«Anything that can be regulated...

by Christoph
 

...will be regulated» Thus goes a lesser‑known but tried-and-tested amendment of Murphy's law among molecular biologists. Practitioners, above all students struggling with their own first PCR and cloning experiments in the lab, are familiar with the original «Anythings that can go wrong will go wrong, and at the worst possible time.» I don't need to dwell on that here. More seasoned molecular biologists are as pleased as newbies every time the amendment is confirmed anew, each year or so. It immediately popped in my mind when, a couple of days ago, I read this abstract of a paper by Shimizu et al. (2024) :
 

(click to enlarge)
Figure 1. Schematic diagram of the modulation of SVH-1 (protease/growth factor) functions regulated by CDD-2 (cytidine deaminase). Source

The pathway for axon regeneration in Caenorhabditis elegans is activated by SVH-1, a growth factor belonging to the HGF/plasminogen family. SVH-1 is a dual-function factor that acts as an HGF-like growth factor to promote axon regeneration and as a protease to regulate early development. It is important to understand how SVH-1 is converted from a protease to a growth factor for axon regeneration. In this study, we demonstrate that cytidine deaminase (CDD) SVH-17/CDD-2 plays a role in the functional conversion of SVH-1. We find that the codon exchange of His-755 to Tyr in the Asp–His–Ser catalytic triad of SVH-1 can suppress the cdd-2 defect in axon regeneration. Furthermore, the stem hairpin structure around the His-755 site in svh-1 mRNA is required for the ac­ti­vation of axon regeneration by SVH-1. These results suggest that CDD-2 promotes axon regeneration by transforming the function of SVH-1 from a protease to a growth factor through modification of svh-1 mRNA.
 

In short, an mRNA is "edited" by a cytidine deaminase such that a specific CAU codon (His‑755) is de­aminated at the C and converted into a UAU codon (Tyr‑755), which then leads to a protein with altered properties upon translation (Fig­ure 1). Wait, what?
 

(click to enlarge)
Figure 2. Stem-loop structure of svh-1 mRNA. (A) Compu­ter modeling of the 400 nucleotide svh-1 mRNA using the CentroidFold program. The C-residue for His-755 is circled in blue. Base pair structure, mutation sites (red letters) and encoded amino acids are shown. The svh-1(s-mut) mutation is shown here, the svh-1(WT) structure is shown in the frontispiece. (B) Percentages of axons that initiated regeneration 24 h after laser surgery. The number of axons examined (n) is shown. Error bars indicate 95% CIs. *P < 0.05 as determined by the Chi-square test and corrected by the false discovery rate (FDR) controlling Benjamini–Hochberg (BH) procedure for multiple comparisons. NS: not significant. Source

The surprise is only on my part, for sure, and is due to my poor study of the literature. I quickly found out that cytidine deaminases as nucleic acid editing enzymes have been known since the mid‑eigthies in Eukaryotes, specifically mammals, and are now very well studied (see here for a review). They are also highly sought-after enzymes among those working on genome edit­­ing.
 

The cherry on the cake of Shimizu et al.'s work is that they can show that deamination of C in His‑755 (CAU) functions in a context-dependent manner. Specifically, it is the mRNA stem‑loop structure adjacent to CAU (frontispiece) that drives deamination resulting in Tyr‑755 (UAU), and which apparently failed to form when the s‑mut mutations (which maintain the reading frame) were introduced in the svh‑1 gene (Figure 2A). They can conclude this from the obser­va­tion that axon regeneration was significantly suppressed in the svh-1 (s‑mut) mutant, while replacement of the Cys codon with a Tyr codon in svh‑1 (s‑mut, H755Y) showed approximately wild-type efficien­cy (Figure 2B). In any case, this is a particularly sophisticated example in the ever-growing basket of mechanisms of post‑transcriptional regulation of gene expression.
 

Do you know of a prokaryotic cytosine deaminase capable of deaminating C in ssDNA or RNA for regulatory reasons, in particular mRNA editing in vivo? Do you want to comment on this post? We would be happy about it! Please comment on Mastodon, Bluesky, or on 𝕏 (formerly Twitter).