|
| Status |
Public on Apr 30, 2022 |
| Title |
Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (ChIP-Seq) |
| Organism |
Caulobacter vibrioides |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package ~5-15 kbp fragments of the host genome that can be subsequently transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the a-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a novel transcription factor, RogA, that represses gafYZ, which are direct activators of GTA gene transcription. Cells lacking rogA or expressing gafYZ produce GTAs harboring an ~8.3 kbp fragment of the genome that can, after cell lysis, promote transfer of DNA into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual horizontal gene transfer mechanism.
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| Overall design |
Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on stationary-phase Caulobacter crescentus (see the supplementary Materials and Methods for the exact treatment that were applied to each strain).
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| Contributor(s) |
Gozzi K, Tran NT, Modell JW, Le TK, Laub MT |
| Citation(s) |
36327213 |
| |
| Submission date |
Sep 20, 2021 |
| Last update date |
Nov 17, 2022 |
| Contact name |
Kevin Gozzi |
| E-mail(s) |
[email protected]
|
| Phone |
2038153995
|
| Organization name |
Massachusetts Institute of Techonology
|
| Street address |
31 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18006 |
Illumina HiSeq 2500 (Caulobacter vibrioides) |
|
| Samples (12)
|
| GSM5589677 |
TLElab_ChIPseq_antiRogA_CcresWT_replicate1 |
| GSM5589678 |
TLElab_ChIPseq_antiRogA_CcresWT_replicate2 |
| GSM5589679 |
TLElab_ChIPseq_antiRogA_Ccres_delta_rogA_replicate1 |
| GSM5589680 |
TLElab_ChIPseq_antiRogA_Ccres_delta_rogA_replicate2 |
| GSM5589681 |
TLElab_ChIPseq_antiGafY_Ccres_delta_rogA_replicate1 |
| GSM5589682 |
TLElab_ChIPseq_antiGafY_Ccres_delta_rogA_replicate2 |
| GSM5589683 |
TLElab_ChIPseq_antiGafY_Ccres_delta_rogAgafY_replicate1 |
| GSM5589684 |
TLElab_ChIPseq_antiGafY_Ccres_delta_rogAgafY_replicate2 |
| GSM5589685 |
TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_replicate1 |
| GSM5589686 |
TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_replicate2 |
| GSM5589687 |
TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_gafZflag_replicate1 |
| GSM5589688 |
TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_gafZflag_replicate2 |
|
| Relations |
| BioProject |
PRJNA764734 |
| SRA |
SRP337949 |
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