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The origin of novel proteins by gene duplication: evolution of translation termination factors

The origin of novel proteins by gene duplication: evolution of translation termination factors. Galina Zhouravleva. Department of Genetics St. Petersburg State University. Part 1. Mechanism of translation termination. Main steps in eukaryotic translation. Start codon. Stop codon. 5 ’.

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The origin of novel proteins by gene duplication: evolution of translation termination factors

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  1. The origin of novel proteins by gene duplication: evolution of translation termination factors Galina Zhouravleva Department of Genetics St. Petersburg State University

  2. Part 1.Mechanism of translation termination

  3. Main steps in eukaryotic translation Start codon Stop codon 5’ mRNA 3’ UAA AUG CAP AAAAAAA 3’ UTR 5’ UTR Initiation Elongation Termination Recycling

  4. Translation factors: Prokariota: EF-Tu, EF-Ts, EF-G RF1, RF2, RF3 IF-1, IF-2, IF-3 Eukaryota: eEF1А, eEF1В, eEF2 eRF1, eRF3 eIF1, eIF1A, eIF2, eIF2B, eIF3, eIF4A, eIF4B, eIF4E, eIF4G, eIF5 Main steps in eukaryotic translation Start codon Stop codon 5’ mRNA 3’ UAA AUG CAP AAAAAAA 3’ UTR 5’ UTR Initiation Elongation Termination

  5. Translation termination in prokaryotes Stop-codon recognition Е Р А Е Р А RF1 (RF2) + RF3 RF2 + RF3 UGA UGA 5’ 3’ Translation termination factors - RF- factors (Release Factors): RF1 (essential) – decodes UAA and UAG 36% amino acid identity Class 1 release factors RF2 (essential) – decodes UAA and UGA Class 2 release factor RF3 - GTPase; promotes RF1/2 release (non-essential)

  6. Stop-codon recognition GGQ Е Р А Е Р А GTP eRF1 + eRF3 UGA AAA UUU UGA AAA UUU Peptidyl-tRNA hydrolysis GGQ GTP hydrolysis eRF1 Recycling? Reinitiation? PAB PAB 3’ Е Р А 4G 4E AAA UUU 5’ UGA GGQ eRF1 eRF3 Е Р А eRF1 GDP eRF3 GTP eRF3 AAA UUU UGA Translation termination in eukaryotes Class 1 release factor eRF1 (essential) – UAA, UAG, UGA (RF1 + RF2) Class 2 release factor (RF3) eRF3 (essential) - GTPase

  7. Part 2. Translation termination factors

  8. Eukaryota Eukaryota Archaea eRF1 – UAA, UAG, UGA eRF3 aRF1 – all 3 stop codons (?) Class 1 release factors Prokaryota RF1 - UAA и UAG RF2 - UAA и UGA Homologous (30% of identity) No sequence similarity Class 2 release factors Prokaryota Archaea RF3 Absent No sequence similarity

  9. The average similarity plot of RF sequences A-G – conserved regions Ito et al., 1996

  10. Comparison of the amino acid sequences of prokaryotic RFs and EF-G of E.coli Ito et al., 1996

  11. tRNA-protein mimicry hypothesis Ito et al., 1996

  12. Phylogenetic tree of aRF1 and eRF1 Mulitcellular eukaryotes Liu, 2005 Inagaki, Doolittle, 2000

  13. Phylogenetic tree of eRF3

  14. Duplication Duplication H. sapiens eRF3a Divergence M. musculus eRF3a H. sapiens eRF3b M. musculus eRF3b lower eukaryotes eRF3 The phylogenetic tree showing the origin of paralogs encoding the factors eRF3a and eRF3b in higher eukaryotes

  15. Difference in the organization of GSPT genes GSPT1 – 15 introns GSPT2 – no introns H.sapiens Х chromosome 16 chromosome Х chromosome 16 chromosome M.musculus

  16. A model of GSPT2 origin by reverse transcription of a processed GSPT1 transcript and its reintegration in X-chromosome GSPT2(Xchromosome) P2 5’UTR/2 Retroposition Splicing P1 P2 5’UTR/2 3’UTR 5’UTR/1 GSPT1(16 chromosome) P1, P2 – promoter sequences

  17. eRF3 family Complementation of S. cerevisiae SUP35 disruption N M C S. cerevisiae Sup35 (1-685) + - - NT + - 57% 14% 13% Amino acid identity between yeast Sup35 and human GSPT1 (1-637) Human GSPT1 (1-635) Mouse GSPT1 Human GSPT2 NT (1-632) Mouse GSPT2 (1-632) X. laevis Sup35 (1-573)

  18. N-terminal domain of eRF3 is not conserved in evolution Identity (%) with yeast Sup35 with mouse GSPT1 Protein Yeast proteome ySup35 mGSPT1 mGSPT2 xSup35 G+Y (%) 8 33 10 5 9 Q+N (%) 10 45 8 4 18 - 100 10 7 14 - 10 100 49 11

