMYRANLSYDLLNKYLN 44

A4YH26_METS5 ...MRSRRTSIEIIADILEVVSSGS..GSKSSIMKNANLSEGLTEKYLS 44 A4YG66_METS5 ...MMIRRTRQEIVLSMLEGCSGIG..TNKTNLMYKSGLNYDSFLRYLN 44

Q973Y2_SULTO ...MSKRLKRTSLEIIYSILGACNNN...STKTRIMYNAGVNLLELTKYLE 45 Q973B3_SULTO ...MRSKRDKFDIVADILENIKDGR..NSKSALMKNANLSFSILKKYID 44 F9VNH4_SULTO ...MKVKFNKKKRTDYEIIYDILNALKDGP..IPKTRLIYRAGLTYLTATKYIP 49

Q970P2_SULTO ...MRISFNKRKRTEYQIMFQILDALSRGP..LPKTKLMYKADLTYVVTEKYLP 49 Q974K1_SULTO ...MTEAQVGRKKRTRYEIIHDILSQC.ENG..AKKTWLMYKANLSYELTNNYIN 49

C3MSQ1_SULIM ...MRVERRKRGTMEIMLDILRSCDPE...CGVTRVIYGAGINYSVAQKYLD 46 C3MV70_SULIM ...MHKKRSSIEVIVSILEACNKGD..IKKTRIMFITYLNPRSFYRYIE 44 C3MUB9_SULIM ...MAKKRSKLEIIQAILEAC.KSG..SPKTRIMYGANLSYALTGRYIK 43

C3MSF1_SULIM ...MR..RTRDDIIGDILEAIDSNI..NRISSIMKNVNLSASLAKKYLS 42 C3MVN3_SULIM ...MIEN.RRRTKTEIIYSILRGCSEG...SKKTRLMYLAKLNYSVFMKYIY 45

C3MVP1_SULIM ...MSRKRNRMEIVANILEGC.KGG..IKKTRLMYKTNLSYRLFCKYTR 43 consensus ****!****!* *!!*** ****!* **!** * *!*

4.3. Results and Discussion I I 80_. 90_. 100_. 110_. 120_. 130_.

Q97V10_SULSO QLVKVGALNIKTENDRKIYEITEKGKLLRTHIEEFIKIRENLYSAKEKVSELLRTDSE... 130

Q97VX8_SULSO MLMDLEIIKQ.EGKQ...YMLTKKGEELLEDIRRFNDMRKNMDQLKEKINSVLS....IK... 95 Q97UL8_SULSO MLAEEGLIQD.DNGE...YKLTEKGRKILEQLRNMRKMELELANIIYEVRKEPVVFH...QFYSK... 100

Q4J7Y2_SULAC RIEKLGLVRVNKEG....YSLTDSGKRELEMIENYLT...IERKLKG... 89 Q4JAD3_SULAC KLVEKQLISQ.KDGL...YYLTDKGKKLLELLKEYKDKKTALDRVTSQIKDIYGED... 102 A4YG75_METS5 DLEQNGFIVT.TGNL...RCLTDKGQRLLDLLVKRENVRKEVEDLEFRISMMTSRAGSLKEIEISKIN... 108

A4YH26_METS5 ILKDKGLIKQ.KDSS...FVLTEKGQQILSNFREIRKLELRLDELLNSTLNELS... 94 A4YG66_METS5 HLMDLGLISF.SEGK...YRLTGEGMKTMDKLRKFKELKKNMQKMMDDIADV... 92

Q973Y2_SULTO LLEKEGYIKKIQSEKRVTYSLTEKGRDALERLEKYIKILKELEEAKKDVIDLIKIVKKKKEVKT... 109 Q973B3_SULTO YLEKNGYVEE.KDGS...YVITDKGLALLDRLNKVRNLEFQLAELINELSKELL... 94 F9VNH4_SULTO YLEKQNLIKKEGDL....YHITEKGEEVRKLLEIYKVKANEIKEIVSKLEKEIGP...EEEL... 104

Q970P2_SULTO YLQNIGAIKKDKEL....YYITQRGQEIRNLLETYIRKAEEIKKVLEELRRTIEMKNNDEGVRTKRESKVIKSDR 120 Q974K1_SULTO KLVEKELIVQ.KDGL...YYLTDKGRKLLDLLKDYKEKKSGLDKVVAQIKEIYGED... 101

C3MSQ1_SULIM QLIKVGALSIKTENGKKIYGITEKGKLLRMHIEEFIKIRENLNLAREKVIELLKTSIR... 104 C3MV70_SULIM ILKSKGFISLNTDET...YELTPKGYDYLNKAKEYLEIKRKLQILKKELD.FNSQN... 96 C3MUB9_SULIM MLMDLEIIKQ.EGKQ...YMLTKKGEELLEDIRRFNDMRKNMDQLKEKINSVLS....IK... 95

C3MSF1_SULIM MLTDDGLIQE.VDGE...YKLTEKGRKVLEHFRNMRKIELELATIIYEVRKELSANKKEDQVSHS... 103 C3MVN3_SULIM KMKQMNLIEFNEGK....CVLTDKGKRVLELLDKYMEMYSELNEVRRKLEELMQTES... 98

C3MVP1_SULIM LLEKKGLITF.VDNE...YRLTAKGYDYLNRVKEYINLMKKLKEMRESLDDLKDEKQLIKR... 100 consensus ! *** * ! *!*!! *** ** * * * * * **

Figure 4.1: ClustalW sequence alignment of Sso10a (Q97VX8) archaeal homologs, including Sso10a2 (Q97V10) and Sso10a3 (Q97UL8) from Sulfolobus solfataricus; Sac10a (Q4JAD3) and a paralog (Q4J7Y2) from Sulfolobus acidocaldarius; similar sequences from Metallosphaera sedula (A4YG75, A4YH26 and A4YG66), Sulfolobus toko- daii (Q973Y2, Q973B3, F9VNH4, Q970P2 and Q974K1), and Sulfolobus islandicus (C3MSQ1, C3MV70, C3MUB9, C3MSF1, C3MVN3 and C3MVP1). The secondary stucture of Sso10a2 is depicted in the first line. Violet and blue shading denote a consensus of more than 80 % and 50 to 80 %, respectively. Residues that are chemically similar, but not identical are shaded in magenta if the similarity exceeds 50 %.