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Volumn 318, Issue 2, 2004, Pages 601-614

Analyzing and enhancing mRNA translational efficiency in an Escherichia coli in vitro expression system

Author keywords

Expression efficiency; In vitro translation system; mRNA secondary structure; mRNA translation; Prediction

Indexed keywords

BACTERIAL RNA; MESSENGER RNA;

EID: 2142639387     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.04.064     Document Type: Article
Times cited : (57)

References (42)
  • 1
    • 0016154301 scopus 로고
    • ′-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites
    • ′ -terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites Proc. Natl. Acad. Sci. USA. 71:1974;1342-1346
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 1342-1346
    • Shine, J.1    Dalgarno, L.2
  • 2
    • 0016610995 scopus 로고
    • Determinant of cistron specificity in bacterial ribosomes
    • Shine J., Dalgarno L. Determinant of cistron specificity in bacterial ribosomes. Nature. 254:1975;34-38
    • (1975) Nature , vol.254 , pp. 34-38
    • Shine, J.1    Dalgarno, L.2
  • 3
    • 0011343769 scopus 로고
    • ′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli
    • ′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli Proc. Natl. Acad. Sci. USA. 72:1975;4734-4738
    • (1975) Proc. Natl. Acad. Sci. USA , vol.72 , pp. 4734-4738
    • Steitz, J.A.1    Jakes, K.2
  • 4
    • 0025166089 scopus 로고
    • Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis
    • deSmit M.H., vanDuin J. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc. Natl. Acad. Sci. USA. 87:1990;7668-7672
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 7668-7672
    • Desmit, M.H.1    Vanduin, J.2
  • 5
    • 0025051883 scopus 로고
    • Translational control of prokaryotic gene expression
    • McCarthy J.E., Gualerzi C. Translational control of prokaryotic gene expression. Trends Genet. 6:1990;78-85
    • (1990) Trends Genet. , vol.6 , pp. 78-85
    • McCarthy, J.E.1    Gualerzi, C.2
  • 6
    • 0028036559 scopus 로고
    • Control of translation by mRNA secondary structure in Escherichia coli. a quantitative analysis of literature data
    • deSmit M.H., vanDuin J. Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. J. Mol. Biol. 244:1994;144-150
    • (1994) J. Mol. Biol. , vol.244 , pp. 144-150
    • Desmit, M.H.1    Vanduin, J.2
  • 7
    • 0029310631 scopus 로고
    • High-level expression of prochymosin in Escherichia coli: Effect of the secondary structure of the ribosome binding site
    • Wang G., Liu N., Yang K. High-level expression of prochymosin in Escherichia coli: effect of the secondary structure of the ribosome binding site. Protein Expr. Purif. 6:1995;284-290
    • (1995) Protein Expr. Purif. , vol.6 , pp. 284-290
    • Wang, G.1    Liu, N.2    Yang, K.3
  • 8
    • 0036161823 scopus 로고    scopus 로고
    • MRNA secondary structure can greatly affect production of recombinant phospholipase A(2) toxins in bacteria
    • Ivanovski G., Gubensek F., Pungercar J. mRNA secondary structure can greatly affect production of recombinant phospholipase A(2) toxins in bacteria. Toxicon. 40:2002;543-549
    • (2002) Toxicon , vol.40 , pp. 543-549
    • Ivanovski, G.1    Gubensek, F.2    Pungercar, J.3
  • 9
    • 0142121656 scopus 로고    scopus 로고
    • High-level expression of porcine liver cytochrome P-450 reductase catalytic domain in Escherichia coli by modulating the predicted local secondary structure of mRNA
    • Kimura S., Iyanagi T. High-level expression of porcine liver cytochrome P-450 reductase catalytic domain in Escherichia coli by modulating the predicted local secondary structure of mRNA. J. Biochem. (Tokyo). 134:2003;403-413
    • (2003) J. Biochem. (Tokyo) , vol.134 , pp. 403-413
    • Kimura, S.1    Iyanagi, T.2
  • 10
    • 0023350617 scopus 로고
    • The involvement of mRNA secondary structure in protein synthesis
    • Pelletier J., Sonenberg N. The involvement of mRNA secondary structure in protein synthesis. Biochem. Cell Biol. 65:1987;576-581
    • (1987) Biochem. Cell Biol. , vol.65 , pp. 576-581
    • Pelletier, J.1    Sonenberg, N.2
  • 11
    • 0021799353 scopus 로고
    • ′ noncoding region of a eukaryotic mRNA reduces translational efficiency
    • ′ noncoding region of a eukaryotic mRNA reduces translational efficiency Cell. 40:1985;515-526
    • (1985) Cell , vol.40 , pp. 515-526
    • Pelletier, J.1    Sonenberg, N.2
  • 13
    • 0025361538 scopus 로고
    • The initiation of translation in E. coli: Apparent base pairing between the 16srRNA and downstream sequences of the mRNA
    • Sprengart M.L., Fatscher H.P., Fuchs E. The initiation of translation in E. coli: apparent base pairing between the 16srRNA and downstream sequences of the mRNA. Nucleic Acids Res. 18:1990;1719-1723
