Deep-Sea Microbial Discovery Reveals Tough New Enzyme for Genome Editing

Deep-sea microorganisms are yielding tough new enzymes that could solve major delivery bottlenecks in precision genome editing. Researchers discovered a remarkably stable monomeric meganuclease originating from a hydrothermal vent environment, showcasing unique cleavage capabilities that expand the molecular toolkit for synthetic biology.

Meganucleases are specialized endonuclease enzymes capable of recognizing and cleaving extended DNA sequences with high fidelity. While tools like CRISPR-Cas systems have revolutionized genetic engineering, their bulky multicomponent structures often suffer from low delivery efficiency inside target cells. In contrast, compact meganucleases under 1 kilobase in size offer a promising alternative, particularly for demanding applications such as mitochondrial genome editing, where delivering guide RNA remains exceptionally difficult.

Historically, discovering new meganucleases meant laboriously culturing microbes in a laboratory. Because fewer than one percent of microbial species can be grown this way, scientists are increasingly turning to metagenomic databases containing billions of uncultured protein sequences. However, traditional homology searches usually just recover slight variations of already known enzymes, missing entirely novel activities. To overcome this limitation, a team led by scientists at AstraZeneca and the University of Cambridge developed a streamlined two-week discovery pipeline combining cell-free protein expression with deep sequencing.

The workflow bypassed the usual protein purification bottlenecks by utilizing cell-free extracts to produce candidate enzymes directly from synthetic DNA templates. Screening sequences harvested from the MGnify microbiome database, the team identified a novel enzyme designated as I-MG11. Originating from subseafloor sediment in the Guaymas Basin, I-MG11 shares only 28.3 percent sequence identity with the classic meganuclease I-SceI and bears no significant matches to annotated proteins in standard uniprot databases.

Detailed functional characterization, published in Nucleic Acids Research, revealed that I-MG11 recognizes a 17-base-pair sequence and creates four-nucleotide palindromic three-prime overhangs. This makes it the first known monomeric meganuclease to generate such cohesive ends from a non-palindromic target site. These overhangs are especially valuable because they facilitate precise gene insertion through homology-directed repair while avoiding the error-prone outcomes typical of non-homologous end joining.

Biochemical assays demonstrated that I-MG11 is exceptionally thermostable, showing optimal DNA cleavage activity at temperatures between 55 and 65 degrees Celsius and a melting temperature of 74 degrees Celsius. The enzyme also displayed an alkaline pH optimum around pH 10, which researchers attribute to its high isoelectric point helping it diffuse efficiently along DNA molecules. Structural modeling using artificial intelligence tools suggested that its high stability and unique specificity stem from specific amino acid insertions and deletions within its DNA-binding pocket.

While these laboratory findings highlight the potential of deep-sea enzymes for biotechnology, further research is required to evaluate their performance in living mammalian cells and to test their precision against off-target genomic sites. The new cell-free screening framework provides a robust blueprint for mining the vast sequence space of unculturable microbes to uncover custom molecular tools.

The research was published in Nucleic acids research on November 10, 2026.