Information storage across a microbial community using universal RNA memory

Abstract

Biological recorders can code information in DNA, but they remain challenging to apply in complex microbial communities. To program microbiome information storage, a synthetic catalytic RNA (cat-RNA) was used to write information in ribosomal RNA (rRNA) about gene transfer host range. By reading out native and modified rRNA using amplicon sequencing, we find that 140 out of 279 wastewater microbial community members from twenty taxonomic orders participate in conjugation and observe differences in information storage across amplicon sequence variants. Twenty of the variants were only observed in modified rRNA amplicons, illustrating information storage sensitivity. This autonomous and reversible RNA-addressable memory (RAM) will enable biosurveillance and microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.

Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity

“…Our findings that sample preparation influences ribozyme activity measurements have broad implications for other ribozyme measurement techniques, particularly those that involve reverse transcription (39,45). These results are also important for characterization of DNAzymes (49), riboswitches (6,50), and ribozymes that perform reactions other than self-cleavage (51)(52)(53)(54)(55). Together these results provide a straightforward and accurate method for measuring ribozyme activity that should generalize to different ribozymes and riboswitches in diverse genetic contexts and transcription environments.…”

“…Our method could also be applied for measurements of aptaswitch activity (6,34,36,50), another important class of RNAs that often use context-dependent cleavage and could be susceptible to structural rearrangements during RNA extraction and reverse transcription. More generally, the method of blocking catalytic activity during sample preparation could be applied to other catalytic nucleic acids, such as ribozymes that perform ligation (51)(52)(53)(54)(55) or DNAzymes (49). Accurate measurements of context-dependent RNA catalysis will ultimately support the discovery of new biology and innovations in RNA synthetic biology, biotechnology, and biomanufacturing.…”

Ribozyme-mediated gene-fragment complementation for non-destructive reporting of DNA transfer within soil

“…14,15 Alternatively, synthetic genetic circuits can code information in the genome or transcriptome through DNA or RNA editing tools, which can be read out without selection using sequencing. 16,17 When studying HGT in soil materials, these techniques all require cell or nucleic acid extraction prior to measurement, which can vary in efficiency with soil properties. 18 As such, these approaches are limited in their ability to provide dynamic gene transfer information without disrupting the sample.…”