Antibiotics as probes of biological complexity.

Antibiotics are critical defenses in the fight against bacterial infections, but they can also be used as probes to explore basic microbiology, including cell division, stress responses and cell wall biosynthesis, and will be valuable tools in deciphering bacterial networks and complexity.

[1]  R. F. Parker,et al.  The Action of Penicillin on Staphylococcus: Further Observations on the Effect of a Short Exposure , 1948, Journal of bacteriology.

[2]  E. Brown,et al.  Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. , 2009, Nature chemical biology.

[3]  M. Gellert,et al.  Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[4]  U. Maitra,et al.  A complex between initiation factor IF2, guanosine triphosphate, and fMet-tRNA: an intermediate in initiation complex formation. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[5]  F. Portillo,et al.  Differential effect of mutational impairment of penicillin-binding proteins 1A and 1B on Escherichia coli strains harboring thermosensitive mutations in the cell division genes ftsA, ftsQ, ftsZ, and pbpB. , 1990 .

[6]  Jeffrey H. Miller,et al.  Determination of Antibiotic Hypersensitivity among 4,000 Single-Gene-Knockout Mutants of Escherichia coli , 2008, Journal of bacteriology.

[7]  A. Emili,et al.  Interaction network containing conserved and essential protein complexes in Escherichia coli , 2005, Nature.

[8]  E. Brown,et al.  Precise Deletion of tagD and Controlled Depletion of Its Product, Glycerol 3-Phosphate Cytidylyltransferase, Leads to Irregular Morphology and Lysis of Bacillus subtilisGrown at Physiological Temperature , 2001, Journal of bacteriology.

[9]  R. Kishony,et al.  Discovery of a small molecule that blocks wall teichoic acid biosynthesis in Staphylococcus aureus. , 2009, ACS chemical biology.

[10]  H. Shinagawa.  SOS response as an adaptive response to DNA damage in prokaryotes. , 1996, EXS.

[11]  Sang Ho Lee,et al.  A Staphylococcus aureus fitness test platform for mechanism-based profiling of antibacterial compounds. , 2009, Chemistry & biology.

[12]  J. Frank,et al.  RF3 Induces Ribosomal Conformational Changes Responsible for Dissociation of Class I Release Factors , 2007, Cell.

[13]  E. Brown,et al.  Wall Teichoic Acid Polymers Are Dispensable for Cell Viability in Bacillus subtilis , 2006, Journal of bacteriology.

[14]  M. Gellert,et al.  Nalidixic acid resistance: a second genetic character involved in DNA gyrase activity. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Neumeister,et al.  Staphylococcus aureus strains lacking D-alanine modifications of teichoic acids are highly susceptible to human neutrophil killing and are virulence attenuated in mice. , 2002, The Journal of infectious diseases.

[16]  J. T. Park.  Uridine-5'-pyrophosphate derivatives. III. Amino acid-containing derivatives. , 1952, The Journal of biological chemistry.

[17]  J. Errington,et al.  Distinct and essential morphogenic functions for wall‐ and lipo‐teichoic acids in Bacillus subtilis , 2009, The EMBO journal.

[18]  Sean R. Collins,et al.  A tool-kit for high-throughput, quantitative analyses of genetic interactions in E. coli , 2008, Nature Methods.

[19]  T. Abo,et al.  Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans‐translation system , 2010, Molecular microbiology.

[20]  Kristin K. Brown,et al.  Type IIA topoisomerase inhibition by a new class of antibacterial agents , 2010, Nature.

[21]  Stanley N Cohen,et al.  DpiA Binding to the Replication Origin of Escherichia coli Plasmids and Chromosomes Destabilizes Plasmid Inheritance and Induces the Bacterial SOS Response , 2003, Journal of bacteriology.

[22]  D. Belin,et al.  Effects of Antibiotics and a Proto-Oncogene Homolog on Destruction of Protein Translocator SecY , 2009, Science.

