Nathan Johns

All Publications

• Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. The ISME journal Gomes, A. L., Johns, N. I., Yang, A., Velez-Cortes, F., Smillie, C. S., Smith, M. B., Alm, E. J., Wang, H. H. 2020

  Abstract

  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 sigma70 motif necessary for transcription initiation. We further confirm the generalizability of this model and find widespread GC content adaptation of the sigma70 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 sigma70 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.

  View details for DOI 10.1038/s41396-020-0696-1

  View details for PubMedID 32514119

• Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems MOLECULAR SYSTEMS BIOLOGY Yim, S., Johns, N., Park, J., Gomes, A. C., McBee, R. M., Richardson, M., Ronda, C., Chen, S. P., Garenne, D., Noireaux, V., Wang, H. H. 2019; 15 (8): e8875

  Abstract

  Cell-free expression systems enable rapid prototyping of genetic programs in vitro. However, current throughput of cell-free measurements is limited by the use of channel-limited fluorescent readouts. Here, we describe DNA Regulatory element Analysis by cell-Free Transcription and Sequencing (DRAFTS), a rapid and robust in vitro approach for multiplexed measurement of transcriptional activities from thousands of regulatory sequences in a single reaction. We employ this method in active cell lysates developed from ten diverse bacterial species. Interspecies analysis of transcriptional profiles from > 1,000 diverse regulatory sequences reveals functional differences in promoter activity that can be quantitatively modeled, providing a rich resource for tuning gene expression in diverse bacterial species. Finally, we examine the transcriptional capacities of dual-species hybrid lysates that can simultaneously harness gene expression properties of multiple organisms. We expect that this cell-free multiplex transcriptional measurement approach will improve genetic part prototyping in new bacterial chassis for synthetic biology.

  View details for Web of Science ID 000484419200006

  View details for PubMedID 31464371

  View details for PubMedCentralID PMC6692573