Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

[1]  Xiongfeng Dai,et al.  Real time determination of bacterial in vivo ribosome translation elongation speed based on LacZα complementation system , 2016, Nucleic acids research.

[2]  A. Valleriani,et al.  Quantitative assessment of ribosome drop-off in E. coli , 2016, Nucleic acids research.

[3]  T. Hwa,et al.  Overflow metabolism in E. coli results from efficient proteome allocation , 2015, Nature.

[4]  T. Hwa,et al.  Inflating bacterial cells by increased protein synthesis , 2015, Molecular systems biology.

[5]  U. Sauer,et al.  Real-time metabolome profiling of the metabolic switch between starvation and growth , 2015, Nature Methods.

[6]  David W. Erickson,et al.  Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria , 2015, Molecular systems biology.

[7]  E. O’Shea,et al.  An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation , 2014, Cell.

[8]  R. Bundschuh,et al.  The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli , 2014, Nucleic acids research.

[9]  David W. Schryer,et al.  The general mode of translation inhibition by macrolide antibiotics , 2014, Proceedings of the National Academy of Sciences.

[10]  David H Burkhardt,et al.  Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources , 2014, Cell.

[11]  Y. Shimizu.  Biochemical aspects of bacterial strategies for handling the incomplete translation processes , 2014, Front. Microbiol..

[12]  T. Hwa,et al.  Molecular crowding limits translation and cell growth , 2013, Proceedings of the National Academy of Sciences.

[13]  T. Hwa,et al.  Coordination of bacterial proteome with metabolism by cyclic AMP signalling , 2013, Nature.

[14]  R. Gillet,et al.  The task force that rescues stalled ribosomes in bacteria. , 2013, Trends in biochemical sciences.

[15]  U. Sauer,et al.  Dissecting specific and global transcriptional regulation of bacterial gene expression , 2013, Molecular systems biology.

[16]  K. Fredrick,et al.  Analysis of polysomes from bacteria. , 2013, Methods in enzymology.

[17]  K. Bettenbrock,et al.  Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar Transport Systems , 2012, Journal of bacteriology.

[18]  P. Uetz,et al.  RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors , 2012, PLoS genetics.

[19]  Thomas A Steitz,et al.  How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis , 2012, Science.

[20]  C. Hayes,et al.  Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis. , 2012, Methods in molecular biology.

[21]  Michael Freeling,et al.  Using Genomic Sequencing for Classical Genetics in E. coli K12 , 2011, PloS one.

[22]  Y. Handa,et al.  YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl–tRNA on stalled ribosomes , 2010, Nucleic acids research.

[23]  T. Hwa,et al.  Interdependence of Cell Growth and Gene Expression: Origins and Consequences , 2010, Science.

[24]  J. Williamson,et al.  Quantitation of the ribosomal protein autoregulatory network using mass spectrometry. , 2010, Analytical chemistry.

[25]  Colin Echeverría Aitken,et al.  Real-time tRNA transit on single translating ribosomes at codon resolution , 2010, Nature.

[26]  Angelo Valleriani,et al.  Global and local depletion of ternary complex limits translational elongation , 2010, Nucleic acids research.

[27]  Natalie I. Tasman,et al.  A guided tour of the Trans‐Proteomic Pipeline , 2010, Proteomics.

[28]  Drew Endy,et al.  Gemini, a Bifunctional Enzymatic and Fluorescent Reporter of Gene Expression , 2009, PloS one.

[29]  A. Mankin,et al.  Erythromycin- and Chloramphenicol-Induced Ribosomal Assembly Defects Are Secondary Effects of Protein Synthesis Inhibition , 2008, Antimicrobial Agents and Chemotherapy.

[30]  Ruedi Aebersold,et al.  Building consensus spectral libraries for peptide identification in proteomics , 2008, Nature Methods.

[31]  J. Williamson,et al.  Quantitative analysis of isotope distributions in proteomic mass spectrometry using least-squares Fourier transform convolution. , 2008, Analytical chemistry.