[23]  M. Ehrenberg,et al.  Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting , 2008, The EMBO journal.

[24]  R. Traut,et al.  THE PUROMYCIN REACTION AND ITS RELATION TO PROTEIN SYNTHESIS. , 1964, Journal of molecular biology.

[25]  J. Abrahams,et al.  Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15. , 2009, Journal of molecular biology.

[26]  J. Strominger,et al.  Multiple penicillin-binding components in Bacillus subtilis, Bacillus cereus, Staphylococcus aureus, and Escherichia coli. , 1972, The Journal of biological chemistry.

[27]  Daniel N. Wilson,et al.  Probing translation with small-molecule inhibitors. , 2010, Chemistry & biology.

[28]  Waldemar Vollmer,et al.  Regulation of peptidoglycan synthesis by outer membrane proteins , 2010, Cell.

[29]  A. Tomasz,et al.  The mechanism of the irreversible antimicrobial effects of penicillins: how the beta-lactam antibiotics kill and lyse bacteria. , 1979, Annual review of microbiology.

[30]  M. Ehrenberg,et al.  A Posttermination Ribosomal Complex Is the Guanine Nucleotide Exchange Factor for Peptide Release Factor RF3 , 2001, Cell.

[31]  R. L. Gonzalez,et al.  Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling , 2009, Nature Structural &Molecular Biology.

[32]  B. Neumeister,et al.  Role of teichoic acids in Staphylococcus aureus nasal colonization, a major risk factor in nosocomial infections , 2004, Nature Medicine.

[33]  M. J. Johnson,et al.  Accumulation of labile phosphate in Staphylococcus aureus grown in the presence of penicillin. , 1949, The Journal of biological chemistry.

[34]  D. Nathans,et al.  PUROMYCIN INHIBITION OF PROTEIN SYNTHESIS: INCORPORATION OF PUROMYCIN INTO PEPTIDE CHAINS. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[35]  M. Delarue,et al.  Structural Insights into the Quinolone Resistance Mechanism of Mycobacterium tuberculosis DNA Gyrase , 2010, PloS one.

[36]  H. Mori,et al.  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. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[37]  J. T. Park.  Uridine-5'-pyrophosphate derivatives. II. A structure common to three derivatives. , 1952, The Journal of biological chemistry.

[38]  S. Joseph,et al.  Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation. , 2008, Molecular cell.

[39]  R. Kishony,et al.  Rapid β-lactam-induced lysis requires successful assembly of the cell division machinery , 2009, Proceedings of the National Academy of Sciences.

[40]  B. Spratt.  Distinct penicillin binding proteins involved in the division, elongation, and shape of Escherichia coli K12. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[41]  R. Kishony,et al.  Functional classification of drugs by properties of their pairwise interactions , 2006, Nature Genetics.

[42]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[43]  Robert P. St.Onge,et al.  The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes , 2008, Science.

[44]  Jun Wang,et al.  Discovery of FabH/FabF Inhibitors from Natural Products , 2006, Antimicrobial Agents and Chemotherapy.

[45]  J. Collins,et al.  Mistranslation of Membrane Proteins and Two-Component System Activation Trigger Antibiotic-Mediated Cell Death , 2008, Cell.

[46]  E. Brown,et al.  Probing teichoic acid genetics with bioactive molecules reveals new interactions among diverse processes in bacterial cell wall biogenesis. , 2009, Chemistry & biology.

[47]  Gary D Bader,et al.  The Genetic Landscape of a Cell , 2010, Science.

[48]  P. D. de Boer,et al.  Bacterial actin MreB assembles in complex with cell shape protein RodZ , 2010, The EMBO journal.

[49]  J. T. Park.  Uridine-5'-pyrophosphate derivatives. II. Isolation from Staphylococcus aureus. , 1952, The Journal of biological chemistry.

