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Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria


While horizontal gene transfer is prevalent across the biosphere, the regulatory features that enable expression and functionalization of foreign DNA remain poorly understood. Here, we combine high-throughput promoter activity measurements and large-scale genomic analysis of regulatory regions to investigate the cross-compatibility of regulatory elements (REs) in bacteria. Functional characterization of thousands of natural REs in three distinct bacterial species revealed distinct expression patterns according to RE and recipient phylogeny. Host capacity to activate foreign promoters was proportional to their genomic GC content, while many low GC regulatory elements were both broadly active and had more transcription start sites across hosts. The difference in expression capabilities could be explained by the influence of the host GC content on the stringency of the AT-rich canonical σ70 motif necessary for transcription initiation. We further confirm the generalizability of this model and find widespread GC content adaptation of the σ70 motif in a set of 1,545 genomes from all major bacterial phyla. Our analysis identifies a key mechanism by which the strength of the AT-rich σ70 motif relative to a host’s genomic GC content governs the capacity for expression of acquired DNA. These findings shed light on regulatory adaptation in the context of evolving genomic composition.

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Fig. 1: Phylogenetic trends in RE library expression.
Fig. 2: Transcription start site utilization in RE library across hosts.
Fig. 3: Recipient and donor RE GC content govern σ70 motif encoding within regulatory sequences.
Fig. 4: Promiscuity and stringency in transcriptional activation depends on recipient and RE GC compositions.
Fig. 5: The signal for σ70 motif is nearly uniform among 1,545 representative genomes after background GC content correction.


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We thank members of the Wang lab for helpful scientific discussions and feedback. HHW acknowledges funding support from the NIH (1DP5OD009172-02, 1U01GM110714-01A1, 1R01AI132403-01), NSF (MCB‐1453219), Sloan Foundation (FR-2015-65795), DARPA (W911NF-15-2-0065), and ONR (N00014-15-1-2704). NIJ was supported by a NSF Graduate Research Fellowship (DGE-16-44869).

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ALCG, NIJ, and HHW designed the study with help from CSS, MBS, and EJA; ALCG, NIJ, and AY performed the experiments and analyzed the data. AG, NIJ, and HHW wrote the paper with input from all authors.

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Correspondence to Harris H. Wang.

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HHW is a member of the Scientific Advisory Board of SNIPR Biome. The authors declare no other competing financial interests.

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Gomes, A.L.C., Johns, N.I., Yang, A. et al. Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. ISME J 14, 2347–2357 (2020).

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