Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR
Abstract
1. Introduction
2. Genetic Engineering in Bacteria
2.1. Techniques and Tools
Tool Name | Access Link | PAM Sequence | Functions | Reference(s) |
---|---|---|---|---|
ATUM | https://www.atum.bio/eCommerce/cas9/input (accessed on 2 September 2024) | NGG, NAG | Knock-in, knock-out | [18] |
Benchling | https://www.benchling.com/crispr (accessed on 2 September 2024) | Custom PAM | Knock-in, knock-out, knock-down | [19] |
CasOFFinder | http://www.rgenome.net/cas-offinder/ (accessed on 2 September 2024) | NGG, NRG, NNAGAAW, NNNNGMTT, NNGRRT, NNNVRYAC, NNNNRYAC, TTTN, TTTV, NNGTGA, TTN, NNNRRT, KYTV, NGCG, NGA, NGT, NG, TTN, ATTN, DTTN, NAAN, NNNNCC, TYCV, TATV, NNNNGNA, YTTV, NCC, NNNNCNR, NNNNCNAA, NNN, NRN, NGC, TTTR, NTTR, TTCN, NRTH, NNGG, NGGNG, NGGNG, NRTA, NNNA, TTNA, TTNA, NRNH, NGNG, NRCH | Knock-in, knock-out, knock-down | [20] |
CCTop | https://cctop.cos.uni-heidelberg.de:8043/ (accessed on 2 September 2024) | NGG, NRG, NG, NG-NRG, NGA, NGCG, TTTN, TTTV, YTN, TTN, YTTN, NNGRRT, NNNNGATT, NNAGAAW, NAAAAC, NNNNRYAC | Knock-in, knock-out | [21,22] |
CHOPCHOP | https://chopchop.cbu.uib.no/ (accessed on 2 September 2024) | NGG, NRG, NG, NG-NRG, NGA, NGCG, TTTN, TTTV, YTN, TTN, YTTN, NNGRRT, NNNNGATT, NNAGAAW, NAAAAC, NNNNRYAC | Knock-in, knock-out, activation, repression, nanopore enrichment | [23] |
CRISPOR | http://crispor.gi.ucsc.edu/ (accessed on 2 September 2024) | NGG, NNG, NGN, NNGT, NAA, NNG, NNG, NNGRRT, NGK, NNNRRT, NGA, NNNNCC, NGCG, NNAGAA, NGGNG, NNNNGMTT, NNNNACA, NNNNRYAC, TTTV, TTTN, ATTN, NTN, TYCV, TATV, TTTA, TCTA, TCCA, CCCA, GGTT, YTTV, TTYN, NNNNCNAA, NNN, NRN, NYN | Knock-in, knock-out | [24] |
CRISPRdirect | https://crispr.dbcls.jp/ (accessed on 2 September 2024) | NGG, NRG, NNGRRT, NG | Knock-in, knock-out | [25] |
CRISPR-ERA | http://crispr-era.stanford.edu/ (accessed on 2 September 2024) | NGG | Gene editing, gene repression, gene activation | [26] |
CRISPick | https://portals.broadinstitute.org/gppx/crispick/public (accessed on 2 September 2024) | NGG, NNGRR, TTTV | Knock-in, knock-out, knock-down | [27] |
IDT | https://www.idtdna.com/site/order/designtool/index/CRISPR_SEQUENCE (accessed on 2 September 2024) | Custom PAM | Knock-in, knock-out, knock-down | [28] |
Off-Spotter | https://cm.jefferson.edu/Off-Spotter/ (accessed on 2 September 2024) | NGG, NAG, NNNNACA, NNGRRT | Knock-in, knock-out | [29] |
Synthego | https://design.synthego.com/#/ (accessed on 2 September 2024) | Custom PAM | Knock-in, knock-out, knock-down | [30] |
TrueDesign Genome Editor | https://www.thermofisher.com/us/en/home/life-science/genome-editing/invitrogen-truedesign-genome-editor.html (accessed on 2 September 2024) | Custom PAM | Knock out a target gene, add a fluorescent or epitope tag, insert, delete, or replace up to 30 bases, long insertion up to 10 kb, generate an SNP | [31] |
2.2. Overall Applications
Microbial Species | Modifications | Importance | Reference(s) |
---|---|---|---|
Bacteria | |||
Acidithiobacillus ferrooxidans DSM 14882 | Knock-down | Utilized for the bioleaching of metals | [40] |
Bacillus methanolicus MGA3 | Knock-down | Methylotrophic bacteria | [41] |
Bacillus smithii DSM 4216T | Knock-in | Moderate thermophile capable of C5 and C6 sugar metabolism | [42,43] |
Bacillus subtilis ATCC 6051a | Knock-in | Producer of industrial enzymes and valuable low-molecular-weight substances | [44] |
Clostridium acetobutylicum 824BO2 | Knock-in | Isopropanol production | [45] |
Clostridium autoethanogenum CAETHG_0928 | Knock-in | Capable of fermenting CO, CO2, and H2 into biofuel ethanol and 2,3-butanediol | [46] |
Clostridium beijerinckii NRRL B-598 | Knock-in | Production strain for biofuels and biochemical | [47] |
Clostridium cellulolyticum ATCC 35319 | Knock-in | Capable of conversion of lignocellulosic biomass to valuable end products | [48] |
Corynebacterium glutamicum ATCC 13032 | Knock-down | Producer of amino acids | [49] |
