**6. Acknowledgments**

This work was supported by the Russian Foundation for Basic Research (10-04-00237) and the Program of the Presidium of the Russian Academy of Sciences, The Origin and the Evolution of the Biosphere.

Gene Duplication and the Origin of Translation Factors 165

Byrne, K.P. & Wolfe, K.H. (2005) The Yeast Gene Order Browser: combining curated

Carr-Schmid, A., Pfund, C., Craig, E.A., & Kinzy, T.G. (2002) Novel G-protein complex

Cavallius, J., Zoll, W., Chakraburtty, K., & Merrick, W.C. (1993) Characterization of yeast

Chapman, B. & Brown, C. (2004) Translation termination in *Arabidopsis thaliana*: characterisation of three versions of release factor 1. *Gene*, Vol.341, pp. 219-225. Chapman, B.A., Bowers, J.E., Feltus, F.A., & Paterson, A.H. (2006) Buffering of crucial

Chen, C.C., Li, W.H., & Sung, H.M. (2007) Patterns of internal gene duplication in the course

Chen, L., Muhlrad, D., Hauryliuk, V., Cheng, Z., Lim, M.K., Shyp, V., Parker, R., & Song, H.

Comai, L., Tyagi, A.P., Winter, K., Holmes-Davis, R., Reynolds, S.H., Stevens, Y., & Byers, B.

Conant, G.C. & Wagner, A. (2005) The rarity of gene shuffling in conserved genes. *Genome* 

Craigen, W.J., Lee, C.C., & Caskey, C.T. (1990) Recent advances in peptide chain

Cui, L., Wall, P.K., Leebens-Mack, J.H., Lindsay, B.G., Soltis, D.E., Doyle, J.J., Soltis, P.S.,

Czaplinski, K., Ruiz-Echevarria, M.J., Paushkin, S.V., Han, X., Weng, Y., Perlick, H.A., Dietz,

Davis, J.C. & Petrov, D.A. (2005) Do disparate mechanisms of duplication add similar genes

Davis, L. & Engebrecht, J. (1998) Yeast *dom34* mutants are defective in multiple

Vol.15, pp. 1456-1461.

Vol.22, pp. 2564-2574.

5801-5811.

*Biol.*, Vol.6, R50.

Vol.149, pp. 45-56.

*Biochim.Biophys.Acta*, Vol.1163, pp. 75-80.

of metazoan evolution. *Gene*, Vol.396, pp. 59-65.

allotetraploids. *Plant Cell*, Vol.12, pp. 1551-1568.

termination. *Mol.Microbiol.*, Vol.4, pp. 861-865.

plants. *Genome Res.*, Vol.16, pp. 738-749.

mRNAs. *Genes Dev.*, Vol.12, pp. 1665-1677.

to the genome? *Trends Genet*, Vol.21, pp. 548-551.

*Nat.Struct.Mol.Biol.* 17, 1233-1240.

homology and syntenic context reveals gene fate in polyploid species. *Genome Res.*,

whose requirement is linked to the translational status of the cell. *Mol.Cell Biol.*,

EF-1 alpha: non-conservation of post-translational modifications.

functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. *Proc.Natl.Acad.Sci.U.S.A.*, Vol.103, pp.2730-2735. Chauvin, C., Salhi, S., Le Goff, C., Viranaicken, W., Diop, D., & Jean-Jean, O. (2005)

Involvement of human release factors eRF3a and eRF3b in translation termination and regulation of the termination complex formation. *Mol.Cell Biol.*, Vol.25, pp.

(2010) Structure of the Dom34-Hbs1 complex and implications for no-go decay.