[50]  D. Hughes,et al.  A vancomycin photoprobe identifies the histidine kinase VanSsc as a vancomycin receptor. , 2010, Nature chemical biology.

[51]  B. Spratt,et al.  Penicillin-binding proteins and cell shape in E. coli , 1975, Nature.

[52]  M. Yarmolinsky,et al.  INHIBITION BY PUROMYCIN OF AMINO ACID INCORPORATION INTO PROTEIN. , 1959, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Stanley N Cohen,et al.  SOS Response Induction by ß-Lactams and Bacterial Defense Against Antibiotic Lethality , 2004, Science.

[54]  N. Krogan,et al.  Phenotypic Landscape of a Bacterial Cell , 2011, Cell.

[55]  J. Strominger,et al.  Mode of Action of Penicillin Biochemical Basis for the Mechanism of Action of Penicillin and for Its Selective Toxicity , 1957 .

[56]  T. Bernhardt,et al.  Daughter cell separation is controlled by cytokinetic ring‐activated cell wall hydrolysis , 2010, The EMBO journal.

[57]  J. Ghuysen,et al.  Sensitivity to ampicillin and cephalothin of enzymes involved in wall peptide crosslinking in Escherichia coli K12, strain 44. , 1974, European journal of biochemistry.

[58]  E. Brown,et al.  Multicopy suppressors for novel antibacterial compounds reveal targets and drug efflux susceptibility. , 2004, Chemistry & biology.

[59]  Jun Wang,et al.  Platensimycin is a selective FabF inhibitor with potent antibiotic properties , 2006, Nature.

[60]  S. L. Wong,et al.  Combining biological networks to predict genetic interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[61]  N. Cozzarelli,et al.  Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[62]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[63]  Boris Hayete,et al.  Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli , 2007 .

[64]  S. Walker,et al.  Lipoprotein Cofactors Located in the Outer Membrane Activate Bacterial Cell Wall Polymerases , 2010, Cell.

[65]  R. Monro.  Catalysis of peptide bond formation by 50 S ribosomal subunits from Escherichia coli. , 1967, Journal of molecular biology.

[66]  T. Silhavy,et al.  Secretion of LamB-LacZ by the Signal Recognition Particle Pathway of Escherichia coli , 2003, Journal of bacteriology.

[67]  J. Beckwith,et al.  Diverse Paths to Midcell: Assembly of the Bacterial Cell Division Machinery , 2005, Current Biology.

[68]  M. Gellert,et al.  DNA gyrase: an enzyme that introduces superhelical turns into DNA. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[69]  T. Rapoport.  Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes , 2007, Nature.

[70]  A. Luttinger,et al.  The twisted ‘life’ of DNA in the cell: bacterial topoisomerases , 1995, Molecular microbiology.

[71]  Wenjun Zhao,et al.  Lesions in Teichoic Acid Biosynthesis in Staphylococcus aureus Lead to a Lethal Gain of Function in the Otherwise Dispensable Pathway , 2006, Journal of bacteriology.

[72]  J. Collins,et al.  Bacterial charity work leads to population-wide resistance , 2010, Nature.

[73]  Huiming Ding,et al.  eSGA: E. coli synthetic genetic array analysis , 2008, Nature Methods.

[74]  J. Collins,et al.  A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics , 2007, Cell.

[75]  Igor Jurisica,et al.  NAViGaTOR: Network Analysis, Visualization and Graphing Toronto , 2009, Bioinform..

[76]  J. Strominger,et al.  PENICILLIN‐SENSITIVE ENZYMES AND PENICILLIN‐BINDING COMPONENTS IN BACTERIAL CELLS * , 1974, Annals of the New York Academy of Sciences.

[77]  Eric D Brown,et al.  Chemical probes of Escherichia coli uncovered through chemical-chemical interaction profiling with compounds of known biological activity. , 2010, Chemistry & biology.

[78]  R. Hegde,et al.  The surprising complexity of signal sequences. , 2006, Trends in biochemical sciences.