Clostridium ljungdahlii ATCC 49587T | Knock-down | Capable of producing ethanol from synthesis gas | [50] |
Clostridium pasteurianum CH4 | Knock-in | Capable of converting waste glycerol to butanol | [51] |
Clostridium thermocellum DSM 1313 | Knock-out | Thermophilic bacteria | [52] |
Clostridium tyrobutyricum ATCC 25755 | Knock-out | Butanol production | [53] |
Corynebacterium glutamicum ATCC 13032 | Knock-down | Producer of amino acids | [49] |
Cupriavidus metallidurans CH34 | Knock-in | Facultative chemolithoautotroph | [54] |
Cupriavidus necator H16 | Knock-in | Facultative chemolithoautotroph | [55] |
Escherichia coli BW25113 | Knock-in, Knock-down, Knock-out | Programmed antimicrobial, recombination, multiplex recombination, CRISPRi, multiplexed CRISPRi, gene circuit, and RNA targeting | [56,57] |
Halomonas bluephagenesis TD01 | Knock-out | 3-Hydroxyvalerate production | [58] |
Hungateiclostridium thermocellum DSM 1313 | Knock-down | Thermophilic bacterium | [59] |
Lactobacillus reuteri DSM 17938 | Knock-in | Probiotic strain and producer of biotherapeutics | [60] |
Methylobacterium extorquens AM1 | Knock-down | Methylotrophic bacterium | [61] |
Pseudomonas putida KT2440 | Knock-down | Exhibits solvent tolerance and highly versatile metabolism | [62] |
Rhodobacter capsulatus DSM 1710 | Knock-down | Facultative photo- and chemolithoautotroph species | [63] |
Rhodococcus ruber THY | Knock-out | Acrylamide production | [64] |
Streptococcus thermophilus Z57 | Knock-in | Probiotic and industrial fermentation strains | [65] |
Streptomyces albus J1074 | Knock-in | Producer of heterologous secondary metabolites | [66] |
Streptomyces coelicolor A3(2) | Knock-in | Source of pharmacologically active and industrially relevant secondary metabolites | [66,67] |
Synechococcus elongatus PCC 7942 | Knock-down | Squalene production | [68] |
Synechococcus sp. PCC 7002 | Knock-down | Lactate production | [69] |
Tatumella citrea CICC 10802 | Knock-in | Producer of vitamin C precursor (2-keto-D-gluconic acid) | [70] |
Vibrio natriegens DSMZ 759 | Knock-down | Fast-growing bacteria | [71] |
Fungi | |||
Aspergillus aculeatus BCC199 | Knock-in | Source of and producer of enzymes | [72] |
Agaricus bisporus var. bisporus | Knock-in | Anti-browning mushroom with extended shelf life and enhanced resistance to blemishes | [73] |
Aspergillus fumigatus AF293 | Knock-in | For studying mechanisms of azole resistance | [74] |
Aspergillus niger AGB | Knock-in | Enhances the expression and secretion of α-galactosidase; improves protein production; facilitates heterologous laccase expression; and boosts glucoamylase secretion | [75,76,77,78] |
Aspergillus oryzae RIB40 | Knock-in | Enhances the expression and secretion of α-galactosidase; improves protein production; facilitates heterologous laccase expression; and boosts glucoamylase secretion | [79,80] |
Candida albicans TL3 | Knock-in | Common production strain, capable of phenol and formaldehyde catabolism | [81,82,83] |
Fusarium graminearum PH-1 | Knock-out | Functional study of 5-oxoprolinase | [84] |
Fusarium fujikuroi IMI 58289 | Knock-out | GA4/GA7 mixtures production | [85] |
Kluyveromyces lactis GG799 | Knock-in | Common production strain | [86] |
Kluyveromyces marxianus DSM 5422 | Knock-out | Ethyl acetate production | [87] |
Magnaporthe oryzae GUY11 | Knock-out | Study of endolysosomal trafficking mechanisms in rice blast | [88] |
Monascus purpureus KL-001 | Knock-out | Monascus red pigment production | [89] |
Myceliophthora thermophile ATCC 42464 | Knock-in | Thermophilic strain and producer of cellulases | [90] |
Neurospora crassa F5 | Knock-in | Hyper-production of cellulases | [91,92] |
Penicillium chrysogenum NRRL 1951 | Knock-in | Producer of β-lactam antibiotics | [93] |
Pichia pastoris X-33 | Knock-in | Common production strain | [94] |
Trichoderma reesei RUT-C30 | Knock-in | Enhancement of cellulase production | [95] |
Saccharomyces cerevisiae S288C | Knock-in, Knock-down | Common production strain | [96,97,98] |
Sclerotinia sclerotiorum 1980 UF-70 | Knock-in | Introduction of large sequence inserts | [99] |