(2000) Phenotypic instability and rapid gene silencing in newly formed arabidopsis

Carlson, J.E., Arumuganathan, K., Barakat, A., Albert, V.A., Ma, H., & dePamphilis, C.W. (2006) Widespread genome duplications throughout the history of flowering

H.C., Ter Avanesyan, M.D., & Peltz, S.W. (1998) The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant

developmental pathways and exhibit decreased levels of polyribosomes. *Genetics*,

### **7. References**


Adams, K.L. & Wendel, J.F. (2005) Polyploidy and genome evolution in plants. *Curr* 

Amrani, N., Dong, S., He, F., Ganesan, R., Ghosh, S., Kervestin, S., Li, C., Mangus, D.A.,

Andersen, G.R., Valente, L., Pedersen, L., Kinzy, T.G., & Nyborg, J. (2001) Crystal structures

Andersson, D.I. & Hughes, D. (2009) Gene Amplification and Adaptive Evolution in

Asano, K., Phan, L., Valasek, L., Schoenfeld, L.W., Shalev, A., Clayton, J., Nielsen, K.,

Atkins, J.F., Weiss, R.B., Thompson, S., & Gesteland, R.F. (1991) Towards a genetic dissection

Atkinson, G.C., Baldauf, S.L., & Hauryliuk, V. (2008) Evolution of nonstop, no-go and

Aury, J.M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B.M., Segurens, B., Daubin, V.,

revealed by the ciliate Paramecium tetraurelia. *Nature*, Vol.444, pp. 171-178. Benard, L., Carroll, K., Valle, R.C., Masison, D.C., & Wickner, R.B. (1999) The Ski7 antiviral

Blanc, G., Hokamp, K., & Wolfe, K.H. (2003) A recent polyploidy superimposed on older

Blanc, G. & Wolfe, K.H. (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. *Plant Cell*, Vol.16, pp. 1667-1678. Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., & Van de, P.Y. (2006) The

Brunet, F.G., Crollius, H.R., Paris, M., Aury, J.M., Gibert, P., Jaillon, O., Laudet, V., &

genome duplication in teleost fishes. *Mol.Biol.Evol.*, Vol.23, pp. 1808-1816.

mediated mRNA decay. *Biochem.Soc.Trans.,* Vol. 34, pp. 39-42.

frame shifts and hops. *Annu.Rev.Genet.*, Vol.25, pp. 201-228.

*Saccharomyces cerevisiae*. *J.Virol.*, Vol.73, pp. 2893-2900.

Spatrick, P., & Jacobson, A. (2006) Aberrant termination triggers nonsense-

of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex.

Donahue, T.F., & Hinnebusch, A.G. (2001) A multifactor complex of eIF1, eIF2, eIF3, eIF5, and tRNA(i)Met promotes initiation complex assembly and couples GTP hydrolysis to AUG recognition. *Cold Spring Harb.Symp.Quant.Biol.*, Vol.66, pp.

of the basis of triplet decoding, and its natural subversion: programmed reading

nonsense-mediated mRNA decay and their termination factor-derived

Anthouard, V., Aiach, N., Arnaiz, O., Billaut, A., Beisson, J., Blanc, I., Bouhouche, K., Camara, F., Duharcourt, S., Guigo, R., Gogendeau, D., Katinka, M., Keller, A.M., Kissmehl, R., Klotz, C., Koll, F., Le Mouel, A., Lepere, G., Malinsky, S., Nowacki, M., Nowak, J.K., Plattner, H., Poulain, J., Ruiz, F., Serrano, V., Zagulski, M., Dessen, P., Betermier, M., Weissenbach, J., Scarpelli, C., Schachter, V., Sperling, L., Meyer, E., Cohen, J., & Wincker, P. (2006) Global trends of whole-genome duplications

protein is an EF1-alpha homolog that blocks expression of non-Poly(A) mRNA in

large-scale duplications in the *Arabidopsis* genome. *Genome Res.*, Vol.13, pp.

gain and loss of genes during 600 million years of vertebrate evolution. *Genome* 

Robinson-Rechavi, M. (2006) Gene loss and evolutionary rates following whole-

**7. References** 

403-415.

137-144.

*Biol.*, Vol.7, R43.

*Opin.Plant Biol.,* Vol. 8, pp. 135-141.

*Nat.Struct.Biol.*, Vol.8, pp. 531-534.

Bacteria. *Annu.Rev.Genet*., Vol.43, pp. 167-95.

components. *BMC.Evol.Biol.*, Vol.8, pp. 290.