[32]  Magnus Johansson,et al.  The kinetics of ribosomal peptidyl transfer revisited. , 2008, Molecular cell.

[33]  M. Rodnina,et al.  The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor , 2006, Proceedings of the National Academy of Sciences.

[34]  Giovanni Bertoni,et al.  One-step high-throughput assay for quantitative detection of beta-galactosidase activity in intact gram-negative bacteria, yeast, and mammalian cells. , 2006, BioTechniques.

[35]  Daniel N. Wilson,et al.  EF-G-dependent GTPase on the ribosome. conformational change and fusidic acid inhibition. , 2006, Biochemistry.

[36]  Robert T Sauer,et al.  Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli , 2005, Molecular microbiology.

[37]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[38]  S. Osawa,et al.  Effects of some antibiotics on the stringent control of RNA synthesis in Escherichia coli , 1975, Molecular and General Genetics MGG.

[39]  C. Kurland,et al.  Translation rates and misreading characteristics of rpsD mutants in Escherichia coli , 2004, Molecular and General Genetics MGG.

[40]  Oleg Paliy,et al.  Physiological Studies of Escherichia coli Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression , 2003, Journal of bacteriology.

[41]  F. Schluenzen,et al.  Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria , 2001, Nature.

[42]  C. Wada,et al.  Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp , 2001, Genes to cells : devoted to molecular & cellular mechanisms.

[43]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[44]  P. Dennis,et al.  mRNA Composition and Control of Bacterial Gene Expression , 2000, Journal of bacteriology.

[45]  M. Ehrenberg,et al.  Decay of rplN and lacZ mRNA in Escherichia coli. , 1999, Journal of molecular biology.

[46]  H. Bujard,et al.  Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.

[47]  C. Kurland,et al.  Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. , 1996, Journal of molecular biology.

[48]  David Vanderbilt,et al.  Origins and Consequences of Surface Stress , 1996 .

[49]  F. Neidhart.  Escherichia coli and Salmonella. , 1996 .

[50]  R. Kolter,et al.  The stationary phase of the bacterial life cycle. , 1993, Annual review of microbiology.

[51]  M. Record,et al.  Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. , 1991, Journal of molecular biology.

[52]  F. Neidhardt,et al.  Physiology of the bacterial cell : a molecular approach , 1990 .

[53]  J. Robertson.  Biological regulation and development. Vol. 3B. Hormone action edited by R. F. Goldberger and K. R. Yamamoto , 1985 .

[54]  S. Pedersen.  Escherichia coli ribosomes translate in vivo with variable rate. , 1984, The EMBO journal.

[55]  M. Ehrenberg,et al.  Costs of accuracy determined by a maximal growth rate constraint , 1984, Quarterly Reviews of Biophysics.

[56]  H. Bremer,et al.  Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate , 1982, Journal of bacteriology.

[57]  Keith R. Yamamoto,et al.  Biological Regulation and Development , 1982, Springer US.

[58]  R. Harvey,et al.  How partially inhibitory concentrations of chloramphenicol affect the growth of Escherichia coli , 1980, Antimicrobial Agents and Chemotherapy.

[59]  O. Maaløe,et al.  Regulation of the Protein-Synthesizing Machinery—Ribosomes, tRNA, Factors, and So On , 1979 .

[60]  I. Chopra,et al.  Bacterial resistance to the tetracyclines. , 1978, Microbiological reviews.

[61]  J. Hughes,et al.  Inhibition of isoleucyl-transfer ribonucleic acid synthetase in Escherichia coli by pseudomonic acid. , 1978, The Biochemical journal.

[62]  H. Bremer,et al.  Rate of ribosomal ribonucleic acid chain elongation in Escherichia coli B/r during chloramphenicol treatment , 1977, Journal of bacteriology.

[63]  P. Dennis,et al.  Role of ribosomal protein S12 in peptide chain elongation: analysis of pleiotropic, streptomycin-resistant mutants of Escherichia coli , 1977, Journal of bacteriology.

