| Apr 14, 2026 |
Bacteria independently evolved similar RNA hairpin structures to fix a wasteful flaw in different CRISPR immune systems, revealing convergent evolution at work.
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(Nanowerk News) The CRISPR-Cas gene-editing system has long been the focus of research as a promising tool in genome editing. However, the emphasis has been on its underlying mechanisms and nucleases. In contrast, little research has examined how CRISPR-Cas systems have evolved and been optimized. In collaboration with the universities of Leipzig, Freiburg, and Michigan (USA), a research team at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg found an optimization mechanism in CRISPR-Cas13, providing insights into the evolution of these systems.
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The results were recently published in The EMBO Journal (“A leader-repeat hairpin blocks extraneous CRISPR RNA production in diverse CRISPR-Cas13 systems”).
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CRISPR-Cas systems are the only known acquired immune systems in bacteria. They can store genetic information from attacking phages—viruses that infect bacteria—to combat future infections. In CRISPR arrays, which are DNA sequences, a DNA fragment of the attacking phage is archived between two fixed sequence repeats. Each viral snippet produces a CRISPR ribonucleic acid (crRNA), which instructs the system to recognize the same intruder in the event of a renewed attack.
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The underlying mechanism is complex and consists of several components that work together simultaneously. However, these components can interfere with one another. For example, in order to store a CRISPR array, it must begin and end with a repeat. This results in one repeat too many at one end, which produces a CRISPR RNA—all without any “viral snippets.”
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“The resulting CRISPR RNA, known as an extraneous CRISPR RNA (ecrRNA), is wasteful at best. At worst, it distracts the CRISPR machinery and prevents it from searching for infecting viruses,” says Chase Beisel, affiliated department head at HIRI and faculty member at the Botnar Institute of Immune Engineering in Basel, Switzerland. Beisel initiated the research, which was recently published in EMBO Journal.
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But nature has a solution: In a 2022 study published in Nature Microbiology, Beisel and his team demonstrated that one type of CRISPR-Cas systems, which use Cas9 nucleases to cut DNA, can prevent ecrRNAs from forming by introducing an additional RNA upstream of the problematic repeat. “The RNA binds to the first repeat and ensures that it is not recognized by the CRISPR machinery,” Beisel explains.
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For a long time, however, it was unclear whether other CRISPR-Cas systems also make use of this solution. Together with scientists from the universities of Leipzig, Freiburg, and Michigan in the US, researchers at the Helmholtz Institute for RNA-based Infection Research (HIRI), a site of the Braunschweig Helmholtz Centre for Infection Research (HZI) in cooperation with the Julius-Maximilians-Universität Würzburg (JMU), investigated whether CRISPR-Cas13 systems—which bear little resemblance to CRISPR-Cas9 systems—produce ecrRNAs and, if so, how they counteract them.
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A cross-system solution
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“We discovered that many CRISPR-Cas13 systems also utilize an RNA to prevent the formation of ecrRNAs,” says Angela Migur, a former postdoctoral researcher in Chase Beisel’s lab. With the first repeat, this protective RNA forms a stable structure resembling a hairpin. This blocks the Cas13 nuclease from binding to the repeat, processing it, and thereby producing an ecrRNA. “The appearance of the ‘hairpin’ was unexpected, since CRISPR-Cas9 and CRISPR-Cas13 systems evolved independently and function very differently,” adds Migur. “Surprisingly, however, the mechanisms that inhibited ecrRNA formation were very similar.”
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These observations point to a remarkable case of convergent evolution: different CRISPR-Cas systems have independently developed mechanisms to overcome common hurdles in immune defense.
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The team also found that not all CRISPR-Cas systems rely on such protective RNA. The decisive factor was whether the additional repeat occurred at the beginning or the end of the CRISPR array. This observation suggests that there are still other distinct strategies to be discovered that enhance the efficacy of CRISPR-Cas systems.
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New Research Perspectives
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Cas13 nucleases are now widely used as research tools and as a non-permanent method for gene editing at the RNA level. The research team’s discovery could help make these systems more effective by ensuring that only the intended CRISPR RNAs are produced. Furthermore, there is the possibility of inhibiting the viral defense by the CRISPR-Cas system using ecrRNAs, making the genetic tool easier to control.
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Although research has already made enormous efforts to characterize new CRISPR-Cas systems, it has primarily focused on the fundamental mechanisms of adaptive immunity, particularly on the properties of the respective nucleases. However, little research has been done so far on how the individual components of these systems are optimally coordinated to ensure their interaction is as efficient as possible. In this study, a drawback of the structure of CRISPR arrays was uncovered, one that can be easily remedied by a simple hairpin RNA.
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“We hope that our work will encourage the research community to investigate the limitations of CRISPR-Cas systems and other bacterial defense mechanisms more intensively. At the same time, it is important to clarify what strategies these systems have developed to overcome such hurdles as effectively as possible,” said Beisel.
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