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bioRxiv · 10.1101/2025.04.29.651329

Controlling the taxonomic composition of biological information storage in 16S ribosomal RNA

Gamas, K. R.·Seamons, T.·Dysart, M.·Fang, L.·Chappell, J.·Stadler, L.·Silberg, J.
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Abstract

Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNA (rRNA) and perform a trans-splicing reaction that adds a barcode to the rRNA. Existing cat-RNA designs were manually generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida, the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNA that store information within user-defined sets of microbes in environmental communities for gene transfer studies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/651329v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@bcc65borg.highwire.dtl.DTLVardef@18288f2org.highwire.dtl.DTLVardef@ecf5c7org.highwire.dtl.DTLVardef@fbe064_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Gamas, K. R., Seamons, T., Dysart, M., Fang, L., Chappell, J., Stadler, L., Silberg, J.. 2025-04-29. Controlling the taxonomic composition of biological information storage in 16S ribosomal RNA. https://doi.org/10.1101/2025.04.29.651329

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