The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
Open accessAbstract
Biological pathways are structured in complex networks of interacting genes. Solving the architecture of such networks may provide valuable information, such as how microorganisms cause disease. Here we present a method (Tn-seq) for accurately determining quantitative genetic interactions on a genome-wide scale in microorganisms. Tn-seq is based on the assembly of a saturated Mariner transposon insertion library. After library selection, changes in frequency of each insertion mutant are determined by sequencing the flanking regions en masse. These changes are used to calculate each mutant's fitness. Using this approach, we determined fitness for each gene of Streptococcus pneumoniae, a causative agent of pneumonia and meningitis. A genome-wide screen for genetic interactions of five query genes identified both alleviating and aggravating interactions that could be divided into seven distinct categories. Owing to the wide activity of the Mariner transposon, Tn-seq has the potential to contribute to the exploration of complex pathways across many different species.
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Cites
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Genes required for mycobacterial growth defined by high density mutagenesis
Sassetti, C. M., Boyd, D. H., & Rubin, E. J. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03425.x · Cited by 2,544
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science · doi:10.1126/science.1065810 · Cited by 2,138
Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.031 · Cited by 870
Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast
Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S. R., Qu, H., Shales, M., Park, H.-O., Hayles, J., et al. (2008) · Science · doi:10.1126/science.1162609 · Cited by 352
Cited by
Griffin, J. E., Gawronski, J. D., DeJesus, M. A., Ioerger, T. R., Akerley, B. J., & Sassetti, C. M. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002251 · Cited by 1,048
DeJesus, M. A., Gerrick, E. R., Xu, W., Park, S. W., Long, J. E., Boutte, C. C., Rubin, E. J., Schnappinger, D., Ehrt, S., Fortune, S. M., et al. (2017) · mBio · doi:10.1128/mbio.02133-16 · Cited by 668
Mutant phenotypes for thousands of bacterial genes of unknown function
Price, M. N., Wetmore, K. M., Waters, R. J., Callaghan, M., Ray, J., Liu, H., Kuehl, J. V., Melnyk, R. A., Lamson, J. S., Suh, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0124-0 · Cited by 576
Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms
van Opijnen, T., & Camilli, A. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3033 · Cited by 494
Self-citationAlsford, S., Turner, D. J., Obado, S. O., Sanchez-Flores, A., Glover, L., Berriman, M., Hertz-Fowler, C., & Horn, D. (2011) · Genome Research · doi:10.1101/gr.115089.110 · Cited by 470
Biofilms and Inflammation in Chronic Wounds
Zhao, G., Usui, M. L., Lippman, S. I., James, G. A., Stewart, P. S., Fleckman, P., & Olerud, J. E. (2013) · Advances in Wound Care · doi:10.1089/wound.2012.0381 · Cited by 448
Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum
Turner, K. H., Wessel, A. K., Palmer, G. C., Murray, J. L., & Whiteley, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419677112 · Cited by 432
Resistance Toward Chlorhexidine in Oral Bacteria – Is There Cause for Concern?
Cieplik, F., Jakubovics, N. S., Buchalla, W., Maisch, T., Hellwig, E., & Al-Ahmad, A. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00587 · Cited by 424
Parsons, J. B., Broussard, T. C., Bose, J. L., Rosch, J. W., Jackson, P., Subramanian, C., & Rock, C. O. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1408797111 · Cited by 182
Fueling the caries process: carbohydrate metabolism and gene regulation by Streptococcus mutans
Moye, Z. D., Zeng, L., & Burne, R. A. (2014) · Journal of Oral Microbiology · doi:10.3402/jom.v6.24878 · Cited by 164
“cated CcpA in 64 genetic interactions (137), and another”
BackgroundSegal, E. S., Gritsenko, V., Levitan, A., Yadav, B., Dror, N., Steenwyk, J. L., Silberberg, Y., Mielich, K., Rokas, A., Gow, N. A. R., et al. (2018) · mBio · doi:10.1128/mbio.02048-18 · Cited by 150
The functional basis of adaptive evolution in chemostats
Gresham, D., & Hong, J. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12082 · Cited by 122
Barquist, L., Langridge, G. C., Turner, D. J., Phan, M.-D., Turner, A. K., Bateman, A., Parkhill, J., Wain, J., & Gardner, P. P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt148 · Cited by 121
Xu, W., DeJesus, M. A., Rücker, N., Engelhart, C. A., Wright, M. G., Healy, C., Lin, K., Wang, R., Park, S. W., Ioerger, T. R., et al. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01334-17 · Cited by 115
Interaction of Salmonella spp. with the Intestinal Microbiota
Ahmer, B. M. M., & Gunn, J. S. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00101 · Cited by 74
Integrated molecular approaches for fermented food microbiome research
Walsh, A. M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., & Cotter, P. D. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad001 · Cited by 56
Structure and function of a spectrin-like regulator of bacterial cytokinesis
Cleverley, R. M., Barrett, J. R., Baslé, A., Bui, N. K., Hewitt, L., Solovyova, A., Xu, Z.-Q., Daniel, R. A., Dixon, N. E., Harry, E. J., et al. (2014) · Nature Communications · doi:10.1038/ncomms6421 · Cited by 50
“The ezrA knockout has been described as lethal to S. aureus 20 , Streptococcus pneumoniae 21,22 and Listeria monocytogenes 23 , and thus constitutes a novel target for antibacterial agents.”
Polar Effects of Transposon Insertion into a Minimal Bacterial Genome
Hutchison, C. A., Merryman, C., Sun, L., Assad-Garcia, N., Richter, R. A., Smith, H. O., & Glass, J. I. (2019) · Journal of Bacteriology · doi:10.1128/jb.00185-19 · Cited by 47
Kim, G.-L., Hooven, T. A., Norambuena, J., Li, B., Boyd, J. M., Yang, J. H., & Parker, D. (2021) · mBio · doi:10.1128/mbio.00814-21 · Cited by 38
The cell wall polymer initiates plasma membrane partitioning in mycobacteria
Kado, T., Akbary, Z., Motooka, D., Sparks, I. L., Melzer, E. S., Nakamura, S., Rojas, E. R., Morita, Y. S., & Siegrist, M. S. (2022) · doi:10.1101/2022.06.12.495848 · Cited by 16
“We performed Tn-seq (Gawronski et al., 2009; Goodman et al., 2009; Langridge et al., 2009; van Opijnen et al., 2009) to identify transposon insertions that are underrepresented 16-24 hours post-benzyl alcohol exposure compared to DMSO vehicle control.”
MethodStuart, W. S., Jenkins, C. H., Ireland, P. M., Isupov, M. N., Norville, I. H., & Harmer, N. J. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108517 · Cited by 1
Metadata
- Authors
- van Opijnen, T., Bodi, K. L., & Camilli, A.
- Venue
- Nature Methods
- Published
- 2009-09-20
- Volume
- 6
- Issue
- 10
- Pages
- 767-772
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2030924818
- Cited by
- 933
- References
- 7
- FWCI
- 13.19
- Type
- journal article
- Language
- en
- Open access
- green
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