Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens
Abstract
:1. Introduction
2. Different CRISPR-Based Tools
3. CRISPR-Based Genome Editing of Plants for Disease Resistance against Pathogens
3.1. Disease Resistance against Bacteria
3.2. Disease Resistance against Fungi
3.3. Diseases Resistance against Oomycetes
3.4. Disease Resistance against Plant Viruses
4. CRISPR-Based Crop Breeding
5. Limitations of CRISPR-Based Tools for Plant Pathogen Resistance
6. Future Research Directions
7. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
- Bahadur Kc, K.; Dias, G.M.; Veeramani, A.; Swanton, C.J.; Fraser, D.; Steinke, D.; Lee, E.; Wittman, H.; Farber, J.M.; Dunfield, K.; et al. When too much isn’t enough: Does current food production meet global nutritional needs? PLoS ONE 2018, 13, e0205683. [Google Scholar] [CrossRef]
- Kleyn, F.J.; Ciacciariello, M. Future demands of the poultry industry: Will we meet our commitments sustainably in developed and develo** economies? Worlds Poult. Sci. J. 2021, 77, 267–278. [Google Scholar] [CrossRef]
- Akoijam, N.; Joshi, S.R.; Akoijam, N. Conservation Metagenomics: Understanding Microbiomes for Biodiversity Sustenance and Conservation. In Molecular Genetics and Genomics Tools in Biodiversity Conservation; Springer: Singapore, 2022; pp. 31–61. [Google Scholar] [CrossRef]
- Lata, S.; Bhardwaj, S.; Garg, R. Nanomaterials for sensing and biosensing: Applications in agri-food diagnostics. Int. J. Environ. Anal. Chem. 2022, 1–12. [Google Scholar] [CrossRef]
- Dong, O.X.; Ronald, P.C. Genetic engineering for disease resistance in plants: Recent progress and future perspectives. Plant Physiol. 2019, 180, 26–38. [Google Scholar] [CrossRef]
- Gupta, R.; Pizarro, L.; Leibman-Markus, M.; Marash, I.; Bar, M. Cytokinin response induces immunity and fungal pathogen resistance, and modulates trafficking of the PRR LeEIX2 in tomato. Mol. Plant Pathol. 2020, 21, 1287–1306. [Google Scholar] [CrossRef]
- Sulima, A.S.; Zhukov, V.A. War and Peas: Molecular Bases of Resistance to Powdery Mildew in Pea (Pisum sativum L.) and Other Legumes. Plants 2022, 11, 339. [Google Scholar] [CrossRef]
- Goode, K.; Mitchum, M.G. Pattern-triggered immunity against root-knot nematode infection: A minireview. Physiol. Plant. 2022, 174, e13680. [Google Scholar] [CrossRef]
- Min, C.W.; Jang, J.W.; Lee, G.H.; Gupta, R.; Yoon, J.; Park, H.J.; Cho, H.S.; Park, S.R.; Kwon, S.W.; Cho, L.H.; et al. TMT-based quantitative membrane proteomics identified PRRs potentially involved in the perception of MSP1 in rice leaves. J. Proteom. 2022, 267, 104687. [Google Scholar] [CrossRef]
- Ke, X.; Wang, J.; Xu, X.; Guo, Y.; Zuo, Y.; Yin, L. Histological and molecular responses of Vigna angularis to Uromyces vignae infection. BMC Plant Biol. 2022, 22, 489. [Google Scholar] [CrossRef]
- Yang, C.; Dolatabadian, A.; Fernando, W.G.D. The wonderful world of intrinsic and intricate immunity responses in plants against pathogens. Can. J. Plant Pathol. 2021, 44, 1–20. [Google Scholar] [CrossRef]
- Waheed, A.; Haxim, Y.; Islam, W.; Kahar, G.; Liu, X.; Zhang, D. Role of pathogen’s effectors in understanding host-pathogen interaction. Mol. Cell Res. 2022, 1869, 119347. [Google Scholar] [CrossRef]
- Chen, D.; Hao, F.; Mu, H.; Ahsan, N.; Thelen, J.J.; Stacey, G. S-acylation of P2K1 mediates extracellular ATP-induced immune signaling in Arabidopsis. Nat. Commun. 2021, 12, 2750. [Google Scholar] [CrossRef]
- Trivedi, P.; Batista, B.D.; Bazany, K.E.; Singh, B.K. Plant–microbiome interactions under a changing world: Responses, consequences and perspectives. New Phytol. 2022, 234, 1951–1959. [Google Scholar] [CrossRef]