Gene Duplication and the Origin of Translation Factors 167

Hahn, M.W. (2009) Distinguishing among evolutionary models for the maintenance of gene

Harms, C.T., Armour, S.L., DiMaio, J.J., Middlesteadt, L.A., Murray, D., Negrotto, D.V.,

Hauryliuk, V., Zavialov, A., Kisselev, L., & Ehrenberg, M. (2006) Class-1 release factor eRF1

He, X. & Zhang, J. (2005) Rapid subfunctionalization accompanied by prolonged and

Hittinger, C.T. & Carroll, S.B. (2007) Gene duplication and the adaptive evolution of a classic

Hoshino, S., Miyazawa, H., Enomoto, T., Hanaoka, F., Kikuchi, Y., Kikuchi, A., & Ui, M.

Hoshino, S., Imai, M., Mizutani, M., Kikuchi, Y., Hanaoka, F., Ui, M., & Katada, T. (1998)

Hoshino, S., Imai, M., Kobayashi, T., Uchida, N., & Katada, T. (1999) The eukaryotic

with polyadenylate-binding protein. *J.Biol.Chem.*, Vol.274, pp. 16677-16680. Hurles, M. (2004) Gene duplication: the genomic trade in spare parts. *PloS.Biol.*, Vol.2,

Inagaki, Y. & Doolittle, F.W. (2000) Evolution of the eukaryotic translation termination

Inge-Vechtomov, S., Zhouravleva, G., & Philippe, M. (2003) Eukaryotic release factors (eRFs)

Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N.,

Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyere, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le, C., I, Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pe, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quetier, F., & Wincker, P. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major

system: origins of release factors. *Mol.Biol.Evol.*, Vol.17, pp. 882-889.

Thompson-Taylor, H., Weymann, K., Montoya, A.L., Shillito, R.D., et al. (1992) Herbicide resistance due to amplification of a mutant acetohydroxyacid synthase

promotes GTP binding by class-2 release factor eRF3. *Biochimie*., Vol.88, pp.

substantial neofunctionalization in duplicate gene evolution. *Genetics*, Vol.169, pp.

(1989) A human homologue of the yeast *GST1* gene codes for a GTP-binding protein and is expressed in a proliferation-dependent manner in mammalian cells.

Molecular cloning of a novel member of the eukaryotic polypeptide chain-releasing factors (eRF). Its identification as eRF3 interacting with eRF1. *J.Biol.Chem.*, Vol.273,

polypeptide chain releasing factor (eRF3/GSPT) carrying the translation termination signal to the 3'-Poly(A) tail of mRNA. Direct association of eRF3/GSPT

duplicates. *J.Hered.* Vol.100, pp. 605-617. Haldane, J. (1932) *The causes of evolution,* NY: Longmans, Green.

gene. *Mol.Gen.Genet*., Vol.233, pp. 427-435.

genetic switch. *Nature*, Vol.449, pp. 677-681.

*EMBO J.*, Vol.8, pp. 3807-3814.

history. *Biol.Cell*, Vol.95, pp. 195-209.

angiosperm phyla. *Nature*, Vol.449, pp. 463-467.

747-757.

1157-1164.

pp. 22254-22259.

E206.


Dehal, P. & Boore, J.L. (2005) Two rounds of whole genome duplication in the ancestral

Dietrich, F.S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pohlmann,

Doma, M.K. & Parker, R. (2006) Endonucleolytic cleavage of eukaryotic mRNAs with stalls

Dontsova, M., Frolova, L., Vassilieva, J., Piendl, W., Kisselev, L., & Garber, M. (2000)

Doolittle, R.F. (1995) The multiplicity of domains in proteins. *Annu.Rev.Biochem.*, Vol.64, pp.

