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Volumn 9, Issue 10, 2013, Pages

Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; RNA POLYMERASE;

EID: 84887306726     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003882     Document Type: Article
Times cited : (43)

References (51)
  • 3
    • 33646130830 scopus 로고    scopus 로고
    • Simple sequence repeats as advantageous mutators in evolution
    • Kashi Y, King DG, (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22: 253-9.
    • (2006) Trends Genet , vol.22 , pp. 253-259
    • Kashi, Y.1    King, D.G.2
  • 4
    • 1642441841 scopus 로고    scopus 로고
    • Catastrophe and what to do about it if you are a bacterium: the importance of frameshift mutants
    • Koch AL, (2004) Catastrophe and what to do about it if you are a bacterium: the importance of frameshift mutants. Crit Rev Microbiol 30: 1-6.
    • (2004) Crit Rev Microbiol , vol.30 , pp. 1-6
    • Koch, A.L.1
  • 5
    • 0028065674 scopus 로고
    • Adaptive evolution of highly mutable loci in pathogenic bacteria
    • Moxon ER, Rainey PB, Nowak MA, Lenski RE, (1994) Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 4: 24-33.
    • (1994) Curr Biol , vol.4 , pp. 24-33
    • Moxon, E.R.1    Rainey, P.B.2    Nowak, M.A.3    Lenski, R.E.4
  • 6
    • 0027303887 scopus 로고
    • Unusual mutational mechanisms and evolution
    • Rainey P, Moxon R, (1993) Unusual mutational mechanisms and evolution. Science 2601958; author reply 1959-60.
    • (1993) Science , vol.260
    • Rainey, P.1    Moxon, R.2
  • 7
    • 77952312601 scopus 로고    scopus 로고
    • Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences
    • Wernegreen JJ, Kauppinen SN, Degnan PH, (2010) Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences. Mol Biol Evol 27: 833-9.
    • (2010) Mol Biol Evol , vol.27 , pp. 833-839
    • Wernegreen, J.J.1    Kauppinen, S.N.2    Degnan, P.H.3
  • 8
    • 0025329221 scopus 로고
    • Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli
    • Wagner LA, Weiss RB, Driscoll R, Dunn DS, Gesteland RF, (1990) Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli. Nucleic Acids Res 18: 3529-35.
    • (1990) Nucleic Acids Res , vol.18 , pp. 3529-3535
    • Wagner, L.A.1    Weiss, R.B.2    Driscoll, R.3    Dunn, D.S.4    Gesteland, R.F.5
  • 9
    • 0029870925 scopus 로고    scopus 로고
    • Programmed translational frameshifting
    • Farabaugh PJ, (1996) Programmed translational frameshifting. Microbiol Rev 60: 103-34.
    • (1996) Microbiol Rev , vol.60 , pp. 103-134
    • Farabaugh, P.J.1
  • 10
    • 0030457112 scopus 로고    scopus 로고
    • Programmed translational frameshifting
    • Farabaugh PJ, (1996) Programmed translational frameshifting. Annu Rev Genet 30: 507-28.
    • (1996) Annu Rev Genet , vol.30 , pp. 507-528
    • Farabaugh, P.J.1
  • 11
    • 0037139583 scopus 로고    scopus 로고
    • Recoding: translational bifurcations in gene expression
    • Baranov PV, Gesteland RF, Atkins JF, (2002) Recoding: translational bifurcations in gene expression. Gene 286: 187-201.
    • (2002) Gene , vol.286 , pp. 187-201
    • Baranov, P.V.1    Gesteland, R.F.2    Atkins, J.F.3
  • 12
    • 0042527531 scopus 로고    scopus 로고
    • Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Sulfolobus solfataricus via chemical rescue of an inactive mutant
    • Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, Moracci M, (2003) Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Sulfolobus solfataricus via chemical rescue of an inactive mutant. Biochemistry 42: 9525-31.
    • (2003) Biochemistry , vol.42 , pp. 9525-9531
    • Cobucci-Ponzano, B.1    Trincone, A.2    Giordano, A.3    Rossi, M.4    Moracci, M.5
  • 13
    • 0038353117 scopus 로고    scopus 로고
    • Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting
    • Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, Moracci M, (2003) Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting. J Biol Chem 278: 14622-31.