- Koseoglou, E.; van der Wolf, J.M.; Visser, R.G.F.; Bai, Y. Susceptibility reversed: Modified plant susceptibility genes for resistance to bacteria. Trends Plant Sci. 2022, 27, 69–79. [Google Scholar] [CrossRef]
- Laflamme, B.; Dillon, M.M.; Martel, A.; Almeida, R.N.D.; Desveaux, D.; Guttman, D.S. The pan-genome effector-triggered immunity landscape of a host-pathogen interaction. Science 2020, 367, 763–768. [Google Scholar] [CrossRef]
- Gaj, T.; Sirk, S.J.; Shui, S.; Liu, J. Genome-Editing Technologies: Principles and Applications. Cold Spring Harb. Perspect. Biol. 2016, 8, 023754. [Google Scholar] [CrossRef]
- Wada, N.; Ueta, R.; Osakabe, Y.; Osakabe, K. Precision genome editing in plants: State-of-the-art in CRISPR/Cas9-based genome engineering. BMC Plant Biol. 2020, 20, 1–12. [Google Scholar] [CrossRef]
- Huang, J.; Zhou, Y.; Li, J.; Lu, A.; Liang, C. CRISPR/Cas systems: Delivery and application in gene therapy. Front. Bioeng. Biotechnol. 2022, 10, 2168. [Google Scholar] [CrossRef]
- Li, J.; Wang, Y.; Wang, B.; Lou, J.; Ni, P.; **, Y.; Chen, S.; Duan, G.; Zhang, R. Application of CRISPR/Cas Systems in the Nucleic Acid Detection of Infectious Diseases. Diagnostics 2022, 12, 2455. [Google Scholar] [CrossRef]
- Lee, H.; Sashital, D.G. Creating memories: Molecular mechanisms of CRISPR adaptation. Trends Biochem. Sci. 2022, 47, 464–476. [Google Scholar] [CrossRef]
- Saber Sichani, A.; Ranjbar, M.; Baneshi, M.; Torabi Zadeh, F.; Fallahi, J. A Review on Advanced CRISPR-Based Genome-Editing Tools: Base Editing and Prime Editing. Mol. Biotechnol. 2022, 1–12. [Google Scholar] [CrossRef] [PubMed]
- Otoupal, P.B.; Cress, B.F.; Doudna, J.A.; Schoeniger, J.S. CRISPR-RNAa: Targeted activation of translation using dCas13 fusions to translation initiation factors. Nucleic Acids Res. 2022, 50, 8986–8998. [Google Scholar] [CrossRef] [PubMed]
- Karmakar, S.; Das, P.; Panda, D.; ** and pathogen diagnostics. Plant Biotechnol. J. 2022, 20, 2418–2429. [Google Scholar] [CrossRef]
- Mohammad, N.; Katkam, S.S.; Wei, Q. Recent Advances in CRISPR-Based Biosensors for Point-of-Care Pathogen Detection. Cris. J. 2022, 5, 500–516. [Google Scholar] [CrossRef]
- Lim, C.K.W.; McCallister, T.X.; Saporito-Magriña, C.; McPheron, G.D.; Krishnan, R.; Zeballos, C.M.A.; Powell, J.E.; Clark, L.V.; Perez-Pinera, P.; Gaj, T. CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes. Mol. Ther. 2022, 30, 3619–3631. [Google Scholar] [CrossRef]
- Roy, R.K.; Debashree, I.; Srivastava, S.; Rishi, N.; Srivastava, A. CRISPR/Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies. Curr. Bioinform. 2021, 17, 119–132. [Google Scholar] [CrossRef]
- Secgin, Z.; Uluisik, S.; Yıldırım, K.; Abdulla, M.F.; Mostafa, K.; Kavas, M. Genome-Wide Identification of the Aconitase Gene Family in Tomato (Solanum lycopersicum) and CRISPR-Based Functional Characterization of SlACO2 on Male-Sterility. Int. J. Mol. Sci. 2022, 23, 13963. [Google Scholar] [CrossRef]
- Editors, A.; Zhang, B.; Alok, A.; Awasthi, P.; Min, T.; Hwarari, D.; Li, D.A.; Movahedi, A.; Yang, L. CRISPR-Based Genome Editing and Its Applications in Woody Plants. Int. J. Mol. Sci. 2022, 23, 10175. [Google Scholar] [CrossRef]
- Roueinfar, M.; Templeton, H.N.; Sheng, J.A.; Hong, K.L. An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology. Molecules 2022, 27, 1114. [Google Scholar] [CrossRef]
- Kantor, A.; McClements, M.E.; Maclaren, R.E. CRISPR-Cas9 DNA Base-Editing and Prime-Editing. Int. J. Mol. Sci. 2020, 21, 6240. [Google Scholar] [CrossRef]