Durand, D. & Hoberman, R. (2006) Diagnosing duplications-can it be done? *Trends Genet*,

Ferris, S.D. & Whitt, G.S. (1979) Evolution of the differential regulation of duplicate genes

Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., & Postlethwait, J. (1999)

Friedman, R. & Hughes, A.L. (2001) Pattern and timing of gene duplication in animal

Friedman, R. & Hughes, A.L. (2003) The temporal distribution of gene duplication events in

Frischmeyer, P.A., van Hoof, A., O'Donnell, K., Guerrerio, A.L., Parker, R., & Dietz, H.C.

Frolova, L.Y., Tsivkovskii, R.Y., Sivolobova, G.F., Oparina, N.Y., Serpinsky, O.I., Blinov,

Graille, M., Chaillet, M., & van Tilbeurgh, H. (2008) Structure of yeast Dom34: a protein

Gu, X., Wang, Y., & Gu, J. (2002) Age distribution of human gene families shows significant

Gu, Z., Cavalcanti, A., Chen, F.C., Bouman, P., & Li, W.H. (2002) Extent of gene duplication

Guigo, R., Muchnik, I., & Smith, T.F. (1996) Reconstruction of ancient molecular phylogeny.

Preservation of duplicate genes by complementary, degenerative mutations.

a set of highly conserved human gene families. *Mol.Biol.Evol.*, Vol.20, pp.

(2002) An mRNA surveillance mechanism that eliminates transcripts lacking

V.M., Tatkov, S.I., & Kisselev, L.L. (1999) Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger

related to translation termination factor eRF1 and involved in No-Go decay.

roles of both large- and small-scale duplications in vertebrate evolution. *Nat.Genet.*,

in the genomes of *Drosophila*, nematode, and yeast. *Mol.Biol.Evol.*, Vol.19, pp.

active with eukaryotic ribosomes. *FEBS Lett.*, Vol.472, pp. 213-216.

R., Luedi, P., Choi, S., Wing, R.A., Flavier, A., Gaffney, T.D., & Philippsen, P. (2004) The *Ashbya gossypii* genome as a tool for mapping the ancient *Saccharomyces* 

Translation termination factor aRF1 from the archaeon *Methanococcus jannaschii* is

vertebrate. *PloS.Biol.*, Vol.3, e314.

287-314.

154-161.

Vol.22, pp. 156-164.

*Genetics*, Vol.151, pp. 1531-1545.

*cerevisiae* genome. *Science*, Vol.304, pp. 304-307.

in translation elongation. *Nature*, Vol.440, pp. 561-564.

after polyploidization. *J.Mol.Evol.*, Vol.12, pp. 267-317.

genomes. *Genome Res.*, Vol.11, pp. 1842-1847.

termination codons. *Science*, Vol.295, pp. 2258-2261.

peptidyl-tRNA hydrolysis. *RNA.*, Vol.5, pp. 1014-1020.

Gilbert, W. (1978) Why genes in pieces? *Nature*, Vol.271, pp. 501.

*J.Biol.Chem.*, Vol.283, No.11, pp. 7145-7153.

*Mol.Phylogenet.Evol.*, Vol.6, pp. 189-213.

Vol.31, pp. 205-209.

256-262.


Gene Duplication and the Origin of Translation Factors 169

Lee, H.S. & Chen, Z.J. (2001) Protein-coding genes are epigenetically regulated in *Arabidopsis*

Lewis, E.B. (1951) Pseudoallelism and gene evolution. *Cold Spring Harb.Symp.Quant.Biol.*,

Liang, A., Brunen-Nieweler, C., Muramatsu, T., Kuchino, Y., Beier, H., & Heckmann, K.

Long, M. (2000) A new function evolved from gene fusion. *Genome Res.*, Vol.10, pp.

Long, M., Betran, E., Thornton, K., & Wang, W. (2003) The origin of new genes: glimpses

Lozupone, C.A., Knight, R.D., & Landweber, L.F. (2001) The molecular basis of nuclear

Lynch, M. & Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes.

