Unlocking non-model organisms with CRISPR-Cas: A roadmap for sustainable biotechnology.
TL;DR
It is concluded that bridging the gap between foundational CRISPR research and its real-world applications is imperative and future efforts should focus on democratizing tools via open-source platforms, advancing delivery systems, and fostering sustainable innovation through synthetic biology integration to fully realize the transformative potential of genome editing in organisms beyond model organisms.
Abstract
The reliance on model organisms in biotechnology has advanced our understanding of fundamental biology but has failed to capture the complexity of real-world ecosystems, limiting applications in agriculture, biomanufacturing, and environmental remediation. This review critically evaluates the challenges and opportunities of applying CRISPR-Cas genome editing to non-model organisms, structured around a framework that systematically addresses host-specific barriers, enabling technical solutions, and real-world applications. Key obstacles are first delineated, such as restrictive genetic tools, inefficient DNA repair pathways (including NHEJ-dominance, HDR-deficiency, and polyploidy), and delivery limitations. Subsequently, innovative solutions are explored, including the engineering of Cas variants with expanded PAM flexibility and reduced toxicity, the development of host-adapted delivery systems such as phage-based vectors and conjugative plasmids, and the integration of synthetic biology tools and machine learning for optimization. Alternative, DSB-free modalities-comprising base editing, prime editing, CRISPR-associated transposases (CAST), and recombinase-assisted engineering-are further expanded upon, offering enhanced precision and expanded capabilities for complex genetic modifications. Major findings indicate that these approaches can unlock the potential of non-conventional hosts to address global challenges, such as low-energy biomanufacturing, environmental bioremediation, and carbon capture. It is concluded that bridging the gap between foundational CRISPR research and its real-world applications is imperative. Future efforts should focus on democratizing tools via open-source platforms, advancing delivery systems, establishing ethical governance-with detailed considerations for environmental release, horizontal gene transfer, regional regulatory frameworks, and biosafety in extremophile engineering-and fostering sustainable innovation through synthetic biology integration to fully realize the transformative potential of genome editing in organisms beyond model organisms.
