Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 21 September 2001:
Vol. 293. no. 5538, pp. 2266 - 2269
DOI: 10.1126/science.1063566
Prev | Table of Contents | Next

Reports

Identification of Critical Staphylococcal Genes Using Conditional Phenotypes Generated by Antisense RNA

Yinduo Ji,1* Barbara Zhang,1dagger Stephanie F. Van , Horn,2 Patrick Warren,2 Gary Woodnutt,1 Martin K. R. Burnham,1 Martin Rosenberg1

Comprehensive genomic analysis of the important human pathogen Staphylococcus aureus was achieved by a strategy involving antisense technology in a regulatable gene expression system. In addition to known essential genes, many genes of unknown or poorly defined biological function were identified. This methodology allowed gene function to be characterized in a comprehensive, defined set of conditionally growth-defective/lethal isogenic strains. Quantitative titration of the conditional growth effect was performed either in bacterial culture or in an animal model of infection. This genomic strategy offers an approach to the identification of staphylococcal gene products that could serve as targets for antibiotic discovery.

1 Department of Microbiology,
2 Genetics Research, GlaxoSmithKline Pharmaceuticals Research and Development, Collegeville, PA 19426, USA.
*   To whom correspondence should be addressed at 1250 South Collegeville Road, UP1345, Collegeville, PA 19426, USA. E-mail: yinduo_ji-1{at}gsk.com

dagger    Present address: Pharmacia Corporation, Peapack, NJ 07977, USA.