Lynch, M., O'Hely, M., Walsh, B., & Force, A. (2001) The probability of preservation of a

Marcotte, E.M., Pellegrini, M., Yeates, T.O., & Eisenberg, D. (1999) A census of protein

Mateyak, M.K. & Kinzy, T.G. (2010) eEF1A: thinking outside the ribosome. *J.Biol.Chem.*,

McLysaght, A., Hokamp, K., & Wolfe, K.H. (2002) Extensive genomic duplication during

Meyer, A. & Schartl, M. (1999) Gene and genome duplications in vertebrates: the one-to-four

Meyer, F., Schmidt, H.J., Plumper, E., Hasilik, A., Mersmann, G., Meyer, H.E., Engstrom, A.,

Nakamura, Y. & Ito, K. (1998) How protein reads the stop codon and terminates translation.

Nakamura, Y. & Ito, K. (2003) Making sense of mimic in translation termination. *Trends* 

Nissen, P., Kjeldgaard, M., & Nyborg, J. (2000) Macromolecular mimicry. *EMBO J.*, Vol.19,

Otto, S.P. & Whitton, J. (2000) Polyploid incidence and evolution. *Annu.Rev.Genet*., Vol.34,

Passos, D.O., Doma, M.K., Shoemaker, C.J., Muhlrad, D., Green, R., Weissman, J., Hollien, J.,

& Parker, R. (2009) Analysis of Dom34 and its function in no-go decay.

(-to-eight in fish) rule and the evolution of novel gene functions. *Curr Opin.Cell* 

& Heckmann, K. (1991) UGA is translated as cysteine in pheromone 3 of *Euplotes* 

(2001) The ciliate *Euplotes octocarinatus* expresses two polypeptide release factors of

polyploids. *Proc.Natl.Acad.Sci.U.S.A*., Vol.98, pp. 6753-6758.

Li, W.H. (1997) *Molecular evolution Sunderland*, Mass: Sinauer Associates.

from the young and old. *Nat.Rev.Genet*., Vol.4, pp. 865-875.

genetic code change in ciliates. *Curr.Biol.*, Vol.11, pp. 65-74.

newly arisen gene duplicate. *Genetics*, Vol.159, pp. 1789-1804.

early chordate evolution. *Nat.Genet.*, Vol.31, pp. 200-204.

*octocarinatus*. *Proc.Natl.Acad.Sci.U.S.A.*, Vol.88, pp. 3758-3761.

Muller, H.J. (1936) Bar duplication. *Science*, Vol.83, pp. 528-530.

Ohno, S. (1970). *Evolution by Gene Duplication*. NY: Springer Verlag.

the type eRF1. *Gene*, Vol.262, pp. 161-168.

*Science*, Vol.290, pp. 1151-1155.

Vol.285, pp. 21209-21213.

*Biol.*, Vol.11, pp. 699-704.

*Genes Cells*, Vol.3, pp. 265-278.

*Biochem.Sci.*, Vol.28, pp. 99-105.

*Mol.Biol.Cell.*, Vol.20, pp. 3025-3032.

pp. 489-495.

pp. 401-437.

repeats. *J.Mol.Biol.*, Vol.293, pp. 151-160.

Vol.16, pp. 159-174.

1655-1657.


Jakobsen, C.G., Segaard, T.M., Jean-Jean, O., Frolova, L., & Justesen, J. (2001) Identification

Jean-Jean, O., Le Goff, X., & Philippe, M. (1996) Is there a human [psi]? *C.R.Acad.Sci.III*.,

Jorgensen, R., Ortiz, P.A., Carr-Schmid, A., Nissen, P., Kinzy, T.G., & Andersen, G.R. (2003)

Kapp, L.D. & Lorsch, J.R. (2004) The molecular mechanics of eukaryotic translation.

Kashkush, K., Feldman, M., & Levy, A.A. (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. *Genetics*., Vol.160, pp. 1651-1659. Kellis, M., Birren, B.W., & Lander, E.S. (2004) Proof and evolutionary analysis of ancient

Kisselev, L., Ehrenberg, M., & Frolova, L. (2003) Termination of translation: interplay of

Kobayashi, K., Kikuno, I., Kuroha, K., Saito, K., Ito, K., Ishitani, R., Inada, T., & Nureki, O.