Synechococcus elongatus PCC 7942 | Knock-in, Knock-out | Succinate production | |
Yarrowia lipolytica PO1f | Knock-in | Lycopene production | [100] |
Oomycetes | |||
Phytophthora capsici PcORP1 | Knock-out | Conferring resistance to oxathiapiprolin | [101] |
Phytophthora infestans JH19 | Knock-out | Increase in transformation efficiency; a modified genetic transformation and genome editing system | [2] |
Phytophthora sojae P6497 | Knock-out | Efficient disruption and replacement of an effector gene. | [102] |
Plasmopara viticola BS5 | Knock-out | Increase in transformation efficiency; a modified genetic transformation and genome editing system | [2] |
Ustilago maydis 521 | Knock-out | Natural producer of valuable biochemicals; causative agent of corn smut | [103,104] |
Yarrowia lipolytica W29 | Knock-in, Knock-out | Natural producer of valuable biochemicals | [100,105] |
2.3. Challenges and Future Directions
3. Genetic Engineering in Fungi
3.1. Transformation Techniques
3.2. CRISPR-Cas9
3.3. Applications
3.4. Challenges and Innovations
4. Genetic Engineering in Oomycetes
4.1. Challenges in Oomycete Genetics
4.2. Recent Advances
4.3. Applications
4.4. Future Prospects
5. Comparative Analysis
5.1. Comparison of Techniques
Organism | Methodologies | Applications | Efficiency | Challenges | Advancements |
---|---|---|---|---|---|
Bacteria | CRISPR-Cas9, CRISPR-Cas12a, base editing, prime editing, CRISPR nickases [162] | Development of crops, gene therapies for diseases like cancer, pathogen detection | Up to 100% success rates in gene editing with optimized systems in some bacterial strains like E. coli [163] | Off-target effects, lethality due to DSBs in certain strains, optimization of delivery methods [107] | Newly engineered CRISPR tools enhancing precision, integration into synthetic biology and diagnostics [164] |
Fungi | CRISPR-Cas9 and CRISPR-Cas12 systems for genetic engineering [72] | Used in research for molecular breeding, improving secondary metabolite production, and developing new fungal strains [124] | Editing efficiencies reported vary, with some studies showing rates as high as 100% for specific targets [72] | Challenges include off-target effects, low transformation efficiency, and optimization of sgRNA design [124] | Recent advancements include the use of CRISPR-Cas12 for enhanced control and efficiency in gene editing in fungi [124] |
Oomycetes | CRISPR-Cas9, Cas12a editing, ribonucleoprotein delivery, complementation [138] | Enhancement of disease resistance in crops and genomic interventions against oomycete pathogens [1] | Editing efficiencies are high but variable depending on specific protocols and methodologies used [1] | Challenges include off-target effects and inefficient gene delivery systems [138] | Developments in ribonucleoprotein delivery and specific editing techniques for oomycetes [138] |
5.2. Case Studies
6. Ethical and Regulatory Considerations
6.1. Safety Concerns
6.2. Regulatory Frameworks
7. Conclusions and Future Directions
Author Contributions
Funding
Conflicts of Interest
References
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Yang, P.; Condrich, A.; Lu, L.; Scranton, S.; Hebner, C.; Sheykhhasan, M.; Ali, M.A. Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR. DNA 2024, 4, 427-454. https://doi.org/10.3390/dna4040030
Yang P, Condrich A, Lu L, Scranton S, Hebner C, Sheykhhasan M, Ali MA. Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR. DNA. 2024; 4(4):427-454. https://doi.org/10.3390/dna4040030
Chicago/Turabian StyleYang, Piao, Abraham Condrich, Ling Lu, Sean Scranton, Camina Hebner, Mohsen Sheykhhasan, and Muhammad Azam Ali. 2024. "Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR" DNA 4, no. 4: 427-454. https://doi.org/10.3390/dna4040030
APA StyleYang, P., Condrich, A., Lu, L., Scranton, S., Hebner, C., Sheykhhasan, M., & Ali, M. A. (2024). Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR. DNA, 4(4), 427-454. https://doi.org/10.3390/dna4040030