[64]  P. Dennis,et al.  Effects of chloramphenicol on the transcriptional activities of ribosomal RNA and ribosomal protein genes in Escherichia coli. , 1976, Journal of Molecular Biology.

[65]  H. Bremer,et al.  Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate. , 1976, The Biochemical journal.

[66]  Synthesis time of beta-galactosidase in Escherichia coli B/r as a function of growth rate. , 1975, The Biochemical journal.

[67]  A. Fowler,et al.  Molecular basis of beta-galactosidase alpha-complementation. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[68]  O. Maaløe,et al.  The effects of fusidic acid on growth, ribosome synthesis and RNA metabolism in Escherichia coli. , 1974, Journal of molecular biology.

[69]  S. Pestka.  Binding of [14C]Erythromycin to Escherichia coli Ribosomes , 1974, Antimicrobial Agents and Chemotherapy.

[70]  F. Neidhardt,et al.  Culture Medium for Enterobacteria , 1974, Journal of bacteriology.

[71]  D. Morris,et al.  Influence of Polyamine Limitation on the Chain Growth Rates of β-Galactosidase and of Its Messenger Ribonucleic Acid , 1973, Journal of bacteriology.

[72]  K. von Meyenburg,et al.  Messenger Ribonucleic Acid Synthesis and Degradation in Escherichia coli During Inhibition of Translation , 1973, Journal of bacteriology.

[73]  R. Schleif,et al.  Induction Kinetics of the l-Arabinose Operon of Escherichia coli , 1973, Journal of bacteriology.

[74]  R. Harvey.  Fraction of Ribosomes Synthesizing Protein as a Function of Specific Growth Rate , 1973, Journal of bacteriology.

[75]  E. Lund,et al.  Metabolism of guanosine tetraphosphate in Escherichia coli. , 1972, European journal of biochemistry.

[76]  Jeffrey H. Miller.  Experiments in molecular genetics , 1972 .

[77]  N. Tanaka,et al.  Formation of fusidic acid-G factor-GDP-ribosome complex and the relationship to the inhibition of GTP hydrolysis. , 1971, The Journal of antibiotics.

[78]  J. Forchhammer,et al.  Growth rate of polypeptide chains as a function of the cell growth rate in a mutant of Escherichia coli 15. , 1971, Journal of molecular biology.

[79]  A. L. Koch,et al.  In vivo assay of protein synthesizing capacity of Escherichia coli from slowly growing chemostat cultures. , 1971, Journal of molecular biology.

[80]  A. L. Koch,et al.  The adaptive responses of Escherichia coli to a feast and famine existence. , 1971, Advances in microbial physiology.

[81]  A. L. Koch,et al.  Protein degradation in Escherichia coli. I. Measurement of rapidly and slowly decaying components. , 1970, The Journal of biological chemistry.

[82]  G. Godson,et al.  Use of Brij lysis as a general method to prepare polyribosomes from Escherichia coli. , 1967, Biochimica et biophysica acta.

[83]  D. Wild,et al.  Inhibition of the growth of Escherichia coli by chlortetracycline. , 1967, The Biochemical journal.

[84]  M. Hoagland,et al.  Polyribosomes of Escherichia coli. Re-formation during recovery from glucose starvation. , 1967, The Journal of biological chemistry.

[85]  L. Day.  Tetracycline Inhibition of Cell-Free Protein Synthesis II. Effect of the Binding of Tetracycline to the Components of the System , 1966, Journal of bacteriology.

[86]  F. Neidhardt,et al.  Studies on the role of ribonucleic acid in the growth of bacteria. , 1960, Biochimica et biophysica acta.

[87]  T. D. Brock,et al.  Similarity in mode of action of chloramphenicol and erythromycin. , 1959, Biochimica et biophysica acta.

[88]  J. Mandelstam.  Turnover of Protein in Starved Bacteria and its Relationship to the Induced Synthesis of Enzyme , 1957, Nature.