메뉴 건너뛰기




Volumn 167, Issue 6, 2016, Pages 1610-1622.e15

Modular Assembly of the Bacterial Large Ribosomal Subunit

Author keywords

50S subunit; macromolecular assembly; quantitative mass spectrometry; Ribosome assembly; RNA folding; single particle cryo electron microscopy

Indexed keywords

BACTERIAL PROTEIN; RIBOSOME PROTEIN; RIBOSOME RNA; BACTERIAL RNA;

EID: 85002374064     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.11.020     Document Type: Article
Times cited : (150)

References (56)
  • 1
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    • Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A., The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289 (2000), 905–920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 2
    • 60549112849 scopus 로고    scopus 로고
    • A hierarchical model for evolution of 23S ribosomal RNA
    • Bokov, K., Steinberg, S.V., A hierarchical model for evolution of 23S ribosomal RNA. Nature 457 (2009), 977–980.
    • (2009) Nature , vol.457 , pp. 977-980
    • Bokov, K.1    Steinberg, S.V.2
  • 3
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • Canton, B., Labno, A., Endy, D., Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26 (2008), 787–793.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 787-793
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 4
    • 84873410888 scopus 로고    scopus 로고
    • Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry
    • Chen, S.S., Williamson, J.R., Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry. J. Mol. Biol. 425 (2013), 767–779.
    • (2013) J. Mol. Biol. , vol.425 , pp. 767-779
    • Chen, S.S.1    Williamson, J.R.2
  • 5
    • 84868095953 scopus 로고    scopus 로고
    • Measuring the dynamics of E. coli ribosome biogenesis using pulse-labeling and quantitative mass spectrometry
    • Chen, S.S., Sperling, E., Silverman, J.M., Davis, J.H., Williamson, J.R., Measuring the dynamics of E. coli ribosome biogenesis using pulse-labeling and quantitative mass spectrometry. Mol. Biosyst. 8 (2012), 3325–3334.
    • (2012) Mol. Biosyst. , vol.8 , pp. 3325-3334
    • Chen, S.S.1    Sperling, E.2    Silverman, J.M.3    Davis, J.H.4    Williamson, J.R.5
  • 6
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    • Datsenko, K.A., Wanner, B.L., One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97 (2000), 6640–6645.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 7
    • 41149155904 scopus 로고    scopus 로고
    • 5S rRNA: Structure and Function from Head to Toe
    • Dontsova, O.A., Dinman, J.D., 5S rRNA: Structure and Function from Head to Toe. Int. J. Biomed. Sci. 1 (2005), 1–7.
    • (2005) Int. J. Biomed. Sci. , vol.1 , pp. 1-7
    • Dontsova, O.A.1    Dinman, J.D.2
  • 8
    • 84872371907 scopus 로고    scopus 로고
    • Comet: an open-source MS/MS sequence database search tool
    • Eng, J.K., Jahan, T.A., Hoopmann, M.R., Comet: an open-source MS/MS sequence database search tool. Proteomics 13 (2013), 22–24.
    • (2013) Proteomics , vol.13 , pp. 22-24
    • Eng, J.K.1    Jahan, T.A.2    Hoopmann, M.R.3
  • 9
    • 84861860481 scopus 로고    scopus 로고
    • (2012). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. MCP 11, O111 016717.
    • Gillet, L.C., Navarro, P., Tate, S., Rost, H., Selevsek, N., Reiter, L., Bonner, R., and Aebersold, R. (2012). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. MCP 11, O111 016717.
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Rost, H.4    Selevsek, N.5    Reiter, L.6    Bonner, R.7    Aebersold, R.8
  • 10
    • 84930634509 scopus 로고    scopus 로고
    • Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
    • Grant, T., Grigorieff, N., Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. eLife, 4, 2015, e06980.
    • (2015) eLife , vol.4 , pp. e06980
    • Grant, T.1    Grigorieff, N.2
  • 11
    • 84974849211 scopus 로고    scopus 로고
    • Frealign: An Exploratory Tool for Single-Particle Cryo-EM
    • Grigorieff, N., Frealign: An Exploratory Tool for Single-Particle Cryo-EM. Methods Enzymol. 579 (2016), 191–226.
    • (2016) Methods Enzymol. , vol.579 , pp. 191-226
    • Grigorieff, N.1
  • 12
    • 84908322596 scopus 로고    scopus 로고
