Guide RNA

Guide RNA (gRNA) or single guide RNA (sgRNA) is a short sequence of RNA that functions as a guide for the Cas9-endonuclease or other Cas-proteins that cut the double-stranded DNA and thereby can be used for gene editing. In bacteria and archaea, gRNAs are a part of the CRISPR-Cas system that serves as an adaptive immune defense that protects the organism from viruses. Here the short gRNAs serve as detectors of foreign DNA and direct the Cas-enzymes that degrades the foreign nucleic acid.

The RNA editing guide RNA was discovered in 1990 by B. Blum, N. Bakalara, and L. Simpson through Northern Blot Hybridization in the mitochondrial maxicircle DNA of the eukaryotic parasite Leishmania tarentolae. Subsequent research throughout the mid-2000s and the following years explored the structure and function of gRNA and the CRISPR-Cas system. A significant breakthrough occurred in 2012 when it was discovered that gRNA could guide the Cas9 endonuclease to introduce target-specific cuts in double-stranded DNA. This discovery led to the 2020 Nobel Prize in Chemistry awarded to Jennifer Doudna and Emmanuelle Charpentier for their contributions to the development of CRISPR-Cas9 gene-editing technology.

Trypanosomatid protists and other kinetoplastids have a post-transcriptional RNA modification process known as "RNA editing" that performs a uridine insertion/deletion inside mitochondria. This mitochondrial DNA is circular and is divided into maxicircles and minicircles. A mitochondrion contains about 50 maxicircles which have both coding and non coding regions and consists of approximately 20 kilo bases (kb). The coding region is highly conserved (16-17kb) and the non-coding region varies depending on the species. Minicircles are small (around 1 kb) but more numerous than maxicircles, a mitochondrion contains several thousands minicircles. Maxicircles can encode "cryptogenes" and some gRNAs; minicircles can encode the majority of gRNAs. Some gRNA genes show identical insertion and deletion sites even if they have different sequences, whereas other gRNA sequences are not complementary to pre-edited mRNA. Maxicircles and minicircles molecules are catenated into a giant network of DNA inside the mitochondrion.

The majority of maxicircle transcripts cannot be translated into proteins due to frameshifts in their sequences. These frameshifts are corrected post-transcriptionally through the insertion and deletion of uridine residues at precise sites, which then create an open reading frame. This open reading frame is subsequently translated into a protein that is homologous to mitochondrial proteins found in other cells. The process of uridine insertion and deletion is mediated by short guide RNAs (gRNAs),which encode the editing information through complementary sequences, and allow for base pairing between guanine and uracil (GU) as well as between guanine and cytosine (GC), facilitating the editing process.

Guide RNAs are mainly transcribed from the intergenic region of DNA maxicircle and have sequences complementary to mRNA. The 3' end of gRNAs contains an oligo 'U' tail (5-24 nucleotides in length) which is in a nonencoded region but interacts and forms a stable complex with A and G rich regions of pre-edited mRNA and gRNA, that are thermodynamically stabilized by a 5' and 3' anchors. This initial hybrid helps in the recognition of specific mRNA site to be edited.

RNA editing typically progresses from the 3' to the 5' end on the mRNA. The initial editing process begins when a gRNA forms an RNA duplex with a complementary mRNA sequence located just downstream of the editing site. This pairing recruits a number of ribonucleoprotein complexes that direct the cleavage of the first mismatched base adjacent to the gRNA-mRNA anchor. Following this, Uridylyltransferase inserts a 'U' at the 3' end, and RNA ligase then joins the two severed ends. The process repeats at the next upstream editing site in a similar manner. A single gRNA usually encodes the information for several editing sites (an editing "block"), the editing of which produces a complete gRNA/mRNA duplex. This process of sequential editing is known as the enzyme cascade model.

In the case of "pan-edited" mRNAs, the duplex unwinds and another gRNA forms a duplex with the edited mRNA sequence, initiating another round of editing. These overlapping gRNAs form an editing "domain". Some genes contain multiple editing domains. The extent of editing for any particular gene varies among trypanosomatid species. The variation consists of the loss of editing at the 3' side, probably due to the loss of minicircle sequence classes that encode specific gRNAs. A retroposition model has been proposed to explain the partial, and in some cases, complete loss of editing through evolution. Although the loss of editing is typically lethal, such losses have been observed in old laboratory strains. The maintenance of editing over the long evolutionary history of these ancient protists suggests the presence of a selective advantage, the exact nature of which is still uncertain.

It is not clear why trypanosomatids utilize such an elaborate mechanism to produce mRNAs. It might have originated in the early mitochondria of the ancestor of the kintoplastid protist lineage, since it is present in the bodonids which are ancestral to the trypanosomatids, and may not be present in the euglenoids, which branched from the same common ancestor as the kinetoplastids.