    • (2003) J Biol Chem , vol.278 , pp. 14622-14631
    • Cobucci-Ponzano, B.1    Trincone, A.2    Giordano, A.3    Rossi, M.4    Moracci, M.5
  • 14
    • 54449100127 scopus 로고    scopus 로고
    • Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts
    • Tamas I, Wernegreen JJ, Nystedt B, Kauppinen SN, Darby AC, et al. (2008) Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proc Natl Acad Sci U S A 105: 14934-9.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14934-14939
    • Tamas, I.1    Wernegreen, J.J.2    Nystedt, B.3    Kauppinen, S.N.4    Darby, A.C.5
  • 15
    • 77954918654 scopus 로고    scopus 로고
    • Visualizing high error levels during gene expression in living bacterial cells
    • Meyerovich M, Mamou G, Ben-Yehuda S, (2010) Visualizing high error levels during gene expression in living bacterial cells. Proc Natl Acad Sci U S A 107: 11543-8.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 11543-11548
    • Meyerovich, M.1    Mamou, G.2    Ben-Yehuda, S.3
  • 16
    • 0025355475 scopus 로고
    • Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme
    • Tsuchihashi Z, Kornberg A, (1990) Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. Proc Natl Acad Sci U S A 87: 2516-20.
    • (1990) Proc Natl Acad Sci U S A , vol.87 , pp. 2516-2520
    • Tsuchihashi, Z.1    Kornberg, A.2
  • 17
    • 0026594057 scopus 로고
    • Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon
    • Tsuchihashi Z, Brown PO, (1992) Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev 6: 511-9.
    • (1992) Genes Dev , vol.6 , pp. 511-519
    • Tsuchihashi, Z.1    Brown, P.O.2
  • 18
    • 84871226912 scopus 로고    scopus 로고
    • Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage
    • DOI: 10.1093/nar/gks944
    • Rockah-Shmuel L, Tawfik DS, (2012) Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage. Nucleic Acids Res DOI: 10.1093/nar/gks944.
    • (2012) Nucleic Acids Res
    • Rockah-Shmuel, L.1    Tawfik, D.S.2
  • 19
    • 0033052969 scopus 로고    scopus 로고
    • A hierarchical approach to protein molecular evolution
    • Bogarad LD, Deem MW, (1999) A hierarchical approach to protein molecular evolution. Proc Natl Acad Sci U S A 96 (6) (): 2591-5.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , Issue.6 , pp. 2591-2595
    • Bogarad, L.D.1    Deem, M.W.2
  • 20
    • 84875601072 scopus 로고    scopus 로고
    • Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space
    • 10.1093/molbev/mst003
    • Toth-Petroczy A, Tawfik DS, (2013) Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space. Mol Biol Evol pp. 10.1093/molbev/mst003.
    • (2013) Mol Biol Evol
    • Toth-Petroczy, A.1    Tawfik, D.S.2
  • 21
    • 76849094347 scopus 로고    scopus 로고
    • Back-translation for discovering distant protein homologies in the presence of frameshift mutations
    • Girdea M, Noe L, Kucherov G, (2009) Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms Mol Biol 5: 6.
    • (2009) Algorithms Mol Biol , vol.5 , pp. 6
    • Girdea, M.1    Noe, L.2    Kucherov, G.3
  • 22
    • 76849094347 scopus 로고    scopus 로고
    • Back-translation for discovering distant protein homologies in the presence of frameshift mutations
    • Girdea M, Noe L, Kucherov G, (2010) Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms Mol Biol 5: 6.
    • (2010) Algorithms Mol Biol , vol.5 , pp. 6
    • Girdea, M.1    Noe, L.2    Kucherov, G.3
  • 23
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Smith JM, (1970) Natural selection and the concept of a protein space. Nature 225: 563-4.
    • (1970) Nature , vol.225 , pp. 563-564
    • Smith, J.M.1
  • 24
    • 33748271469 scopus 로고    scopus 로고
    • An initial map of insertion and deletion (INDEL) variation in the human genome
    • Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, et al. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16: 1182-90.