    • (1990) Nucleic Acids Res. , vol.18 , pp. 1719-1723
    • Sprengart, M.L.1    Fatscher, H.P.2    Fuchs, E.3
  • 14
    • 0030064682 scopus 로고    scopus 로고
    • The downstream box: An efficient and independent translation initiation signal in Escherichia coli
    • Sprengart M.L., Fuchs E., Porter A.G. The downstream box: an efficient and independent translation initiation signal in Escherichia coli. EMBO J. 15:1996;665-674
    • (1996) EMBO J. , vol.15 , pp. 665-674
    • Sprengart, M.L.1    Fuchs, E.2    Porter, A.G.3
  • 15
    • 0032834312 scopus 로고    scopus 로고
    • A sequence downstream of the initiation codon is essential for cold shock induction of cspB of Escherichia coli
    • Etchegaray J.P., Inouye M. A sequence downstream of the initiation codon is essential for cold shock induction of cspB of Escherichia coli. J. Bacteriol. 181:1999;5852-5854
    • (1999) J. Bacteriol. , vol.181 , pp. 5852-5854
    • Etchegaray, J.P.1    Inouye, M.2
  • 16
    • 0029811326 scopus 로고    scopus 로고
    • Downstream box-anti-downstream box interactions are dispensable for translation initiation of leaderless mRNAs
    • Resch A., Tedin K., Grundling A., Mundlein A., Blasi U. Downstream box-anti-downstream box interactions are dispensable for translation initiation of leaderless mRNAs. EMBO J. 15:1996;4740-4748
    • (1996) EMBO J. , vol.15 , pp. 4740-4748
    • Resch, A.1    Tedin, K.2    Grundling, A.3    Mundlein, A.4    Blasi, U.5
  • 17
    • 0032142818 scopus 로고    scopus 로고
    • The low level expression of chloramphenicol acetyltransferase (CAT) mRNA in Escherichia coli is not dependent on either Shine-Dalgarno or the downstream boxes in the CAT gene
    • Odjakova M., Golshani A., Ivanov G., AbouHaidar M., Ivanov I. The low level expression of chloramphenicol acetyltransferase (CAT) mRNA in Escherichia coli is not dependent on either Shine-Dalgarno or the downstream boxes in the CAT gene. Microbiol. Res. 153:1998;173-178
    • (1998) Microbiol. Res. , vol.153 , pp. 173-178
    • Odjakova, M.1    Golshani, A.2    Ivanov, G.3    Abouhaidar, M.4    Ivanov, I.5
  • 18
    • 0033752611 scopus 로고    scopus 로고
    • Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box
    • LaTeana A., Brandi A., O'Connor M., Freddi S., Pon C.L. Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box. RNA. 6:2000;1393-1402
    • (2000) RNA , vol.6 , pp. 1393-1402
    • Lateana, A.1    Brandi, A.2    O'Connor, M.3    Freddi, S.4    Pon, C.L.5
  • 19
    • 0033529890 scopus 로고    scopus 로고
    • Enhancement of translation by the downstream box does not involve base pairing of mRNA with the penultimate stem sequence of 16S rRNA
    • O'Connor M., Asai T., Squires C.L., Dahlberg A.E. Enhancement of translation by the downstream box does not involve base pairing of mRNA with the penultimate stem sequence of 16S rRNA. Proc. Natl. Acad. Sci. USA. 96:1999;8973-8978
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 8973-8978
    • O'Connor, M.1    Asai, T.2    Squires, C.L.3    Dahlberg, A.E.4
  • 20
    • 0035026057 scopus 로고    scopus 로고
    • Evidence against an interaction between the mRNA downstream box and 16S rRNA in translation initiation
    • Moll I., Huber M., Grill S., Sairafi P., Mueller F., Brimacombe R., Londei P., Blasi U. Evidence against an interaction between the mRNA downstream box and 16S rRNA in translation initiation. J. Bacteriol. 183:2001;3499-3505
    • (2001) J. Bacteriol. , vol.183 , pp. 3499-3505
    • Moll, I.1    Huber, M.2    Grill, S.3    Sairafi, P.4    Mueller, F.5    Brimacombe, R.6    Londei, P.7    Blasi, U.8
  • 22
    • 0032959546 scopus 로고    scopus 로고
    • Heat-induced synthesis of sigma 32 in Escherichia coli: Structural and functional dissection of rpoH mRNA secondary structure
    • Morita M., Kanemori M., Yanagi H., Yura T. Heat-induced synthesis of sigma 32 in Escherichia coli: structural and functional dissection of rpoH mRNA secondary structure. J. Bacteriol. 181:1999;401-410
    • (1999) J. Bacteriol. , vol.181 , pp. 401-410
    • Morita, M.1    Kanemori, M.2    Yanagi, H.3    Yura, T.4
  • 23
    • 0025144939 scopus 로고
    • RNA primary sequence or secondary structure in the translational initiation region controls expression of two variant interferon-beta genes in Escherichia coli
    • Gross G., Mielke C., Hollatz I., Blocker H., Frank R. RNA primary sequence or secondary structure in the translational initiation region controls expression of two variant interferon-beta genes in Escherichia coli. J. Biol. Chem. 265:1990;17627-17636
    • (1990) J. Biol. Chem. , vol.265 , pp. 17627-17636
    • Gross, G.1    Mielke, C.2    Hollatz, I.3    Blocker, H.4    Frank, R.5
  • 24
    • 0026774169 scopus 로고
