New Role of CRISPR-Cas System Identified by Researchers

A team of researchers led by Dr. Alexander Probst has identified that the CRISPR-Cas system is utilized by archaea – microorganisms closely resembling bacteria – to counteract parasites. This discovery was made through an exhaustive analysis of over 7,000 genomes via cutting-edge sequencing technology.

The CRISPR-Cas system is employed by microorganisms as a protective measure against viral attacks. In genetic engineering, this bacterial immune system is repurposed for precise alterations of genetic material.

The research group, directed by microbiologist Professor Dr. Alexander Probst of the Research Center One Health Ruhr at the Research Alliance Ruhr, has now determined another function of this specific genomic sequence: archaea use it to battle parasites.

The results of the study have recently been published in the journal Nature Microbiology.

Dr. Alexander Probst. Credit: UDE/Bettina Engel-Albustin

Emmanuelle Charpentier and Jennifer Doudna, biochemists, were awarded the Nobel Prize in 2020 for the biotechnological application of the CRISPR-Cas systems, often referred to as ‘genetic scissors’, in genetic engineering. Yet, many aspects of this genetic tool remain uninvestigated. For instance, could microorganisms use them to fend off parasitic microorganisms?

Investigating this hypothesis, Alexander Probst studied the genetic material of microbes deep within the Earth’s crust. He points out, ‘Over 70 percent of the Earth’s microorganisms are found in the deep biosphere. If we wish to understand our planet’s diversity, it is worth exploring the deep.’

Together with his team, Probst analysed water samples from a geyser in the USA and samples from the Horonobe underground laboratory in Japan. The focus of their study was archaea, which exist in the ecosystem as both hosts and parasites. These minute microbes, although closely resembling bacteria in cell size, possess significantly different physiological characteristics.

The outcome of their genomic analysis was revealing: host organisms had few parasites nearby and demonstrated genetic resistance to parasites. The scientists identified the ‘genetic scissors’ within the microorganisms’ genomes as the cause. Probst explains, ‘Over time, the archaea have integrated the parasitic DNA. When a parasite with matching DNA attacks the organism, the foreign genetic material is likely recognized by the CRISPR system and possibly disassembled.’ Probst’s expertise lies in the analysis of genetic material from environmental samples and his lab employs advanced methods such as Oxford Nanopore technology, which allows quick and thorough sequencing of the material.

To discount the possibility of mere isolated occurrences, the research extended their analysis to over 7,000 genomes and frequently observed the phenomenon. This discovery will aid in differentiating between beneficial symbionts and harmful parasites in future studies. If the CRISPR system recognizes a microorganism, it is likely a parasite. This will possibly enhance the understanding of key metabolic processes, like carbon flow in ecosystems, in the future.

Reference: “A predicted CRISPR-mediated symbiosis between uncultivated archaea” by Sarah P. Esser, Janina Rahlff, Weishu Zhao, Michael Predl, Julia Plewka, Katharina Sures, Franziska Wimmer, Janey Lee, Panagiotis S. Adam, Julia McGonigle, Victoria Turzynski, Indra Banas, Katrin Schwank, Mart Krupovic, Till L. V. Bornemann, Perla Abigail Figueroa-Gonzalez, Jessica Jarett, Thomas Rattei, Yuki Amano, Ian K. Blaby, Jan-Fang Cheng, William J. Brazelton, Chase L. Beisel, Tanja Woyke, Ying Zhang and Alexander J. Probst, 27 July 2023, Nature Microbiology.
DOI: 10.1038/s41564-023-01439-2

Frequently Asked Questions (FAQs) about CRISPR-Cas system function

More about CRISPR-Cas system function

• Nature Microbiology
• CRISPR-Cas System
• Research on Archaea
• Genetic Engineering
• Oxford Nanopore Technology