The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Bacterial insertion sequences: their genomic impact and diversity
Open accessAbstract
Insertion sequences (ISs), arguably the smallest and most numerous autonomous transposable elements (TEs), are important players in shaping their host genomes. This review focuses on prokaryotic ISs. We discuss IS distribution and impact on genome evolution. We also examine their effects on gene expression, especially their role in activating neighbouring genes, a phenomenon of particular importance in the recent upsurge of bacterial antibiotic resistance. We explain how ISs are identified and classified into families by a combination of characteristics including their transposases (Tpases), their overall genetic organisation and the accessory genes which some ISs carry. We then describe the organisation of autonomous and nonautonomous IS-related elements. This is used to illustrate the growing recognition that the boundaries between different types of mobile element are becoming increasingly difficult to define as more are being identified. We review the known Tpase types, their different catalytic activities used in cleaving and rejoining DNA strands during transposition, their organisation into functional domains and the role of this in regulation. Finally, we consider examples of prokaryotic IS domestication. In a more speculative section, we discuss the necessity of constructing more quantitative dynamic models to fully appreciate the continuing impact of TEs on prokaryotic populations.
Overview
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
Cites
Statistics
Verification
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.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
ISfinder: the reference centre for bacterial insertion sequences
Siguier, P. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj014 · Cited by 2,767
Self-citationGenomic Islands in Pathogenic and Environmental Microorganisms
Dobrindt, U., Hochhut, B., Hentschel, U., & Hacker, J. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro884 · Cited by 1,188
Comparative genomics: the bacterial pan-genome
Tettelin, H., Riley, D., Cattuto, C., & Medini, D. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.006 · Cited by 1,120
Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., Thomson, N., Harris, D. E., Holden, M. T. G., Churcher, C. M., Bentley, S. D., Mungall, K. L., et al. (2003) · Nature Genetics · doi:10.1038/ng1227 · Cited by 1,037
Reassembly of shattered chromosomes in Deinococcus radiodurans
Zahradka, K., Slade, D., Bailone, A., Sommer, S., Averbeck, D., Petranovic, M., Lindner, A. B., & Radman, M. (2006) · Nature · doi:10.1038/nature05160 · Cited by 444
Multi-scale modelling and simulation in systems biology
Dada, J. O., & Mendes, P. (2011) · Integrative Biology · doi:10.1039/c0ib00075b · Cited by 213
Richardson, J. M., Colloms, S. D., Finnegan, D. J., & Walkinshaw, M. D. (2009) · Cell · doi:10.1016/j.cell.2009.07.012 · Cited by 145 · cited 2×
“Other ISs such as the IS630 family, related to the eukaryote mariner/Tc superfamily, employ a mechanism in which the initial H2O-catalysed cleavage of the nontransferred strand occurs with a small offset of 2 bases into the IS prior to cleavage of the transferred strand (Feng & Colloms, 2007) as do their eukaryotic co…”
BackgroundBarabas, O., Ronning, D. R., Guynet, C., Hickman, A. B., Ton-Hoang, B., Chandler, M., & Dyda, F. (2008) · Cell · doi:10.1016/j.cell.2007.12.029 · Cited by 143 · cited 5×
“Although the founding family member, IS200, was identified in Salmonella 30 years ago (Lam & Roth, 1983), their activities have only recently been unravelled (Ronning et al., 2005; Ton-Hoang et al., 2005, 2010; Barabas et al., 2008; Guynet et al., 2008, 2009).”
BackgroundInfluentialSelf-citationThe Mu transpososome structure sheds light on DDE recombinase evolution
Montaño, S. P., Pigli, Y. Z., & Rice, P. A. (2012) · Nature · doi:10.1038/nature11602 · Cited by 137
Cited by
Horizontal gene transfer and adaptive evolution in bacteria.
Arnold, B. J., Huang, I.-T., & Hanage, W. P. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00650-4 · Cited by 869
The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases
Altae-Tran, H., Kannan, S., Demircioglu, F. E., Oshiro, R., Nety, S. P., McKay, L. J., Dlakić, M., Inskeep, W. P., Makarova, K. S., Macrae, R. K., et al. (2021) · Science · doi:10.1126/science.abj6856 · Cited by 407
Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease
Karvelis, T., Druteika, G., Bigelyte, G., Budre, K., Zedaveinyte, R., Silanskas, A., Kazlauskas, D., Venclovas, Č., & Siksnys, V. (2021) · Nature · doi:10.1038/s41586-021-04058-1 · Cited by 348
Bridge RNAs direct programmable recombination of target and donor DNA
Durrant, M. G., Perry, N. T., Pai, J. J., Jangid, A. R., Athukoralage, J. S., Hiraizumi, M., McSpedon, J. P., Pawluk, A., Nishimasu, H., Konermann, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07552-4 · Cited by 163
Considerations for determining safety of probiotics: A USP perspective
Roe, A. L., Boyte, M.-E., Elkins, C. A., Goldman, V. S., Heimbach, J., Madden, E., Oketch-Rabah, H., Sanders, M. E., Sirois, J., & Smith, A. (2022) · Regulatory Toxicology and Pharmacology · doi:10.1016/j.yrtph.2022.105266 · Cited by 136
The transposon-encoded protein TnpB processes its own mRNA into ωRNA for guided nuclease activity
Nety, S. P., Altae-Tran, H., Kannan, S., Demircioglu, F. E., Faure, G., Hirano, S., Mears, K., Zhang, Y., Macrae, R. K., & Zhang, F. (2023) · The CRISPR Journal · doi:10.1089/crispr.2023.0015 · Cited by 35
“These IS200/ 605 transposon loci are flanked by transposon ends.(3) The 3¢ transposon end (right end or RE) demarcates the 3¢ end of the xRNA scaffold, which is followed by a”
BackgroundSuenaga, H., Fujihara, H., Kimura, N., Hirose, J., Watanabe, T., Futagami, T., Goto, M., Shimodaira, J., & Furukawa, K. (2017) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12561 · Cited by 26
Metadata
- Authors
- Siguier, P., Gourbeyre, E., & Chandler, M.
- Venue
- FEMS Microbiology Reviews
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-09
- Volume
- 38
- Issue
- 5
- Pages
- 865-891
- ISSN
- 0168-6445 (ISSN-L)
- 1574-6976
- OpenAlex
- W1985886752
- Cited by
- 726
- References
- 10
- FWCI
- 21.00
- 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.