  19. N-terminal domain of eRF3 is not conserved in evolution G-stretch mGSPT1 -----------------MDPGSGGGGGGGGGGSSSSSDSAPDCWDQTDME------------------ -----------------ccttccccccccccccccccccccccccccccc------------------ mGSPT2 -----------------MDLGS-------------SNDSAPDCWDQVDME------------------ -----------------eeecc-------------cccccccccceeeec------------------ xSup35 -----------------ITGTTLFPPTWEVLPTLPTPCLTPSAPLIKQLV------------------ -----------------ecccccccccceecccccccccccccchhheee------------------ ySup35 MSDSNQGNNQQNYQQYSQNGNQQQGNNRYQGYQAYNAQAQPAGGYYQNYQGYSGYQQGGYQQYNPDAG eccccccccccceeeeccccccccccccccchhhhhhtccccccceecttccttcccttcccccttcc . * : mGSPT1 APGPGPCGGG---GSGSGSMAAVAEAQR---ENLSAAFSRQLNVNAKPFVPN--- cccccccccc---cccchhhhhhhhhhh---hhhhhhhhhhhcccccccccc--- mGSPT2 GPGSAPSGDGIAPAAMAAAEAAEAEAQR---KHLSLAFSSQLNIHAKPFVPS--- cccccccccccchhhhhhhhhhhhhhhh---hhhhhhhhhhccccccccccc--- xSup35 YPNPTHPEMDASDSAPDSWEQADMEATE---AQLNNSMA-ALNVNAKPFVPN--- ccccccccccccccccchhhhhhhhhhh---hhhhhhhh-hhhccccccccc--- ySup35 YQQQYNPQGGYQQYNPQGGYQQQFNPQGGRGNYKNFNYNNNLQGYQAGFQPQSQG ceeecccttccccccttccceeeccccccccceeeecccccccchettccccctt . . :. . *: * *. QN-stretch Oligopeptide (PQGGYQQ-YN) repeats Pab1- interacting region Oligopeptide (PQGGYQQ-YN) repeats Alpha helix – h, extended strand – e, random coil – c, beta turn - t SOPM (Self-Optimized Prediction Method) - secondary structure prediction method (Geourjon and Deleage, 1994) http://npsa-pbil.ibcp.fr/cgi-bin/

  20. Part 3.Prionization of translation termination factor eRF3 in yeast

  21. Composition of yeast eRF3 (Sup35) 1 254 685 124 N M C PFD Translation termination EF1-A-like domain 6 33 97 PFD R6 R4 R5 R3 R1 R2 QN OR QN: the N-terminal QN-rich stretch. OR: R1-R6 – oligopeptide repeats of the consensus sequence PQGGYQQ-YN (P – proline, Q – glutamine, G – glycine, Y – tyrosine, N – asparagine)

  22. Evolutionary comparison of the N-terminal domains of Sup35 proteins from budding and fission yeast N-domain QN-stretch OR-region Q(%) N(%) QN OR 132 • 39 15 • 43 17 • 35 30 • 16 22 • 26 • 12 • 38 9 • 45 14 • 15 • 39 7 (GYQNYNQ)5.5 D. hansenii Debaryomyces 137 K. lactis (QGYNNAQQ)6 Kluyveromyces P. methanolica (NRGGYSNYN)5 161 Pichia 106 (QGYQXY)4 P. pastoris S. cerevisiae 123 (PQGGYQQ-YN)5.5 Saccharomyces Z. rouxii 103 (GGYGGY)5 Zygosaccharomyces Y. lipolytica 157 (QGGYQGGYQGGY)5 Yarrowia Ascomycota S. ludwigii (GYQAYQQYNAQPQQQ)4.5 121 Saccharomycodes C. albicans (GGYQQNYN)6.5 129 Candida C. maltosa 144 (GGYQQNYNNR)4.5 Schizosaccharomyces No QN-stretch No repeats S. pombe 112

  23. Evolutionary origin of eRF3 Eukarya eEF-2 Archaea aEF-2 EF-G EF-G EF-G RF3 Eubacteria Ancient GTPase EF-Tu Archaea aEF-1A EF-Tu eEF-1A Eukarya eEF-1A eRF3 EF – elongation factor, RF- release factor. (1-465) Giardia intestinalis Sup35 (1-685) Saccharomyces cerevisiae Sup35 N M C

  24. Part 4.Molecular mimicry: translation termination factors as tRNA

  25. tRNA-protein mimicry hypothesis Ito et al., 1996

  26. Molecular Mimicry EF-Tu tRNA tRNA-EF-Tu-GTP EF-G-GTP

  27. (Ramakrishnan 2002)

  28. Macromolecular mimicry in termination and ribosome recycling Human eRF1 Yeast tRNAPhe E. coli RF2

  29. Part 5.Duplication in the evolutionary history of translation elongation and termination factors

  30. A scheme for the evolution of elongation and release factors in Bacteria, Archaea, and Eukarya. (Inagaki and Ford, 2000)

  31. The evolutionary origin of translation termination factors EF - elongation factors EF-G RF3 RF – termination (release) factors EF-G eEF-2 Hbs1 RF1 EF RF2 eRF1 Duplication EF-Tu Divergence Hbs1 e - eukaryotic EF-Tu eRF3 eEF-1A

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