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Plasmid-Based System for High-Level Gene Expression and Antisense Gene Knockdown in Bartonella henselae.
D. Gillaspie, I. Perkins, K. Larsen, A. McCord, S. Pangonis, D. Sweger, M. N. Seleem, N. Sriranganathan, and B. E. Anderson (2009)
Appl. Envir. Microbiol. 75, 5434-5436
   Abstract »    Full Text »    PDF »
Grasping at Shadows: Revealing the Elusive Nature of Essential Genes.
T. Msadek (2009)
J. Bacteriol. 191, 4701-4704
   Full Text »    PDF »
Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli.
N. Nakashima and T. Tamura (2009)
Nucleic Acids Res. 37, e103
   Abstract »    Full Text »    PDF »
Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets.
D.-S. Lee, H. Burd, J. Liu, E. Almaas, O. Wiest, A.-L. Barabasi, Z. N. Oltvai, and V. Kapatral (2009)
J. Bacteriol. 191, 4015-4024
   Abstract »    Full Text »    PDF »
Specific gene silencing by artificial trans-encoded small noncoding RNAs in bacteria.
R. Cheng, C. Miao, Q. Gong, Y. Gu, X. Lu, F. Han, and W. Yu (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes.
R. Zhang and Y. Lin (2009)
Nucleic Acids Res. 37, D455-D458
   Abstract »    Full Text »    PDF »
Hairpin ribozyme-antisense RNA constructs can act as molecular lassos.
A. Dallas, S. V. Balatskaya, T.-C. Kuo, H. Ilves, A. V. Vlassov, R. L. Kaspar, K. O. Kisich, S. A. Kazakov, and B. H. Johnston (2008)
Nucleic Acids Res. 36, 6752-6766
   Abstract »    Full Text »    PDF »
Staphylococcus aureus Cell Wall Stress Stimulon Gene-lacZ Fusion Strains: Potential for Use in Screening for Cell Wall-Active Antimicrobials.
R. Steidl, S. Pearson, R. E. Stephenson, N. Ledala, S. Sitthisak, B. J. Wilkinson, and R. K. Jayaswal (2008)
Antimicrob. Agents Chemother. 52, 2923-2925
   Abstract »    Full Text »    PDF »
Characterization and Application of a Glucose-Repressible Promoter in Francisella tularensis.
J. Horzempa, D. M. Tarwacki, P. E. Carlson Jr., C. M. Robinson, and G. J. Nau (2008)
Appl. Envir. Microbiol. 74, 2161-2170
   Abstract »    Full Text »    PDF »
New Insights into the WalK/WalR (YycG/YycF) Essential Signal Transduction Pathway Reveal a Major Role in Controlling Cell Wall Metabolism and Biofilm Formation in Staphylococcus aureus.
S. Dubrac, I. G. Boneca, O. Poupel, and T. Msadek (2007)
J. Bacteriol. 189, 8257-8269
   Abstract »    Full Text »    PDF »
DNA Helicase Activity of PcrA Is Not Required for the Displacement of RecA Protein from DNA or Inhibition of RecA-Mediated Strand Exchange.
S. P. Anand, H. Zheng, P. R. Bianco, S. H. Leuba, and S. A. Khan (2007)
J. Bacteriol. 189, 4502-4509
   Abstract »    Full Text »    PDF »
Tight Modulation of Escherichia coli Bacterial Biofilm Formation through Controlled Expression of Adhesion Factors.
S. Da Re, B. Le Quere, J.-M. Ghigo, and C. Beloin (2007)
Appl. Envir. Microbiol. 73, 3391-3403
   Abstract »    Full Text »    PDF »
Evaluation of the metS and murB Loci for Antibiotic Discovery Using Targeted Antisense RNA Expression Analysis in Bacillus anthracis.
G. C. Kedar, V. Brown-Driver, D. R. Reyes, M. T. Hilgers, M. A. Stidham, K. J. Shaw, J. Finn, and R. J. Haselbeck (2007)
Antimicrob. Agents Chemother. 51, 1708-1718
   Abstract »    Full Text »    PDF »
Discovery of platencin, a dual FabF and FabH inhibitor with in vivo antibiotic properties.
J. Wang, S. Kodali, S. H. Lee, A. Galgoci, R. Painter, K. Dorso, F. Racine, M. Motyl, L. Hernandez, E. Tinney, et al. (2007)
PNAS 104, 7612-7616
   Abstract »    Full Text »    PDF »
Catalytic Properties of Staphylococcus aureus and Bacillus Members of the Secondary Cation/Proton Antiporter-3 (Mrp) Family Are Revealed by an Optimized Assay in an Escherichia coli Host.
T. H. Swartz, M. Ito, T. Ohira, S. Natsui, D. B. Hicks, and T. A. Krulwich (2007)
J. Bacteriol. 189, 3081-3090
   Abstract »    Full Text »    PDF »
Conditional Mutation of an Essential Putative Glycoprotease Eliminates Autolysis in Staphylococcus aureus.
L. Zheng, C. Yu, K. Bayles, I. Lasa, and Y. Ji (2007)
J. Bacteriol. 189, 2734-2742
   Abstract »    Full Text »    PDF »
Genes Required for Glycolipid Synthesis and Lipoteichoic Acid Anchoring in Staphylococcus aureus.
A. Grundling and O. Schneewind (2007)
J. Bacteriol. 189, 2521-2530
