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A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress [MNase-seq]

ABSTRACT: A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress [MNase-seq]

PROVIDER: PRJNA1047058 | ENA |

REPOSITORIES: ENA

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A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress [MNase-seq]

Project description:Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism.

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Project description:High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation, and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu-stress was down-regulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu-stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.

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