Koonin, E.V., Bork, P., & Sander, C. (1994) A novel RNA-binding motif in omnipotent

Kushnirov, V.V. & Ter Avanesyan, M.D. (1998) Structure and replication of yeast prions.

Larhammar, D., Lundin, L.G., & Hallbook, F. (2002) The human Hox-bearing chromosome

Lavorgna, G., Patthy, L., & Boncinelli, E. (2001) Were protein internal repeats formed by

Le Goff, C., Zemlyanko, O., Moskalenko, S., Berkova, N., Inge-Vechtomov, S., Philippe, M.,

Lecompte, O., Ripp, R., Thierry, J.C., Moras, D., & Poch, O. (2002) Comparative analysis of

Lee, H.H., Kim, Y.S., Kim, K.H., Heo, I., Kim, S.K., Kim, O., Kim, H.K., Yoon, J.Y., Kim, H.S.,

component of no-go mRNA decay. *Mol.Cell*., Vol.27, pp. 938-950.

EF1alpha complex. *Proc.Natl.Acad.Sci.U.S.A.*, Vol.107, pp. 17575-17579. Kodama, H., Ito, K., & Nakamura, Y. (2007) The role of N-terminal domain of translational

mRNA, rRNAs and release factors? *EMBO J.*, Vol.22, pp. 175-182.

modification enzyme? *Nucleic Acids Res.*, Vol.22, pp. 2166-2167.

ribosomal translocase. *Nat.Struct.Biol.*, Vol. 10, pp. 379-385.

in vivo. *Mol.Biol.(Mosk)*, Vol.35, pp. 672-681.

*Annu.Rev.Biochem.*, Vol.73, pp. 657-704.

Vol.319, pp. 487-492.

*Cells*, Vol.12, pp. 639-650.

*Cell*, Vol. 94, pp. 13-16.

*Res.*, Vol.12, pp. 1910-1920.

"bricolage"? *Trends Genet*, Vol.17, pp. 120-123.

eRF3 in vivo. *Genes Cells*, Vol.7, pp. 1043-1057.

domain scale. *Nucleic Acids Res.*, Vol.30, pp. 5382-5390.

617-624.

of a novel termination release factor eRF3b expressing the eRF3 activity in vitro and

Two crystal structures demonstrate large conformational changes in the eukaryotic

genome duplication in the yeast *Saccharomyces cerevisiae*. *Nature*, Vol.428, pp.

(2010) Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound

release factor eRF3 for the control of functionality and stability in *S. cerevisiae*. *Genes* 

suppressors of translation termination, ribosomal proteins and a ribosome

regions did arise by block or chromosome (or even genome) duplications. *Genome* 

& Zhouravleva, G. (2002) Mouse GSPT2, but not GSPT1, can substitute for yeast

ribosomal proteins in complete genomes: an example of reductive evolution at the

Kim, d.J., Lee, S.J., Yoon, H.J., Kim, S.J., Lee, B.G., Song, H.K., Kim, V.N., Park, C.M., & Suh, S.W. (2007) Structural and functional insights into Dom34, a key


Gene Duplication and the Origin of Translation Factors 171

Stark, H., Rodnina, M.V., Wieden, H.J., Zemlin, F., Wintermeyer, W., & van Heel, M. (2002)

Sturtevant, A.H. (1925) The Effects of Unequal Crossing over at the Bar Locus in Drosophila.

Taylor, J.S. & Raes, J. (2004) Duplication and divergence: the evolution of new genes and old

Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N.,

Urbero, B., Eurwilaichitr, L., Stansfield, I., Tassan, J.P., Le Goff, X., Kress, M., & Tuite, M.F.