- Bashor, C.J.; Hilton, I.B.; Bandukwala, H.; Smith, D.M.; Veiseh, O. Engineering the next generation of cell-based therapeutics. Nat. Rev. Drug Discov. 2022, 21, 655–675. [Google Scholar] [CrossRef]
- Weeks, D.P.; Spalding, M.H.; Yang, B. Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol. J. 2016, 14, 483–495. [Google Scholar] [CrossRef]
- Faber, N.R.; McFarlane, G.R.; Gaynor, R.C.; Pocrnic, I.; Whitelaw, C.B.A.; Gorjanc, G. Novel combination of CRISPR-based gene drives eliminates resistance and localises spread. Sci. Rep. 2021, 11, 3791. [Google Scholar] [CrossRef]
- Gurr, G.M.; Johnson, A.C.; Ash, G.J.; Wilson, B.A.L.; Ero, M.M.; Pilotti, C.A.; Dewhurst, C.F.; You, M.S. Coconut lethal yellowing diseases: A phytoplasma threat to palms of global economic and social significance. Front. Plant Sci. 2016, 7, 1521. [Google Scholar] [CrossRef]
- Touzdjian Pinheiro Kohlrausch Távora, F.; de Assis dos Santos Diniz, F.; de Moraes Rêgo-Machado, C.; Chagas Freitas, N.; Barbosa Monteiro Arraes, F.; Chumbinho de Andrade, E.; Furtado, L.L.; Osiro, K.O.; Lima de Sousa, N.; Cardoso, T.B.; et al. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front. Bioeng. Biotechnol. 2022, 10, 28. [Google Scholar] [CrossRef]
Sr. No. | Cas Nucleases | Targeted Plants | PAM Sequences 5′-3′ | Organisms | References |
---|---|---|---|---|---|
1 | SpRY | Rice | NGD and NAN | Streptococcus pyogenes | [41] |
2 | SpG | Rice | NGD | Streptococcus pyogenes | [41] |
3 | SpCas9 | Many plants | NGG | Streptococcus pyogenes | [47] |
4 | Cas3d/Cas5d/Cas6d/Cas7d/Cas10d | Rice and Tomato | GTH | Microcystis aeruginosa | [48] |
5 | NmeCas9 | Rice | NNNNGATT | Neisseria meningitidis | [49] |
6 | CjCas9 | Various plants | NNNNRYAC | Campylobacter jejuni | [50] |
7 | Cas14 | - | T-rich PAM sequences, eg. TTTA for dsDNA cleavage, no PAM sequence requirement for ssDNA | Uncultivated archea | [51] |
8 | Cas3 | - | No PAM sequence needed | in silico analysis of various prokaryotic genomes | [52] |
9 | ScCas9 | Rice | NNG | Streptococcus canis | [44] |
10 | LbCpf1 (Cas12a) | Rice and Arabidopsis | TTTN (TTTV) (V = A/G/C) | Lachnospiraceae bacterium ND2006 | [53] |
11 | SaCas9 | Arabidopsis, Rice, and Tobacco | NNGRRT | Staphylococcus aureus | [54] |
12 | St1Cas9 | Arabidopsis | NNAGAAW | Streptococcus thermophiles | [55] |
13 | FnCas12a | Rice and Tobacco | TTN | Francisella novicida | [56] |
14 | AsCas12a | Rice | TTTN | Acidaminococcus sp. BV3L6 | [57] |
15 | AacCas12b | Cotton | TTN | Alicyclobacillus acidiphilus | [58] |
16 | BhCas12b v4 | Arabidopsis | ATTN, TTTN, and GTTN | Bacillus hisashii | [59] |
17 | AsCpf1 (Cas12a) | Cotton | TTTV | Acidaminococcus sp. | [60] |
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Ijaz, M.; Khan, F.; Zaki, H.E.M.; Khan, M.M.; Radwan, K.S.A.; Jiang, Y.; Qian, J.; Ahmed, T.; Shahid, M.S.; Luo, J.; et al. Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens. Plants 2023, 12, 1911. https://doi.org/10.3390/plants12091911
Ijaz M, Khan F, Zaki HEM, Khan MM, Radwan KSA, Jiang Y, Qian J, Ahmed T, Shahid MS, Luo J, et al. Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens. Plants. 2023; 12(9):1911. https://doi.org/10.3390/plants12091911
Chicago/Turabian StyleIjaz, Munazza, Fahad Khan, Haitham E. M. Zaki, Muhammad Munem Khan, Khlode S. A. Radwan, Yugen Jiang, Jiahui Qian, Temoor Ahmed, Muhammad Shafiq Shahid, **yan Luo, and et al. 2023. "Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens" Plants 12, no. 9: 1911. https://doi.org/10.3390/plants12091911