One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

Open access

Datsenko, Kirill A., Wanner, Barry L.·2000·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.120163297

Open this paper in CoChat — free account

Abstract

We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage λ Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB , cyaA , lacZYA , ompR - envZ , phnR , pstB , pstCA , pstS , pstSCAB - phoU , recA , and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1073/pnas.120163297

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858
Self-citation
A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics
Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A., & Collins, J. J. (2007) · Cell · doi:10.1016/j.cell.2007.06.049 · Cited by 2,982
A Deep Learning Approach to Antibiotic Discovery
Stokes, J. M., Yang, K., Swanson, K., Jin, W., Cubillos-Ruiz, A., Donghia, N. M., MacNair, C. R., French, S., Carfrae, L. A., Bloom-Ackermann, Z., et al. (2020) · Cell · doi:10.1016/j.cell.2020.01.021 · Cited by 2,463
Intestinal inflammation targets cancer-inducing activity of the microbiota
Arthur, J. C., Perez-Chanona, E., Mühlbauer, M., Tomkovich, S., Uronis, J. M., Fan, T.-J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., et al. (2012) · Science · doi:10.1126/science.1224820 · Cited by 2,263
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., & Gardner, T. S. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050008 · Cited by 1,563
Femtomolar Sensitivity of Metalloregulatory Proteins Controlling Zinc Homeostasis
Outten, C. E., & O'Halloran, A. T. V. (2001) · Science · doi:10.1126/science.1060331 · Cited by 1,489
Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system
Jiang, Y., Chen, B., Duan, C., Sun, B., Yang, J., & Yang, S. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.04023-14 · Cited by 1,362
Interaction network containing conserved and essential protein complexes in Escherichia coli
Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., et al. (2005) · Nature · doi:10.1038/nature03239 · Cited by 1,201
SOS response promotes horizontal dissemination of antibiotic resistance genes
Beaber, J. W., Hochhut, B., & Waldor, M. K. (2004) · Nature · doi:10.1038/nature02241 · Cited by 1,186
Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut
Winter, S. E., Winter, M. G., Xavier, M. N., Thiennimitr, P., Poon, V., Keestra, A. M., Laughlin, R. C., Gomez, G., Wu, J., Lawhon, S. D., et al. (2013) · Science · doi:10.1126/science.1232467 · Cited by 1,019
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013) · Nature · doi:10.1038/nature12503 · Cited by 1,035
The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity
Parry, B. R., Surovtsev, I. V., Cabeen, M. T., O’Hern, C. S., Dufresne, E. R., & Jacobs-Wagner, C. (2014) · Cell · doi:10.1016/j.cell.2013.11.028 · Cited by 822
The Molecular Diversity of Adaptive Convergence
Tenaillon, O., Rodríguez-Verdugo, A., Gaut, R. L., McDonald, P., Bennett, A. F., Long, A. D., & Gaut, B. S. (2012) · Science · doi:10.1126/science.1212986 · Cited by 815
Integrating high-throughput and computational data elucidates bacterial networks
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature · doi:10.1038/nature02456 · Cited by 792
An engineered microbial platform for direct biofuel production from brown macroalgae
Wargacki, A. J., Leonard, E., Win, M. N., Regitsky, D. D., Santos, C. N. S., Kim, P. B., Cooper, S. R., Raisner, R. M., Herman, A., Sivitz, A. B., et al. (2012) · Science · doi:10.1126/science.1214547 · Cited by 734
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
Schwer, B., Bunkenborg, J., Verdin, R. O., Andersen, J. S., & Verdin, E. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603968103 · Cited by 705
Growth Rate-Dependent Global Effects on Gene Expression in Bacteria
Klumpp, S., Zhang, Z., & Hwa, T. (2009) · Cell · doi:10.1016/j.cell.2009.12.001 · Cited by 703
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
Lee, H., Popodi, E., Tang, H., & Foster, P. L. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210309109 · Cited by 681
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