   Abstract »    Full Text »    PDF »
Adaptation of a Luciferase Gene Reporter and lac Expression System to Borrelia burgdorferi.
J. S. Blevins, A. T. Revel, A. H. Smith, G. N. Bachlani, and M. V. Norgard (2007)
Appl. Envir. Microbiol. 73, 1501-1513
   Abstract »    Full Text »    PDF »
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
L. K. McNeil, C. Reich, R. K. Aziz, D. Bartels, M. Cohoon, T. Disz, R. A. Edwards, S. Gerdes, K. Hwang, M. Kubal, et al. (2007)
Nucleic Acids Res. 35, D347-D353
   Abstract »    Full Text »    PDF »
Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli.
N. Nakashima, T. Tamura, and L. Good (2006)
Nucleic Acids Res. 34, e138
   Abstract »    Full Text »    PDF »
Functional analysis of 11 putative essential genes in Bacillus subtilis..
A. Hunt, J. P. Rawlins, H. B. Thomaides, and J. Errington (2006)
Microbiology 152, 2895-2907
   Abstract »    Full Text »    PDF »
Mapping the Pathways to Staphylococcal Pathogenesis by Comparative Secretomics.
M. J. J. B. Sibbald, A. K. Ziebandt, S. Engelmann, M. Hecker, A. de Jong, H. J. M. Harmsen, G. C. Raangs, I. Stokroos, J. P. Arends, J. Y. F. Dubois, et al. (2006)
Microbiol. Mol. Biol. Rev. 70, 755-788
   Abstract »    Full Text »    PDF »
Inactivation of a Two-Component Signal Transduction System, SaeRS, Eliminates Adherence and Attenuates Virulence of Staphylococcus aureus..
X. Liang, C. Yu, J. Sun, H. Liu, C. Landwehr, D. Holmes, and Y. Ji (2006)
Infect. Immun. 74, 4655-4665
   Abstract »    Full Text »    PDF »
Good old-fashioned (anti)sense.
S. S. Golden (2006)
PNAS 103, 6781-6782
   Full Text »    PDF »
Discovery of FabH/FabF Inhibitors from Natural Products.
K. Young, H. Jayasuriya, J. G. Ondeyka, K. Herath, C. Zhang, S. Kodali, A. Galgoci, R. Painter, V. Brown-Driver, R. Yamamoto, et al. (2006)
Antimicrob. Agents Chemother. 50, 519-526
   Abstract »    Full Text »    PDF »
Essential genes of a minimal bacterium.
J. I. Glass, N. Assad-Garcia, N. Alperovich, S. Yooseph, M. R. Lewis, M. Maruf, C. A. Hutchison III, H. O. Smith, and J. C. Venter (2006)
PNAS 103, 425-430
   Abstract »    Full Text »    PDF »
Identification of a Novel Essential Two-Component Signal Transduction System, YhcSR, in Staphylococcus aureus.
J. Sun, L. Zheng, C. Landwehr, J. Yang, and Y. Ji (2005)
J. Bacteriol. 187, 7876-7880
   Abstract »    Full Text »    PDF »
Integrative elements for Bacillus subtilis yielding tetracycline-dependent growth phenotypes.
R. Bertram, M. Kostner, J. Muller, J. V. Ramos, and W. Hillen (2005)
Nucleic Acids Res. 33, e153
   Abstract »    Full Text »    PDF »
Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection.
X.-X. Tan, J. K. Actor, and Y. Chen (2005)
Antimicrob. Agents Chemother. 49, 3203-3207
   Abstract »    Full Text »    PDF »
Staphylococcus aureus Aminopeptidase S Is a Founding Member of a New Peptidase Clan.
S. G. Odintsov, I. Sabala, G. Bourenkov, V. Rybin, and M. Bochtler (2005)
J. Biol. Chem. 280, 27792-27799
   Abstract »    Full Text »    PDF »
Inducible Antisense RNA Expression in the Characterization of Gene Functions in Streptococcus mutans.
B. Wang and H. K. Kuramitsu (2005)
Infect. Immun. 73, 3568-3576
   Abstract »    Full Text »    PDF »
Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis.
D. Hoper, U. Volker, and M. Hecker (2005)
J. Bacteriol. 187, 2810-2826
   Abstract »    Full Text »    PDF »
Tetracycline-Dependent Conditional Gene Knockout in Bacillus subtilis.
A. Kamionka, R. Bertram, and W. Hillen (2005)
Appl. Envir. Microbiol. 71, 728-733
   Abstract »    Full Text »    PDF »
Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor.
S. Ehrt, X. V. Guo, C. M. Hickey, M. Ryou, M. Monteleone, L. W. Riley, and D. Schnappinger (2005)
Nucleic Acids Res. 33, e21
   Abstract »    Full Text »    PDF »
Tetracycline-inducible gene regulation in mycobacteria.
M. C. J. Blokpoel, H. N. Murphy, R. O'Toole, S. Wiles, E. S. C. Runn, G. R. Stewart, D. B. Young, and B. D. Robertson (2005)
Nucleic Acids Res. 33, e22
   Abstract »    Full Text »    PDF »
Group A Streptococcus Transcriptome Dynamics during Growth in Human Blood Reveals Bacterial Adaptive and Survival Strategies.