Valente, L. & Kinzy, T.G. (2003) Yeast as a sensor of factors affecting the accuracy of protein

Valle, M., Sengupta, J., Swami, N.K., Grassucci, R.A., Burkhardt, N., Nierhaus, K.H.,

van Hoof, A., Frischmeyer, P.A., Dietz, H.C., & Parker, R. (2002) Exosome-mediated

van Rijk, A. & Bloemendal, H. (2003) Molecular mechanisms of exon shuffling: illegitimate

Vasudevan, S., Peltz, S.W., & Wilusz, C.J. (2002) Non-stop decay-a new mRNA surveillance

tRNA in the accommodation process. *EMBO J.*, Vol. 21, pp. 3557-3567. van den Elzen, A.M., Henri, J., Lazar, N., Gas, M.E., Durand, D., Lacroute, F., Nicaise, M.,

yeast and mammalian tissues. *Biochimie*, Vol.79, pp. 27-36.

synthesis. *Cell Mol.Life Sci.*, Vol.60, pp. 2115-2130.

*Nat.Struct.Mol.Biol.* Vol.17, pp. 1446-1452.

recombination. *Genetica*, Vol.18, pp. 245-249.

pathway. *Bioessays*, Vol.24, pp. 785-788.

Vol.295, pp. 2262-2264.

(1997) Expression of the release factor eRF1 (Sup45p) gene of higher eukaryotes in

Agrawal, R.K., & Frank, J. (2002) Cryo-EM reveals an active role for aminoacyl-

van Tilbeurgh, H., Seraphin, B., & Graille, M. (2010) Dissection of Dom34-Hbs1 reveals independent functions in two RNA quality control pathways.

recognition and degradation of mRNAs lacking a termination codon. *Science*,

recognition complex. *Nat.Struct.Biol.*, Vol.9, pp. 849-854.

*Genetics*, Vol.10, pp. 117-147.

ideas. *Annu.Rev.Genet*., Vol.38, pp. 615-643.

& Gray). *Science*, Vol. 313, pp. 1596-1604.

Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-

Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., Depamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C.J., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de, P.Y., & Rokhsar, D. (2006) The genome of black cottonwood, *Populus trichocarpa* (Torr.


Piatigorsky, J. (2003) Crystallin genes: specialization by changes in gene regulation may precede gene duplication. *J.Struct.Funct.Genomics*, Vol.3, pp. 131-137. Piatigorsky, J., O'Brien, W.E., Norman, B.L., Kalumuck, K., Wistow, G.J., Borras, T.,

argininosuccinate lyase. *Proc.Natl.Acad.Sci.U.S.A*., Vol.85, pp. 3479-3483. Piskur, J. (2001) Origin of the duplicated regions in the yeast genomes. *Trends Genet*., Vol.17,

Ramakrishnan, V. (2002) Ribosome structure and the mechanism of translation. *Cell*, Vol.108,

Reams, A.B. & Neidle, E.L. (2004) Selection for gene clustering by tandem duplication.

Rodin, S.N. & Riggs, A.D. (2003) Epigenetic silencing may aid evolution by gene

Romero, D. & Palacios, R. (1997) Gene amplification and genomic plasticity in prokaryotes.

Saito, K., Kobayashi, K., Wada, M., Kikuno, I., Takusagawa, A., Mochizuki, M., Uchiumi, T.,

Scannell, D.R., Byrne, K.P., Gordon, J.L., Wong, S., & Wolfe, K.H. (2006) Multiple rounds of

Seit-Nebi, A., Frolova, L., Justesen, J., & Kisselev, L. (2001) Class-1 translation termination

Seoighe, C. & Gehring, C. (2004) Genome duplication led to highly selective expansion of

Seoighe, C. & Wolfe, K.H. (1999) Yeast genome evolution in the post-genome era. *Curr* 

Serio, T.R. & Lindquist, S.L. (1999) [*PSI+*]: an epigenetic modulator of translation

Shoemaker, C.J., Eyler, D.E., & Green, R. (2010) Dom34:Hbs1 promotes subunit dissociation

Shyr, Y.Y., Hepburn, A.G., & Widholm, J.M. (1992) Glyphosate selected amplification of the

Sonenberg, N. & Dever, T.E. (2003) Eukaryotic translation initiation factors and regulators.

Spring, J. (1997) Vertebrate evolution by interspecific hybridisation – are we polyploid?

and peptidyl-tRNA drop-off to initiate no-go decay. *Science*, Vol.330, pp.