Yosef, I., Goren, M. G., & Qimron, U. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks216 · Cited by 655
Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron
Deriu, E., Liu, J. Z., Pezeshki, M., Edwards, R. A., Ochoa, R. J., Contreras, H., Libby, S. J., Fang, F. C., & Raffatellu, M. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.06.007 · Cited by 550
Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system
Datsenko, K. A., Pougach, K., Tikhonov, A., Wanner, B. L., Severinov, K., & Semenova, E. (2012) · Nature Communications · doi:10.1038/ncomms1937 · Cited by 561
Self-citation
A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging
Zhang, W., Li, J., Suzuki, K., Qu, J., Wang, P., Zhou, J., Liu, X., Ren, R., Xu, X., Ocampo, A., et al. (2015) · Science · doi:10.1126/science.aaa1356 · Cited by 551
Microcins mediate competition among Enterobacteriaceae in the inflamed gut
Sassone-Corsi, M., Nuccio, S.-P., Liu, H., Hernandez, D., Vu, C. T., Takahashi, A. A., Edwards, R. A., & Raffatellu, M. (2016) · Nature · doi:10.1038/nature20557 · Cited by 549
Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver
Bertocchi, A., Carloni, S., Ravenda, P. S., Bertalot, G., Spadoni, I., Lo Cascio, A., Gandini, S., Lizier, M., Braga, D., Asnicar, F., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.03.004 · Cited by 515
Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease
van Kessel, S. P., Frye, A. K., El-Gendy, A. O., Castejon, M., Keshavarzian, A., van Dijk, G., & El Aidy, S. (2019) · Nature Communications · doi:10.1038/s41467-019-08294-y · Cited by 521
Fucose sensing regulates bacterial intestinal colonization
Pacheco, A. R., Curtis, M. M., Ritchie, J. M., Munera, D., Waldor, M. K., Moreira, C. G., & Sperandio, V. (2012) · Nature · doi:10.1038/nature11623 · Cited by 499
Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models
Hwang, I. Y., Koh, E., Wong, A., March, J. C., Bentley, W. E., Lee, Y. S., & Chang, M. W. (2017) · Nature Communications · doi:10.1038/ncomms15028 · Cited by 472
Evolution of high-level resistance during low-level antibiotic exposure
Wistrand-Yuen, E., Knopp, M., Hjort, K., Koskiniemi, S., Berg, O. G., & Andersson, D. I. (2018) · Nature Communications · doi:10.1038/s41467-018-04059-1 · Cited by 466
Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells
Bakshi, S., Siryaporn, A., Goulian, M., & Weisshaar, J. C. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08081.x · Cited by 456
Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation
Riglar, D. T., Giessen, T. W., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., Kotula, J. W., Gerber, G. K., Way, J. C., & Silver, P. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3879 · Cited by 426
Mechanism of Transcriptional Bursting in Bacteria
Chong, S., Chen, C., Ge, H., & Xie, X. S. (2014) · Cell · doi:10.1016/j.cell.2014.05.038 · Cited by 428
Selective small-molecule inhibition of an RNA structural element
Howe, J. A., Wang, H., Fischmann, T. O., Balibar, C. J., Xiao, L., Galgoci, A. M., Malinverni, J. C., Mayhood, T., Villafania, A., Nahvi, A., et al. (2015) · Nature · doi:10.1038/nature15542 · Cited by 407
Shadow Enhancers Foster Robustness of Drosophila Gastrulation
Perry, M. W., Boettiger, A. N., Bothma, J. P., & Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.07.043 · Cited by 396
Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine
Fabich, A. J., Jones, S. A., Chowdhury, F. Z., Cernosek, A., Anderson, A., Smalley, D., McHargue, J. W., Hightower, G. A., Smith, J. T., Autieri, S. M., et al. (2008) · Infection and Immunity · doi:10.1128/iai.01386-07 · Cited by 380
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., Banerjee, O., Feng, Z., Losic, B., Mahajan, M. C., Jabado, O. J., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2432 · Cited by 360
Intracellular Copper Does Not Catalyze the Formation of Oxidative DNA Damage in Escherichia coli
Macomber, L., Rensing, C., & Imlay, J. A. (2007) · Journal of Bacteriology · doi:10.1128/jb.01357-06 · Cited by 356
Roles of NapF, NapG and NapH, subunits of the Escherichia coli periplasmic nitrate reductase, in ubiquinol oxidation: Roles of NapF, G and H in ubiquinol oxidation in E. coli