    • Functional interaction between ribosomal protein L6 and RbgA during ribosome assembly
    • Gulati, M., Jain, N., Davis, J.H., Williamson, J.R., Britton, R.A., Functional interaction between ribosomal protein L6 and RbgA during ribosome assembly. PLoS Genet., 10, 2014, e1004694.
    • (2014) PLoS Genet. , vol.10 , pp. e1004694
    • Gulati, M.1    Jain, N.2    Davis, J.H.3    Williamson, J.R.4    Britton, R.A.5
  • 13
    • 0023664556 scopus 로고
    • Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes
    • Herold, M., Nierhaus, K.H., Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes. J. Biol. Chem. 262 (1987), 8826–8833.
    • (1987) J. Biol. Chem. , vol.262 , pp. 8826-8833
    • Herold, M.1    Nierhaus, K.H.2
  • 16
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A., Nesvizhskii, A.I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74 (2002), 5383–5392.
    • (2002) Anal. Chem. , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 17
    • 33646568438 scopus 로고    scopus 로고
    • Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research
    • Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., Mori, H., Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 (2005), 291–299.
    • (2005) DNA Res. , vol.12 , pp. 291-299
    • Kitagawa, M.1    Ara, T.2    Arifuzzaman, M.3    Ioka-Nakamichi, T.4    Inamoto, E.5    Toyonaga, H.6    Mori, H.7
  • 18
    • 84894623755 scopus 로고    scopus 로고
    • Quantifying the local resolution of cryo-EM density maps
    • Kucukelbir, A., Sigworth, F.J., Tagare, H.D., Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11 (2014), 63–65.
    • (2014) Nat. Methods , vol.11 , pp. 63-65
    • Kucukelbir, A.1    Sigworth, F.J.2    Tagare, H.D.3
  • 19
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., King, N., Stein, S.E., Aebersold, R., Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7 (2007), 655–667.
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6    Aebersold, R.7
  • 21
    • 84881491558 scopus 로고    scopus 로고
    • Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit
    • Li, N., Chen, Y., Guo, Q., Zhang, Y., Yuan, Y., Ma, C., Deng, H., Lei, J., Gao, N., Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. Nucleic Acids Res. 41 (2013), 7073–7083.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 7073-7083
    • Li, N.1    Chen, Y.2    Guo, Q.3    Zhang, Y.4    Yuan, Y.5    Ma, C.6    Deng, H.7    Lei, J.8    Gao, N.9
  • 22
    • 84880848354 scopus 로고    scopus 로고
    • Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
    • Li, X., Mooney, P., Zheng, S., Booth, C.R., Braunfeld, M.B., Gubbens, S., Agard, D.A., Cheng, Y., Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10 (2013), 584–590.
    • (2013) Nat. Methods , vol.10 , pp. 584-590
    • Li, X.1    Mooney, P.2    Zheng, S.3    Booth, C.R.4    Braunfeld, M.B.5    Gubbens, S.6    Agard, D.A.7    Cheng, Y.8
  • 23
    • 0033377664 scopus 로고    scopus 로고
    • EMAN: semiautomated software for high-resolution single-particle reconstructions
    • Ludtke, S.J., Baldwin, P.R., Chiu, W., EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128 (1999), 82–97.
    • (1999) J. Struct. Biol. , vol.128 , pp. 82-97
    • Ludtke, S.J.1    Baldwin, P.R.2    Chiu, W.3
  • 24
    • 84883447961 scopus 로고    scopus 로고
    • Likelihood-based classification of cryo-EM images using FREALIGN
    • Lyumkis, D., Brilot, A.F., Theobald, D.L., Grigorieff, N., Likelihood-based classification of cryo-EM images using FREALIGN. J. Struct. Biol. 183 (2013), 377–388.
    • (2013) J. Struct. Biol. , vol.183 , pp. 377-388
    • Lyumkis, D.1    Brilot, A.F.2    Theobald, D.L.3    Grigorieff, N.4
  • 25
    • 84888059421 scopus 로고    scopus 로고
    • Optimod-an automated approach for constructing and optimizing initial models for single-particle electron microscopy
    • Lyumkis, D., Vinterbo, S., Potter, C.S., Carragher, B., Optimod-an automated approach for constructing and optimizing initial models for single-particle electron microscopy. J. Struct. Biol. 184 (2013), 417–426.
    • (2013) J. Struct. Biol. , vol.184 , pp. 417-426
    • Lyumkis, D.1    Vinterbo, S.2    Potter, C.S.3    Carragher, B.4