5-enolpyruvylshikimate-3-phosphate synthase gene in cultured carrot cells.

the *Arabidopsis thaliana* proteome. *Trends Genet*., Vol.20, pp. 461-464.

termination efficiency. *Annu.Rev.Cell Dev.Biol.*, Vol.15, pp. 661-703.

Ishitani, R., Nureki, O., & Ito, K. (2010) Omnipotent role of archaeal elongation factor 1 alpha (EF1alpha) in translational elongation and termination, and quality control of protein synthesis. *Proc.Natl.Acad.Sci.U.S.A*. Vol.107, pp. 19242-19247. Scannell, D.R., Butler, G., & Wolfe, K.H. (2007) Yeast genome evolution--the origin of the

speciation associated with reciprocal gene loss in polyploid yeasts. *Nature*, Vol.440,

factors: invariant GGQ minidomain is essential for release activity and ribosome binding but not for stop codon recognition. *Nucleic Acids Res.*, Vol.29, pp.

pp. 302-303.

pp. 557-572.

pp. 341-345.

3982-3987.

369-372.

*Annu.Rev.Microbiol.*, Vol.58, pp. 119-142.

*Annu.Rev.Genet*., Vol.31, pp. 91-111.

species. *Yeast*, Vol.24, pp. 929-942.

*Opin.Microbiol.*, Vol.2, pp. 548-554.

*Mol.Gen.Genet.*, Vol.232, pp. 377-382.

*FEBS Lett.*, Vol.400, pp. 2-8.

*Curr Opin.Struct.Biol.*, Vol.13, pp. 56-63.

duplication. *J.Mol.Evol.*, Vol.56, pp. 718-729.

Nickerson, J.M., & Wawrousek, E.F. (1988) Gene sharing by delta-crystallin and


**10** 

**Analysis of Duplicate Gene Families in Microbial** 

Though considerable sequence information from different organisms was available prior to the recent advances in genome sequencing technology, the foundation for our current understanding of the mechanisms of bacterial pathogenesis was laid by the release of the first complete genome sequence of *Heamophilus influenza* in 1995 (Fraser-Liggett, 2005). Ever since, significant progress in the availability of data for different genomes has been possible due to the contribution of various genome sequencing projects (Koonin & Wolf, 2008). Despite the complete genome sequences of many pathogenic organisms being available, the mortality rates due to these infectious agents still remains a problem, highlighting the need to decipher the complex molecular mechanisms responsible for survival of the bacteria. The wealth of complete genome information for pathogens can be effectively explored using comparative genomic tools for the identification of common and unique sets of genes involved in the propagation of virulence. Sequence comparison tools have been developed to identify homologous genes from the complete genomes of microorganisms. Homologous genes which arise from speciation tend to maintain functions similar to that of their ancestral molecule and are known as orthologs, while the genes originating from duplication events often evolve new functions and are defined as

The world of microbes is highly diverse with genome complexity differing across a wide range of microorganisms. In general, the difference in the complexity of genomes is dictated by the life style and environment of the organism (Cordero & Hogeweg, 2009). Life style plays an important role in regulating the genome dynamics of an organism, and functional novelty provided by gene duplication is thought to enhance the adaptation capability of the organism. In addition, horizontal transfer of operons or functional units of genes from external sources may provide an immediate functional benefit to the organism, thereby adding to the functional complexity of the genomes. The availability of complete genome sequences of important mycobacteria such as *Mycobacterium tuberculosis, Mycobacterium ulcerans, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium paratuberculosis, Mycobacterium avium* and others, can be used to gain deeper insights into possible

**1. Introduction** 

paralogs (Tatusov *et al.,* 1997).

**Genomes and Application to the Study of Gene** 

*Computational Biology Group, Department of Clinical Laboratory Sciences Institute of Infectious Diseases and Molecular Medicine, Health Science Faculty* 

**Duplication in** *M. tuberculosis*

Venu Vuppu and Nicola Mulder

*University of Cape Town* 

*South Africa* 