Brondijk, T. H. C., Fiegen, D., Richardson, D. J., & Cole, J. A. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02875.x · Cited by 342
The Synchronization of Replication and Division Cycles in Individual E. coli Cells
Wallden, M., Fange, D., Lundius, E. G., Baltekin, Ö., & Elf, J. (2016) · Cell · doi:10.1016/j.cell.2016.06.052 · Cited by 331
A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils
Claessen, D., Rink, R., de Jong, W., Siebring, J., de Vreugd, P., Boersma, F. G. H., Dijkhuizen, L., & Wösten, H. A. B. (2003) · Genes & Development · doi:10.1101/gad.264303 · Cited by 327
A robust system for production of minicircle DNA vectors
Kay, M. A., He, C.-Y., & Chen, Z.-Y. (2010) · Nature Biotechnology · doi:10.1038/nbt.1708 · Cited by 329
Engineering an allosteric transcription factor to respond to new ligands
Taylor, N. D., Garruss, A. S., Moretti, R., Chan, S., Arbing, M. A., Cascio, D., Rogers, J. K., Isaacs, F. J., Kosuri, S., Baker, D., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3696 · Cited by 328
Adaptive laboratory evolution — harnessing the power of biology for metabolic engineering
Portnoy, V. A., Bezdan, D., & Zengler, K. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.03.007 · Cited by 309
The antimicrobial compound reuterin (3-hydroxypropionaldehyde) induces oxidative stress via interaction with thiol groups
Schaefer, L., Auchtung, T. A., Hermans, K. E., Whitehead, D., Borhan, B., & Britton, R. A. (2010) · Microbiology · doi:10.1099/mic.0.035642-0 · Cited by 310
Rapid gut dysbiosis induced by stroke exacerbates brain infarction in turn
Xu, K., Gao, X., Xia, G., Chen, M., Zeng, N., Wang, S., You, C., Tian, X., Di, H., Tang, W., et al. (2021) · Gut · doi:10.1136/gutjnl-2020-323263 · Cited by 308
Nutritional Basis for Colonization Resistance by Human Commensal Escherichia coli Strains HS and Nissle 1917 against E. coli O157:H7 in the Mouse Intestine
Maltby, R., Leatham-Jensen, M. P., Gibson, T., Cohen, P. S., & Conway, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053957 · Cited by 285
“Null alleles were constructed in E. coli Nissle 1917 by using the Lambda Red allelic replacement system, first described by Datsenko and Wanner [39].”
Influential
Genomically encoded analog memory with precise in vivo DNA writing in living cell populations
Farzadfard, F., & Lu, T. K. (2014) · Science · doi:10.1126/science.1256272 · Cited by 298
Bricks and blueprints: methods and standards for DNA assembly.
Casini, A., Storch, M., Baldwin, G. S., & Ellis, T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4014 · Cited by 286
A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth
Constantinidou, C., Hobman, J. L., Griffiths, L., Patel, M. D., Penn, C. W., Cole, J. A., & Overton, T. W. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512312200 · Cited by 280
Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy
Pryor, R., Norvaisas, P., Marinos, G., Best, L., Thingholm, L. B., Quintaneiro, L. M., De Haes, W., Esser, D., Waschina, S., Lujan, C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.003 · Cited by 274
Bacterial Adaptation through Loss of Function
Hottes, A. K., Freddolino, L., Khare, A., Donnell, Z. N., Liu, J. C., & Tavazoie, S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003617 · Cited by 270
Redundancy and Specificity of Escherichia coli Iron Acquisition Systems during Urinary Tract Infection
Garcia, E. C., Brumbaugh, A. R., & Mobley, H. L. T. (2011) · Infection and Immunity · doi:10.1128/iai.01222-10 · Cited by 256
Indole production by the tryptophanase TnaA in escherichia coli is determined by the amount of exogenous tryptophan
Li, G., & Young, K. D. (2013) · Microbiology · doi:10.1099/mic.0.064139-0 · Cited by 266
The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor
Elliot, M. A., Karoonuthaisiri, N., Huang, J., Bibb, M. J., Cohen, S. N., Kao, C. M., & Buttner, M. J. (2003) · Genes & Development · doi:10.1101/gad.264403 · Cited by 246
Locoregional Effects of Microbiota in a Preclinical Model of Colon Carcinogenesis