    • (2006) Genome Res , vol.16 , pp. 1182-1190
    • Mills, R.E.1    Luttig, C.T.2    Larkins, C.E.3    Beauchamp, A.4    Tsui, C.5
  • 25
    • 0023256559 scopus 로고
    • Slipped-strand mispairing: a major mechanism for DNA sequence evolution
    • Levinson G, Gutman GA, (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-21.
    • (1987) Mol Biol Evol , vol.4 , pp. 203-221
    • Levinson, G.1    Gutman, G.A.2
  • 26
    • 0036897944 scopus 로고    scopus 로고
    • Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review
    • Li YC, Korol AB, Fahima T, Beiles A, Nevo E, (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11: 2453-65.
    • (2002) Mol Ecol , vol.11 , pp. 2453-2465
    • Li, Y.C.1    Korol, A.B.2    Fahima, T.3    Beiles, A.4    Nevo, E.5
  • 27
    • 0042531995 scopus 로고    scopus 로고
    • Polymerase slippage in relation to the uniformity of tetrameric repeat stretches
    • Klintschar M, Wiegand P, (2003) Polymerase slippage in relation to the uniformity of tetrameric repeat stretches. Forensic Sci Int 135: 163-6.
    • (2003) Forensic Sci Int , vol.135 , pp. 163-166
    • Klintschar, M.1    Wiegand, P.2
  • 28
    • 0036893298 scopus 로고    scopus 로고
    • A DNA sequence evolution analysis generalized by simulation and the markov chain monte carlo method implicates strand slippage in a majority of insertions and deletions
    • Nishizawa M, Nishizawa K, (2002) A DNA sequence evolution analysis generalized by simulation and the markov chain monte carlo method implicates strand slippage in a majority of insertions and deletions. J Mol Evol 55: 706-17.
    • (2002) J Mol Evol , vol.55 , pp. 706-717
    • Nishizawa, M.1    Nishizawa, K.2
  • 29
    • 58449126084 scopus 로고    scopus 로고
    • The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
    • Moran NA, McLaughlin HJ, Sorek R, (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323: 379-82.
    • (2009) Science , vol.323 , pp. 379-382
    • Moran, N.A.1    McLaughlin, H.J.2    Sorek, R.3
  • 30
    • 12344307147 scopus 로고    scopus 로고
    • Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes
    • Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA, (2005) Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 14: 59-69.
    • (2005) Hum Mol Genet , vol.14 , pp. 59-69
    • Bhangale, T.R.1    Rieder, M.J.2    Livingston, R.J.3    Nickerson, D.A.4
  • 31
    • 67649369319 scopus 로고    scopus 로고
    • Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria
    • Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, et al. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26: 1523-31.
    • (2009) Mol Biol Evol , vol.26 , pp. 1523-1531
    • Chen, J.Q.1    Wu, Y.2    Yang, H.3    Bergelson, J.4    Kreitman, M.5
  • 32
    • 37549023418 scopus 로고    scopus 로고
    • DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage
    • de la Chaux N, Messer PW, Arndt PF, (2007) DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. BMC Evol Biol 7: 191.
    • (2007) BMC Evol Biol , vol.7 , pp. 191
    • de la Chaux, N.1    Messer, P.W.2    Arndt, P.F.3
  • 33
    • 0018966254 scopus 로고
    • Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli
    • Szomolanyi E, Kiss A, Venetianer P, (1980) Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene 10: 219-25.
    • (1980) Gene , vol.10 , pp. 219-225
    • Szomolanyi, E.1    Kiss, A.2    Venetianer, P.3
  • 34
    • 44349161622 scopus 로고    scopus 로고
    • Intense neutral drifts yield robust and evolvable consensus proteins
    • Bershtein S, Goldin K, Tawfik DS, (2008) Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 379: 1029-44.
    • (2008) J Mol Biol , vol.379 , pp. 1029-1044
    • Bershtein, S.1    Goldin, K.2    Tawfik, D.S.3
  • 35
    • 0035883519 scopus 로고    scopus 로고
    • Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
    • Kobayashi I, (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Research 29: 3742-3756.
