High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
Abstract Background Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5187-7 |
| _version_ | 1818960787235930112 |
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| author | Daniel G. Mediati Catherine M. Burke Shirin Ansari Elizabeth J. Harry Iain G. Duggin |
| author_facet | Daniel G. Mediati Catherine M. Burke Shirin Ansari Elizabeth J. Harry Iain G. Duggin |
| author_sort | Daniel G. Mediati |
| collection | DOAJ |
| description | Abstract Background Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. Results We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. Conclusions The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation. |
| first_indexed | 2024-12-20T12:03:05Z |
| format | Article |
| id | doaj.art-ed2852df6cb94fd0abd1bf6db160359a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T12:03:05Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ed2852df6cb94fd0abd1bf6db160359a2022-12-21T19:41:30ZengBMCBMC Genomics1471-21642018-10-0119111610.1186/s12864-018-5187-7High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell divisionDaniel G. Mediati0Catherine M. Burke1Shirin Ansari2Elizabeth J. Harry3Iain G. Duggin4The ithree institute, University of Technology SydneyThe ithree institute, University of Technology SydneyThe ithree institute, University of Technology SydneyThe ithree institute, University of Technology SydneyThe ithree institute, University of Technology SydneyAbstract Background Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. Results We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. Conclusions The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation.http://link.springer.com/article/10.1186/s12864-018-5187-7Cell divisionUropathogenic E. coliHigh-throughputGenetic screenDNA sequencingFilamentation |
| spellingShingle | Daniel G. Mediati Catherine M. Burke Shirin Ansari Elizabeth J. Harry Iain G. Duggin High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division BMC Genomics Cell division Uropathogenic E. coli High-throughput Genetic screen DNA sequencing Filamentation |
| title | High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division |
| title_full | High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division |
| title_fullStr | High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division |
| title_full_unstemmed | High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division |
| title_short | High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division |
| title_sort | high throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division |
| topic | Cell division Uropathogenic E. coli High-throughput Genetic screen DNA sequencing Filamentation |
| url | http://link.springer.com/article/10.1186/s12864-018-5187-7 |
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