Tomkovich, S., Yang, Y., Winglee, K., Gauthier, J., Mühlbauer, M., Sun, X., Mohamadzadeh, M., Liu, X., Martin, P., Wang, G. P., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-3472 · Cited by 252
Genomic and Functional Analyses of SXT, an Integrating Antibiotic Resistance Gene Transfer Element Derived from Vibrio cholerae
Beaber, J. W., Hochhut, B., & Waldor, M. K. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.15.4259-4269.2002 · Cited by 248
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
Conrad, T. M., Frazier, M., Joyce, A. R., Cho, B.-K., Knight, E. M., Lewis, N. E., Landick, R., & Palsson, B. Ø. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911253107 · Cited by 241
The QseC Adrenergic Signaling Cascade in Enterohemorrhagic E. coli (EHEC)
Hughes, D. T., Clarke, M. B., Yamamoto, K., Rasko, D. A., & Sperandio, V. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000553 · Cited by 244
Enterohemorrhagic Escherichia coli Reduces Mucus and Intermicrovillar Bridges in Human Stem Cell-Derived Colonoids
In, J., Foulke-Abel, J., Zachos, N. C., Hansen, A.-M., Kaper, J. B., Bernstein, H. D., Halushka, M., Blutt, S., Estes, M. K., Donowitz, M., et al. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2015.10.001 · Cited by 239
High-Affinity Zn2+Uptake System ZnuABC Is Required for Bacterial Zinc Homeostasis in Intracellular Environments and Contributes to the Virulence of Salmonella enterica
Ammendola, S., Pasquali, P., Pistoia, C., Petrucci, P., Petrarca, P., Rotilio, G., & Battistoni, A. (2007) · Infection and Immunity · doi:10.1128/iai.00559-07 · Cited by 235
FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress
Grass, G., Otto, M., Fricke, B., Haney, C. J., Rensing, C., Nies, D. H., & Munkelt, D. (2005) · Archives of Microbiology · doi:10.1007/s00203-004-0739-4 · Cited by 233
Identity and function of a large gene network underlying mutagenic repair of DNA breaks
Al Mamun, A. A. M., Lombardo, M.-J., Shee, C., Lisewski, A. M., Gonzalez, C., Lin, D., Nehring, R. B., Saint-Ruf, C., Gibson, J. L., Frisch, R. L., et al. (2012) · Science · doi:10.1126/science.1226683 · Cited by 224
Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption
Romano, K. A., Martinez-del Campo, A., Kasahara, K., Chittim, C. L., Vivas, E. I., Amador-Noguez, D., Balskus, E. P., & Rey, F. E. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.07.021 · Cited by 224
Respiration of Escherichia coli in the Mouse Intestine
Jones, S. A., Chowdhury, F. Z., Fabich, A. J., Anderson, A., Schreiner, D. M., House, A. L., Autieri, S. M., Leatham, M. P., Lins, J. J., Jorgensen, M., et al. (2007) · Infection and Immunity · doi:10.1128/iai.00484-07 · Cited by 223
Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria
Karberg, M., Guo, H., Zhong, J., Coon, R., Perutka, J., & Lambowitz, A. M. (2001) · Nature Biotechnology · doi:10.1038/nbt1201-1162 · Cited by 222
Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli
Laganenka, L., Colin, R., & Sourjik, V. (2016) · Nature Communications · doi:10.1038/ncomms12984 · Cited by 218
Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition
Fulde, M., Sommer, F., Chassaing, B., van Vorst, K., Dupont, A., Hensel, M., Basic, M., Klopfleisch, R., Rosenstiel, P., Bleich, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0395-5 · Cited by 206
Functioning of a metabolic flux sensor in Escherichia coli
Kochanowski, K., Volkmer, B., Gerosa, L., Haverkorn van Rijsewijk, B. R., Schmidt, A., & Heinemann, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202582110 · Cited by 196
Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome
Meydan, S., Marks, J., Klepacki, D., Sharma, V., Baranov, P. V., Firth, A. E., Margus, T., Kefi, A., Vázquez-Laslop, N., & Mankin, A. S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.017 · Cited by 184
Indoles from commensal bacteria extend healthspan
Sonowal, R., Swimm, A., Sahoo, A., Luo, L., Matsunaga, Y., Wu, Z., Bhingarde, J. A., Ejzak, E. A., Ranawade, A., Qadota, H., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706464114 · Cited by 197
QseC Mediates Salmonella enterica Serovar Typhimurium Virulence In Vitro and In Vivo
Moreira, C. G., Weinshenker, D., & Sperandio, V. (2010) · Infection and Immunity · doi:10.1128/iai.01038-09 · Cited by 195