  • 26
    • 33750979860 scopus 로고    scopus 로고
    • General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
    • MacLean, B., Eng, J.K., Beavis, R.C., McIntosh, M., General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22 (2006), 2830–2832.
    • (2006) Bioinformatics , vol.22 , pp. 2830-2832
    • MacLean, B.1    Eng, J.K.2    Beavis, R.C.3    McIntosh, M.4
  • 28
    • 84894582458 scopus 로고    scopus 로고
    • A day in the life of the spliceosome
    • Matera, A.G., Wang, Z., A day in the life of the spliceosome. Nat. Rev. Mol. Cell Biol. 15 (2014), 108–121.
    • (2014) Nat. Rev. Mol. Cell Biol. , vol.15 , pp. 108-121
    • Matera, A.G.1    Wang, Z.2
  • 29
    • 0038441501 scopus 로고    scopus 로고
    • Accurate determination of local defocus and specimen tilt in electron microscopy
    • Mindell, J.A., Grigorieff, N., Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142 (2003), 334–347.
    • (2003) J. Struct. Biol. , vol.142 , pp. 334-347
    • Mindell, J.A.1    Grigorieff, N.2
  • 31
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A.I., Keller, A., Kolker, E., Aebersold, R., A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75 (2003), 4646–4658.
    • (2003) Anal. Chem. , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 33
    • 84995356971 scopus 로고
    • Enzyme Induction as an All-or-None Phenomenon
    • Novick, A., Weiner, M., Enzyme Induction as an All-or-None Phenomenon. Proc. Natl. Acad. Sci. USA 43 (1957), 553–566.
    • (1957) Proc. Natl. Acad. Sci. USA , vol.43 , pp. 553-566
    • Novick, A.1    Weiner, M.2
  • 35
    • 77952581453 scopus 로고    scopus 로고
    • Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
    • Pintilie, G.D., Zhang, J., Goddard, T.D., Chiu, W., Gossard, D.C., Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170 (2010), 427–438.
    • (2010) J. Struct. Biol. , vol.170 , pp. 427-438
    • Pintilie, G.D.1    Zhang, J.2    Goddard, T.D.3    Chiu, W.4    Gossard, D.C.5
  • 37
    • 0346816491 scopus 로고    scopus 로고
    • FindEM-a fast, efficient program for automatic selection of particles from electron micrographs
    • Roseman, A.M., FindEM-a fast, efficient program for automatic selection of particles from electron micrographs. J. Struct. Biol. 145 (2004), 91–99.
    • (2004) J. Struct. Biol. , vol.145 , pp. 91-99
    • Roseman, A.M.1
  • 38
    • 84946473054 scopus 로고    scopus 로고
    • Alignment of cryo-EM movies of individual particles by optimization of image translations
    • Rubinstein, J.L., Brubaker, M.A., Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 192 (2015), 188–195.
    • (2015) J. Struct. Biol. , vol.192 , pp. 188-195
    • Rubinstein, J.L.1    Brubaker, M.A.2
  • 39
    • 84917709175 scopus 로고    scopus 로고
    • Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy
    • Russo, C.J., Passmore, L.A., Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy. Science 346 (2014), 1377–1380.
    • (2014) Science , vol.346 , pp. 1377-1380
    • Russo, C.J.1    Passmore, L.A.2
  • 40
    • 84937823133 scopus 로고    scopus 로고
    • A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli
    • Sashital, D.G., Greeman, C.A., Lyumkis, D., Potter, C.S., Carragher, B., Williamson, J.R., A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. eLife, 3, 2014, e04491.
    • (2014) eLife , vol.3 , pp. e04491
    • Sashital, D.G.1    Greeman, C.A.2    Lyumkis, D.3    Potter, C.S.4    Carragher, B.5    Williamson, J.R.6
  • 41
    • 84868444740 scopus 로고    scopus 로고
    • RELION: implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres, S.H., RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180 (2012), 519–530.
    • (2012) J. Struct. Biol. , vol.180 , pp. 519-530
    • Scheres, S.H.1
  • 42
    • 78449268845 scopus 로고    scopus 로고
    • Interdependence of cell growth and gene expression: origins and consequences
    • Scott, M., Gunderson, C.W., Mateescu, E.M., Zhang, Z., Hwa, T., Interdependence of cell growth and gene expression: origins and consequences. Science 330 (2010), 1099–1102.
    • (2010) Science , vol.330 , pp. 1099-1102
    • Scott, M.1    Gunderson, C.W.2    Mateescu, E.M.3    Zhang, Z.4    Hwa, T.5
  • 45