    • (2001) Nucleic Acids Research , vol.29 , pp. 3742-3756
    • Kobayashi, I.1
  • 36
    • 43349095997 scopus 로고    scopus 로고
    • Real-time kinetics of restriction-modification gene expression after entry into a new host cell
    • Mruk I, Blumenthal RM, (2008) Real-time kinetics of restriction-modification gene expression after entry into a new host cell. Nucleic Acids Res 36: 2581-93.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2581-2593
    • Mruk, I.1    Blumenthal, R.M.2
  • 38
    • 70349333227 scopus 로고    scopus 로고
    • The evolutionary consequences of erroneous protein synthesis
    • Drummond DA, Wilke CO, (2009) The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 10: 715-24.
    • (2009) Nat Rev Genet , vol.10 , pp. 715-724
    • Drummond, D.A.1    Wilke, C.O.2
  • 39
    • 0022872027 scopus 로고
    • Escherichia coli K-12 restricts DNA containing 5-methylcytosine
    • Raleigh EA, Wilson G, (1986) Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A 83: 9070-4.
    • (1986) Proc Natl Acad Sci U S A , vol.83 , pp. 9070-9074
    • Raleigh, E.A.1    Wilson, G.2
  • 40
    • 79959807202 scopus 로고    scopus 로고
    • Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences
    • McDonald MJ, Wang WC, Huang HD, Leu JY, (2010) Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol 9: e1000622.
    • (2010) PLoS Biol , vol.9
    • McDonald, M.J.1    Wang, W.C.2    Huang, H.D.3    Leu, J.Y.4
  • 41
    • 77952082576 scopus 로고    scopus 로고
    • Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus
    • Cobucci-Ponzano B, Guzzini L, Benelli D, Londei P, Perrodou E, et al. (2010) Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus. J Proteome Res 9: 2496-507.
    • (2010) J Proteome Res , vol.9 , pp. 2496-2507
    • Cobucci-Ponzano, B.1    Guzzini, L.2    Benelli, D.3    Londei, P.4    Perrodou, E.5
  • 42
    • 33644747335 scopus 로고    scopus 로고
    • Why are phenotypic mutation rates much higher than genotypic mutation rates?
    • Burger R, Willensdorfer M, Nowak MA, (2006) Why are phenotypic mutation rates much higher than genotypic mutation rates? Genetics 172: 197-206.
    • (2006) Genetics , vol.172 , pp. 197-206
    • Burger, R.1    Willensdorfer, M.2    Nowak, M.A.3
  • 43
    • 65549084298 scopus 로고    scopus 로고
    • Potential role of phenotypic mutations in the evolution of protein expression and stability
    • Goldsmith M, Tawfik DS, (2009) Potential role of phenotypic mutations in the evolution of protein expression and stability. Proc Natl Acad Sci U S A 106: 6197-202.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 6197-6202
    • Goldsmith, M.1    Tawfik, D.S.2
  • 45
    • 79551622326 scopus 로고    scopus 로고
    • Evolution of molecular error rates and the consequences for evolvability
    • Rajon E, Masel J, (2011) Evolution of molecular error rates and the consequences for evolvability. Proc Natl Acad Sci U S A 108: 1082-7.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 1082-1087
    • Rajon, E.1    Masel, J.2
  • 46
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 47
    • 79959842126 scopus 로고    scopus 로고
    • Genomic island variability facilitates Prochlorococcus-virus coexistence
    • Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D, (2011) Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474: 604-8.
    • (2011) Nature , vol.474 , pp. 604-608
    • Avrani, S.1    Wurtzel, O.2    Sharon, I.3    Sorek, R.4    Lindell, D.5
  • 49
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38: W529-33.
    • (2010) Nucleic Acids Res , vol.38
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 50
    • 0029068629 scopus 로고
    • The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing
    • Reinisch KM, Chen L, Verdine GL, Lipscomb WN, (1995) The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82: 143-53.
    • (1995) Cell , vol.82 , pp. 143-153
    • Reinisch, K.M.1    Chen, L.2    Verdine, G.L.3    Lipscomb, W.N.4


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