ZupT Is a Zn(II) Uptake System in Escherichia coli
Grass, G., Wong, M. D., Rosen, B. P., Smith, R. L., & Rensing, C. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.3.864-866.2002 · Cited by 197
Biosynthesis and IroC‐dependent export of the siderophore salmochelin are essential for virulence of Salmonella enterica serovar Typhimurium
Crouch, M. V., Castor, M., Karlinsey, J. E., Kalhorn, T., & Fang, F. C. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.06089.x · Cited by 187
Application of different types of CRISPR/Cas-based systems in bacteria
Liu, Z., Dong, H., Cui, Y., Cong, L., & Zhang, D. (2020) · Microbial Cell Factories · doi:10.1186/s12934-020-01431-z · Cited by 185
Disparate Impact of Oxidative Host Defenses Determines the Fate of Salmonella during Systemic Infection in Mice
Burton, N. A., Schürmann, N., Casse, O., Steeb, A. K., Claudi, B., Zankl, J., Schmidt, A., & Bumann, D. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2013.12.006 · Cited by 175
Acinetobacter baumannii can use multiple siderophores for iron acquisition, but only acinetobactin is required for virulence
Sheldon, J. R., & Skaar, E. P. (2020) · PLOS Pathogens · doi:10.1371/journal.ppat.1008995 · Cited by 177
Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems
Bobonis, J., Mitosch, K., Mateus, A., Karcher, N., Kritikos, G., Selkrig, J., Zietek, M., Monzon, V., Pfalz, B., Garcia-Santamarina, S., et al. (2022) · Nature · doi:10.1038/s41586-022-05091-4 · Cited by 165
Fur Regulates Expression of the Salmonella Pathogenicity Island 1 Type III Secretion System through HilD
Ellermeier, J. R., & Slauch, J. M. (2008) · Journal of Bacteriology · doi:10.1128/jb.00926-07 · Cited by 160
ECMDB: the E-coli Metabolome Database
Guo, A. C., Jewison, T., Wilson, M., Liu, Y., Knox, C., Djoumbou, Y., Lo, P., Mandal, R., Krishnamurthy, R., & Wishart, D. S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks992 · Cited by 164
EfeUOB (YcdNOB) is a tripartite, acid‐induced and CpxAR‐regulated, low‐pH Fe2+ transporter that is cryptic in Escherichia coli K‐12 but functional in E. coli O157:H7
Cao, J., Woodhall, M. R., Alvarez, J., Cartron, M. L., & Andrews, S. C. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05802.x · Cited by 163
Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source,l-1,2-Propanediol
Lee, D.-H., & Palsson, B. Ø. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00373-10 · Cited by 160
Genetic characterization of the β-glucuronidase enzyme from a human intestinal bacterium, Ruminococcus gnavus
Beaud, D., Tailliez, P., & Anba-Mondoloni, J. (2005) · Microbiology · doi:10.1099/mic.0.27712-0 · Cited by 160
Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut
Moreira, C. G., Russell, R., Mishra, A. A., Narayanan, S., Ritchie, J. M., Waldor, M. K., Curtis, M. M., Winter, S. E., Weinshenker, D., & Sperandio, V. (2016) · mBio · doi:10.1128/mbio.00826-16 · Cited by 157
“Nonpolar mutants of qseE and qseEC in C. rodentium were constructed through the use of a lambda Red system (81).”
Severe Zinc Depletion of Escherichia coli
Graham, A. I., Hunt, S., Stokes, S. L., Bramall, N., Bunch, J., Cox, A. G., McLeod, C. W., & Poole, R. K. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.001503 · Cited by 156
The Ferritin-Like Dps Protein Is Required for Salmonella enterica Serovar Typhimurium Oxidative Stress Resistance and Virulence
Halsey, T. A., Vazquez-Torres, A., Gravdahl, D. J., Fang, F. C., & Libby, S. J. (2004) · Infection and Immunity · doi:10.1128/iai.72.2.1155-1158.2004 · Cited by 155
The Y ersinia pestis siderophore, yersiniabactin, and the ZnuABC system both contribute to zinc acquisition and the development of lethal septicaemic plague in mice
Bobrov, A. G., Kirillina, O., Fetherston, J. D., Miller, M. C., Burlison, J. A., & Perry, R. D. (2014) · Molecular Microbiology · doi:10.1111/mmi.12693 · Cited by 149
Structure of the SecY channel during initiation of protein translocation
Park, E., Ménétret, J.-F., Gumbart, J. C., Ludtke, S. J., Li, W., Whynot, A., Rapoport, T. A., & Akey, C. W. (2014) · Nature · doi:10.1038/nature12720 · Cited by 148
Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system
Yu, B. J., Sung, B. H., Koob, M. D., Lee, C. H., Lee, J. H., Lee, W. S., Kim, M. S., & Kim, S. C. (2002) · Nature Biotechnology · doi:10.1038/nbt740 · Cited by 145
An Outer Membrane Receptor of Neisseria meningitidis Involved in Zinc Acquisition with Vaccine Potential
Stork, M., Bos, M. P., Jongerius, I., de Kok, N., Schilders, I., Weynants, V. E., Poolman, J. T., & Tommassen, J. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000969 · Cited by 141
A Novel Two-Component Signaling System That Activates Transcription of an Enterohemorrhagic Escherichia coli Effector Involved in Remodeling of Host Actin
Reading, N. C., Torres, A. G., Kendall, M. M., Hughes, D. T., Yamamoto, K., & Sperandio, V. (2007) · Journal of Bacteriology · doi:10.1128/jb.01848-06 · Cited by 140
The role of ferritins in the physiology of Salmonella enterica sv. Typhimurium: a unique role for ferritin B in iron‐sulphur cluster repair and virulence
Velayudhan, J., Castor, M., Richardson, A., Main‐Hester, K. L., & Fang, F. C. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05600.x · Cited by 140
Interplay between Siderophores and Colibactin Genotoxin Biosynthetic Pathways in Escherichia coli
Martin, P., Marcq, I., Magistro, G., Penary, M., Garcie, C., Payros, D., Boury, M., Olier, M., Nougayrède, J.-P., Audebert, M., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003437 · Cited by 138
The StcE Protease Contributes to Intimate Adherence of Enterohemorrhagic Escherichia coli O157:H7 to Host Cells
Grys, T. E., Siegel, M. B., Lathem, W. W., & Welch, R. A. (2005) · Infection and Immunity · doi:10.1128/iai.73.3.1295-1303.2005 · Cited by 138
A new ferrous iron‐uptake transporter, EfeU (YcdN), from Escherichia coli
Große, C., Scherer, J., Koch, D., Otto, M., Taudte, N., & Grass, G. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05326.x · Cited by 137
Submicromolar hydrogen peroxide disrupts the ability of Fur protein to control free‐iron levels in Escherichia coli
Varghese, S., Wu, A., Park, S., Imlay, K. R. C., & Imlay, J. A. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05701.x · Cited by 133
The Zur-Regulated ZinT Protein Is an Auxiliary Component of the High-Affinity ZnuABC Zinc Transporter That Facilitates Metal Recruitment during Severe Zinc Shortage
Petrarca, P., Ammendola, S., Pasquali, P., & Battistoni, A. (2010) · Journal of Bacteriology · doi:10.1128/jb.01310-09 · Cited by 129
Linkage between Catecholate Siderophores and the Multicopper Oxidase CueO in Escherichia coli
Grass, G., Thakali, K., Klebba, P. E., Thieme, D., Müller, A., Wildner, G. F., & Rensing, C. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.17.5826-5833.2004 · Cited by 124
Roles of the Extraintestinal Pathogenic Escherichia coli ZnuACB and ZupT Zinc Transporters during Urinary Tract Infection
Sabri, M., Houle, S., & Dozois, C. M. (2009) · Infection and Immunity · doi:10.1128/iai.01082-08 · Cited by 118
Reducing Ribosome Biosynthesis Promotes Translation during Low Mg 2+ Stress
Pontes, M. H., Yeom, J., & Groisman, E. A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.008 · Cited by 115
Stable-isotope labeling with amino acids in nematodes
Larance, M., Bailly, A. P., Pourkarimi, E., Hay, R. T., Buchanan, G., Coulthurst, S., Xirodimas, D. P., Gartner, A., & Lamond, A. I. (2011) · Nature Methods · doi:10.1038/nmeth.1679 · Cited by 120
Anaerobic biosynthesis of the lower ligand of vitamin B 12
Hazra, A. B., Han, A. W., Mehta, A. P., Mok, K. C., Osadchiy, V., Begley, T. P., & Taga, M. E. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509132112 · Cited by 116

Authors: Datsenko, K. A., & Wanner, B. L.
Venue: Proceedings of the National Academy of Sciences
Publisher: Proceedings of the National Academy of Sciences
Published: 2000-05-30
Volume: 97
Issue: 12
Pages: 6640-6645
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.120163297
OpenAlex: W2116137883
Cited by: 14,782
References: 0
FWCI: 57.51
Type: journal article
Language: en
Open access: green

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cited by

Metadata

Record

About these checks

Data sources