Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters
Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and fi...
| Main Authors: | , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Berlin Heidelberg
2016
|
| Online Access: | http://hdl.handle.net/1721.1/104375 https://orcid.org/0000-0003-0437-3157 |
| _version_ | 1826194188055609344 |
|---|---|
| author | Gonçalves, Geisa A. L. Oliveira, Pedro H. Gomes, Ana G. Lewis, Leslie A. Monteiro, Gabriel A. Jones, Kristala L. Prazeres, Duarte Miguel |
| author2 | MIT-Portugal Program |
| author_facet | MIT-Portugal Program Gonçalves, Geisa A. L. Oliveira, Pedro H. Gomes, Ana G. Lewis, Leslie A. Monteiro, Gabriel A. Jones, Kristala L. Prazeres, Duarte Miguel |
| author_sort | Gonçalves, Geisa A. L. |
| collection | MIT |
| description | Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3′ region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability. |
| first_indexed | 2024-09-23T09:51:59Z |
| format | Article |
| id | mit-1721.1/104375 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:51:59Z |
| publishDate | 2016 |
| publisher | Springer Berlin Heidelberg |
| record_format | dspace |
| spelling | mit-1721.1/1043752022-09-26T14:12:46Z Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters Gonçalves, Geisa A. L. Oliveira, Pedro H. Gomes, Ana G. Lewis, Leslie A. Monteiro, Gabriel A. Jones, Kristala L. Prazeres, Duarte Miguel MIT-Portugal Program Massachusetts Institute of Technology. Department of Chemical Engineering Monteiro, Gabriel A. Jones, Kristala L. Prazeres, Duarte Miguel Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3′ region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability. Fundação para a Ciência e a Tecnologia (PTDC/EBB-EBI/113650/2009) MIT-Portugal Program 2016-09-22T21:24:20Z 2016-09-22T21:24:20Z 2014-04 2014-03 2016-08-18T15:24:29Z Article http://purl.org/eprint/type/JournalArticle 0175-7598 1432-0614 http://hdl.handle.net/1721.1/104375 Gonçalves, Geisa A. L. et al. “Evidence That the Insertion Events of IS2 Transposition Are Biased towards Abrupt Compositional Shifts in Target DNA and Modulated by a Diverse Set of Culture Parameters.” Applied Microbiology and Biotechnology 98.15 (2014): 6609–6619. https://orcid.org/0000-0003-0437-3157 en http://dx.doi.org/10.1007/s00253-014-5695-6 Applied Microbiology and Biotechnology Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ Springer-Verlag Berlin Heidelberg application/pdf Springer Berlin Heidelberg Springer Berlin Heidelberg |
| spellingShingle | Gonçalves, Geisa A. L. Oliveira, Pedro H. Gomes, Ana G. Lewis, Leslie A. Monteiro, Gabriel A. Jones, Kristala L. Prazeres, Duarte Miguel Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters |
| title | Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters |
| title_full | Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters |
| title_fullStr | Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters |
| title_full_unstemmed | Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters |
| title_short | Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters |
| title_sort | evidence that the insertion events of is2 transposition are biased towards abrupt compositional shifts in target dna and modulated by a diverse set of culture parameters |
| url | http://hdl.handle.net/1721.1/104375 https://orcid.org/0000-0003-0437-3157 |
| work_keys_str_mv | AT goncalvesgeisaal evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters AT oliveirapedroh evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters AT gomesanag evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters AT lewislesliea evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters AT monteirogabriela evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters AT joneskristalal evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters AT prazeresduartemiguel evidencethattheinsertioneventsofis2transpositionarebiasedtowardsabruptcompositionalshiftsintargetdnaandmodulatedbyadiversesetofcultureparameters |