M. R. Graham, K. Virtaneva, S. F. Porcella, W. T. Barry, B. B. Gowen, C. R. Johnson, F. A. Wright, and J. M. Musser (2005)
Am. J. Pathol. 166, 455-465
   Abstract »    Full Text »    PDF »
Determination of the Core of a Minimal Bacterial Gene Set.
R. Gil, F. J. Silva, J. Pereto, and A. Moya (2004)
Microbiol. Mol. Biol. Rev. 68, 518-537
   Abstract »    Full Text »    PDF »
Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing.
T. Bae, A. K. Banger, A. Wallace, E. M. Glass, F. Aslund, O. Schneewind, and D. M. Missiakas (2004)
PNAS 101, 12312-12317
   Abstract »    Full Text »    PDF »
Identification of Genes Required for Embryo Development in Arabidopsis.
I. Tzafrir, R. Pena-Muralla, A. Dickerman, M. Berg, R. Rogers, S. Hutchens, T. C. Sweeney, J. McElver, G. Aux, D. Patton, et al. (2004)
Plant Physiology 135, 1206-1220
   Abstract »    Full Text »    PDF »
Conditional Lethal Amber Mutations in Essential Escherichia coli Genes.
C. D. Herring and F. R. Blattner (2004)
J. Bacteriol. 186, 2673-2681
   Abstract »    Full Text »    PDF »
A modular minimal cell model: Purine and pyrimidine transport and metabolism.
M. Castellanos, D. B. Wilson, and M. L. Shuler (2004)
PNAS 101, 6681-6686
   Abstract »    Full Text »    PDF »
Identification of Antibiotic Stress-Inducible Promoters: A Systematic Approach to Novel Pathway-Specific Reporter Assays for Antibacterial Drug Discovery.
H. P. Fischer, N. A. Brunner, B. Wieland, J. Paquette, L. Macko, K. Ziegelbauer, and C. Freiberg (2004)
Genome Res. 14, 90-98
   Abstract »    Full Text »    PDF »
DEG: a database of essential genes.
R. Zhang, H.-Y. Ou, and C.-T. Zhang (2004)
Nucleic Acids Res. 32, D271-272
   Abstract »    Full Text »    PDF »
Discovery of a Small Molecule That Inhibits Cell Division by Blocking FtsZ, a Novel Therapeutic Target of Antibiotics.
J. Wang, A. Galgoci, S. Kodali, K. B. Herath, H. Jayasuriya, K. Dorso, F. Vicente, A. Gonzalez, D. Cully, D. Bramhill, et al. (2003)
J. Biol. Chem. 278, 44424-44428
   Abstract »    Full Text »    PDF »
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655.
S. Y. Gerdes, M. D. Scholle, J. W. Campbell, G. Balazsi, E. Ravasz, M. D. Daugherty, A. L. Somera, N. C. Kyrpides, I. Anderson, M. S. Gelfand, et al. (2003)
J. Bacteriol. 185, 5673-5684
   Abstract »    Full Text »    PDF »
MOLECULAR GENETIC ANALYSIS OF THE VIRULENCE OF ORAL BACTERIAL PATHOGENS: AN HISTORICAL PERSPECTIVE.
H. K. Kuramitsu (2003)
Critical Reviews in Oral Biology & Medicine 14, 331-344
   Abstract »    Full Text »    PDF »
A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: Application to Mycobacterium tuberculosis.
G. Lamichhane, M. Zignol, N. J. Blades, D. E. Geiman, A. Dougherty, J. Grosset, K. W. Broman, and W. R. Bishai (2003)
PNAS 100, 7213-7218
   Abstract »    Full Text »    PDF »
Identification of Listeria monocytogenes Genes Involved in Salt and Alkaline-pH Tolerance.
R. Gardan, P. Cossart, The European Listeria Genome Consortium,, and J. Labadie (2003)
Appl. Envir. Microbiol. 69, 3137-3143
   Abstract »    Full Text »    PDF »
The YSIRK-G/S Motif of Staphylococcal Protein A and Its Role in Efficiency of Signal Peptide Processing.
T. Bae and O. Schneewind (2003)
J. Bacteriol. 185, 2910-2919
   Abstract »    Full Text »    PDF »
Essential Bacillussubtilis genes.
K. Kobayashi, S. D. Ehrlich, A. Albertini, G. Amati, K. K. Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P. Bessieres, et al. (2003)
PNAS 100, 4678-4683
   Abstract »    Full Text »    PDF »
The role of genomics in antimicrobial discovery.
S. D. Mills (2003)
J. Antimicrob. Chemother. 51, 749-752
   Full Text »    PDF »
Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae.
J. A. Thanassi, S. L. Hartman-Neumann, T. J. Dougherty, B. A. Dougherty, and M. J. Pucci (2002)
Nucleic Acids Res. 30, 3152-3162
   Abstract »    Full Text »    PDF »
Mycobacterial Genetics: The Sensibility of Antisense.
S. C. Woolwine and W. R. Bishai (2002)
Am. J. Respir. Crit. Care Med. 165, 318-319
   Full Text »    PDF »
A genome-scale analysis for identification of genes required for growth or survival of Haemophilusinfluenzae.
B. J. Akerley, E. J. Rubin, V. L. Novick, K. Amaya, N. Judson, and J. J. Mekalanos (2002)
PNAS 99, 966-971
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)