    • Molecular cloning of a cDNA encoding chicken T-protein of the glycine cleavage system and expression of the functional protein in Escherichia coli. Effect of mRNA secondary structure in the translational initiation region on expression
    • Okamura-Ikeda K., Fujiwara K., Motokawa Y. Molecular cloning of a cDNA encoding chicken T-protein of the glycine cleavage system and expression of the functional protein in Escherichia coli. Effect of mRNA secondary structure in the translational initiation region on expression. J. Biol. Chem. 267:1992;18284-18290
    • (1992) J. Biol. Chem. , vol.267 , pp. 18284-18290
    • Okamura-Ikeda, K.1    Fujiwara, K.2    Motokawa, Y.3
  • 25
    • 0035941484 scopus 로고    scopus 로고
    • ′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli
    • ′ -side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli Gene. 263:2001;273-284
    • (2001) Gene , vol.263 , pp. 273-284
    • Stenstrom, C.M.1    Jin, H.2    Major, L.L.3    Tate, W.P.4    Isaksson, L.A.5
  • 28
    • 0029670330 scopus 로고    scopus 로고
    • Improved green fluorescent protein by molecular evolution using DNA shuffling
    • Crameri A., Whitehorn E.A., Tate E., Stemmer W.P. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14:1996;315-319
    • (1996) Nat. Biotechnol. , vol.14 , pp. 315-319
    • Crameri, A.1    Whitehorn, E.A.2    Tate, E.3    Stemmer, W.P.4
  • 29
    • 0023650543 scopus 로고
    • The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp P.M., Li W.H. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1987;1281-1295
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 30
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31:2003;3429-3431
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 31
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:1981;133-148
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 32
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 33
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill J.S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 29:1990;1105-1119
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 34
    • 0028143014 scopus 로고
    • Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
    • Walter A.E., Turner D.H. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry. 33:1994;12715-12719
    • (1994) Biochemistry , vol.33 , pp. 12715-12719
    • Walter, A.E.1    Turner, D.H.2
  • 35
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 37
    • 0022374873 scopus 로고
    • Initiator tRNA may recognize more than the initiation codon in mRNA: A model for translational initiation
    • Ganoza M.C., Marliere P., Kofoid E.C., Louis B.G. Initiator tRNA may recognize more than the initiation codon in mRNA: a model for translational initiation. Proc. Natl. Acad. Sci. USA. 82:1985;4587-4591
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 4587-4591
    • Ganoza, M.C.1    Marliere, P.2    Kofoid, E.C.3    Louis, B.G.4
  • 38
    • 0026033684 scopus 로고
    • Influence of mRNA determinants on translation initiation in Escherichia coli
    • Hartz D., McPheeters D.S., Gold L. Influence of mRNA determinants on translation initiation in Escherichia coli. J. Mol. Biol. 218:1991;83-97
    • (1991) J. Mol. Biol. , vol.218 , pp. 83-97
    • Hartz, D.1    McPheeters, D.S.2    Gold, L.3
  • 39
    • 0024232373 scopus 로고
    • Messenger RNA recognition in Escherichia coli: A possible second site of interaction with 16S ribosomal RNA
    • Petersen G.B., Stockwell P.A., Hill D.F. Messenger RNA recognition in Escherichia coli: a possible second site of interaction with 16S ribosomal RNA. EMBO J. 7:1988;3957-3962
    • (1988) EMBO J. , vol.7 , pp. 3957-3962
    • Petersen, G.B.1    Stockwell, P.A.2    Hill, D.F.3
  • 40
    • 0028094403 scopus 로고
    • Footprinting mRNA-ribosome complexes with chemical probes
    • Huttenhofer A., Noller H.F. Footprinting mRNA-ribosome complexes with chemical probes. EMBO J. 13:1994;3892-3901
    • (1994) EMBO J. , vol.13 , pp. 3892-3901
    • Huttenhofer, A.1    Noller, H.F.2
  • 41
    • 0035958587 scopus 로고    scopus 로고
    • The path of messenger RNA through the ribosome
    • Yusupova G.Z., Yusupov M.M., Cate J.H., Noller H.F. The path of messenger RNA through the ribosome. Cell. 106:2001;233-241
    • (2001) Cell , vol.106 , pp. 233-241
    • Yusupova, G.Z.1    Yusupov, M.M.2    Cate, J.H.3    Noller, H.F.4
  • 42
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: Status for the year 2000
    • Nakamura Y., Gojobori T., Ikemura T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28:2000;292
    • (2000) Nucleic Acids Res. , vol.28 , pp. 292
    • Nakamura, Y.1    Gojobori, T.2    Ikemura, T.3


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