    • 80053387432 scopus 로고    scopus 로고
    • Nesvizhskii, A.I. (2011). iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. MCP 10, M111 007690.
    • Shteynberg, D., Deutsch, E.W., Lam, H., Eng, J.K., Sun, Z., Tasman, N., Mendoza, L., Moritz, R.L., Aebersold, R., and Nesvizhskii, A.I. (2011). iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. MCP 10, M111 007690.
    • Shteynberg, D.1    Deutsch, E.W.2    Lam, H.3    Eng, J.K.4    Sun, Z.5    Tasman, N.6    Mendoza, L.7    Moritz, R.L.8    Aebersold, R.9
  • 46
    • 0030759410 scopus 로고    scopus 로고
    • Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations
    • Siegele, D.A., Hu, J.C., Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations. Proc. Natl. Acad. Sci. USA 94 (1997), 8168–8172.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 8168-8172
    • Siegele, D.A.1    Hu, J.C.2
  • 47
    • 85027926010 scopus 로고    scopus 로고
    • RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
    • Siegfried, N.A., Busan, S., Rice, G.M., Nelson, J.A., Weeks, K.M., RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat. Methods 11 (2014), 959–965.
    • (2014) Nat. Methods , vol.11 , pp. 959-965
    • Siegfried, N.A.1    Busan, S.2    Rice, G.M.3    Nelson, J.A.4    Weeks, K.M.5
  • 50
    • 46849117040 scopus 로고    scopus 로고
    • Quantitative analysis of isotope distributions in proteomic mass spectrometry using least-squares Fourier transform convolution
    • Sperling, E., Bunner, A.E., Sykes, M.T., Williamson, J.R., Quantitative analysis of isotope distributions in proteomic mass spectrometry using least-squares Fourier transform convolution. Anal. Chem. 80 (2008), 4906–4917.
    • (2008) Anal. Chem. , vol.80 , pp. 4906-4917
    • Sperling, E.1    Bunner, A.E.2    Sykes, M.T.3    Williamson, J.R.4
  • 51
    • 84931280756 scopus 로고    scopus 로고
    • Discovery of a small molecule that inhibits bacterial ribosome biogenesis
    • Stokes, J.M., Davis, J.H., Mangat, C.S., Williamson, J.R., Brown, E.D., Discovery of a small molecule that inhibits bacterial ribosome biogenesis. eLife, 3, 2014, e03574.
    • (2014) eLife , vol.3 , pp. e03574
    • Stokes, J.M.1    Davis, J.H.2    Mangat, C.S.3    Williamson, J.R.4    Brown, E.D.5
  • 52
    • 67650303382 scopus 로고    scopus 로고
    • A complex assembly landscape for the 30S ribosomal subunit
    • Sykes, M.T., Williamson, J.R., A complex assembly landscape for the 30S ribosomal subunit. Annu. Rev. Biophys. 38 (2009), 197–215.
    • (2009) Annu. Rev. Biophys. , vol.38 , pp. 197-215
    • Sykes, M.T.1    Williamson, J.R.2
  • 53
    • 85002409335 scopus 로고    scopus 로고
    • Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit
    • Published online July 5, 2016
    • Thurlow, B., Davis, J.H., Leong, V., F Moraes, T., Williamson, J.R., Ortega, J., Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. Nucleic Acids Res., 2016, 10.1093/nar/gkw613 Published online July 5, 2016.
    • (2016) Nucleic Acids Res.
    • Thurlow, B.1    Davis, J.H.2    Leong, V.3    F Moraes, T.4    Williamson, J.R.5    Ortega, J.6
  • 54
    • 84878942836 scopus 로고    scopus 로고
    • Molecular architecture and assembly of the eukaryotic proteasome
    • Tomko, R.J. Jr., Hochstrasser, M., Molecular architecture and assembly of the eukaryotic proteasome. Annu. Rev. Biochem. 82 (2013), 415–445.
    • (2013) Annu. Rev. Biochem. , vol.82 , pp. 415-445
    • Tomko, R.J.1    Hochstrasser, M.2
  • 55
    • 63649113687 scopus 로고    scopus 로고
    • DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy
    • Voss, N.R., Yoshioka, C.K., Radermacher, M., Potter, C.S., Carragher, B., DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. J. Struct. Biol. 166 (2009), 205–213.
    • (2009) J. Struct. Biol. , vol.166 , pp. 205-213
    • Voss, N.R.1    Yoshioka, C.K.2    Radermacher, M.3    Potter, C.S.4    Carragher, B.5
  • 56
    • 84955216953 scopus 로고    scopus 로고
    • Gctf: Real-time CTF determination and correction
    • Zhang, K., Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193 (2016), 1–12.
    • (2016) J. Struct. Biol. , vol.193 , pp. 1-12
    • Zhang, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.