Rojano-Nisimura, A. M. | Search bioRxiv

bioRxiv2024

Concentration dependent CsrA regulation of the uxuB transcript leads to development of post-transcriptional BANDPASS Filter

Post-transcriptional control systems offer new avenues to design synthetic circuits that offer reduced burden and less synthetic regulatory components compared to transcriptionally based tools. Herein, we repurpose a newly identified post-transcriptional interaction between the uxuB leader sequence and the E. coli CsrA regulatory protein to design a biological post-transcriptional BANDPASS filter. In this work, we characterize the uxuB mRNA as heterogenous target of the Carbon Storage Regulatory A (CsrA) protein, where the protein can both activate and repress uxuB activity depending on its intracellular concentration. We leverage this interaction to implement a novel strategy of regulation within the 5UTR of an mRNA. Specifically, we report a hierarchical binding strategy that may be leveraged by CsrA within uxuB to result in a dose- dependent response in regulatory outcomes. In our semi-synthetic circuit, the uxuB mRNA leader sequence is used as a scaffold that is fused to a gene of interest, which allows the circuit to transition between ON/OFF states based on a range of free native concentration of the CsrA regulatory protein. Notably, this system exerts regulation comparable to previously developed transcriptional BANDPASS filters while reducing the number of circuit components and can be used in concert with additional controlled circuits to achieve complex multi-signal control. We anticipate that future characterization of native regulatory RNA-protein systems will allow for development of more complex RNP-based circuits for synthetic biology applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/615595v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@107348dorg.highwire.dtl.DTLVardef@b4be0org.highwire.dtl.DTLVardef@1a272a3org.highwire.dtl.DTLVardef@1443c3_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

A high-throughput search for intracellular factors that affect RNA folding identifies E. coli proteins PepA and YagL as RNA chaperones that promote RNA remodeling

General RNA chaperones are RNA-binding proteins (RBPs) that interact transiently and non-specifically with RNA substrates and assist in their folding into native state. In bacteria, these chaperones impact both coding and non-coding RNAs and are particularly important for large, structured RNAs which are prone to becoming kinetically trapped in misfolded states. Currently, due to the limited number of well-characterized examples and the lack of a consensus structural or sequence motif, it is difficult to identify general RNA chaperones in bacteria. Here, we adapted a previously published in vivo RNA regional accessibility probing assay to screen genome wide for intracellular factors in E. coli affecting RNA folding, among which we aimed to uncover novel RNA chaperones. Through this method, we identified and validated eight proteins whose deletion gives changes in regional accessibility within the exogenously expressed Tetrahymena group I intron ribozyme. Further, we purified and measured in vitro properties of two of these proteins, YagL and PepA, which were especially attractive as general chaperone candidates. We showed that both proteins bind RNA and that YagL accelerates native refolding of the ribozyme from a long-lived misfolded state. Further dissection of YagL showed that a putative helix-turn-helix (HTH) domain is responsible for most of its RNA binding activity but only the full protein shows chaperone activity. Altogether, this work expands the current repertoire of known general RNA chaperones in bacteria.

molecular biology↗