Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents?
Abstract
:1. Introduction
2. Cellular Mechanisms of HM Bioremediation in Microalgae
3. Genetic and Metabolic Engineering Tools for Microalgal Strain Improvement
4. Genetic Engineering Targets to Improve Microalgal HM Bioremediation Capacity
4.1. Metal Transportation
4.2. Metal Chelation
4.3. Metal Biotransformation
4.4. Oxidative Stress Response Regulation
4.5. Metal Stress Response Regulation
4.6. Cell-Surface Bioengineering
5. Discussion
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genetic and Metabolic Engineering Tools | Type | Specifics | Advantages and Disadvantages |
---|---|---|---|
CRISPR/Cas systems | Gene editing | A single guide RNA (sgRNA) drives the Cas protein to a matching DNA sequence on the host cell genome—which is degraded by Cas protein to create knockout and deletion mutants; and replaced by a new gene to generate insertion and knockdown mutants, with the aid of non-homologous, end-joining machinery | Allows manipulation of any DNA sequences; multiple mutations are possible; comparably more whole genome data are required; possibility of off-target events; large size of Cas makes cell delivery challenging |
ZFNs | Gene editing | An array of site-specific DNA-binding domains that recognizes two sequences flanking a specific site, attached to the endonuclease domain of bacterial FokI restriction enzyme; upon binding, FokI domains dimerize and cleave DNA at the site, which will be repaired by the DNA repair machinery of the cell | Comparably high probability of off-target events; complicated programming is required; limited possible genomic target sites; only single mutations are possible |
TALENs | Gene editing | Tandem arrays with 10 to 30 repeats that bind and recognize extended DNA sequences, attached to the endonuclease domain of bacterial FokI restriction enzyme; upon binding, FokI domains dimerize and cleave DNA at the site, which will be repaired by the DNA repair machinery of the cell | Comparably high probability of off-target events; complicated programming is required; limited possible genomic target sites. large TALENs hard to express or transfect into the cell; only single mutations are possible |
Cre/loxP recombination systems | Gene editing | Two loxP sequences flanking the target gene interact with Cre recombinase for insertion of a new gene fragment or deletion of the one targeted | Simple and efficient; allows multiple genome integration; occasional off-target events are possible; toxicity of Cre for Cre-expressing cells |
Modular cloning systems | Synthetic biology | Design and construction of expression vectors by providing a library of genetic building blocks (e.g., promoters, UTRs, terminators, tags, reporters, antibiotic resistance genes, introns) | Simple and efficient; high flexibility; expression of multiple transgenes possible; developed for limited range of species |
RNAi technology | Gene silencing | Small RNA molecules bind to target mRNAs to form double-stranded RNAs, which are degraded by RNA-induced silencing complex (RISC)—and cause sequence-specific suppression of gene expression, through translational or transcriptional repression | Simple and efficient; occasional off-target effects; produces hypomorphic phenotypes, which do not always mirror the complete loss-of-function that often occurs with genetic mutation; nuclear transcripts—e.g., long non-coding RNAs or lncRNAs, more difficult to effectively target |
Multiomics technologies | Omics | Analysis of whole-cell biochemical information of cell through genomics, transcriptomics, proteomics, metabolomics, interactomics, phenomics, meta-omics, etc. | Provide snapshot of response of cell or whole ecosystem to environmental changes; improves data comparability; time-consuming; high cost; sophisticated, expensive equipment required |
Online databases | Bioinformatics | Integrated online platforms e.g., ChlamyCys, Greenhouse, Diatom EST database, Alga-PrAs, Cyan-Omics, and KEGG | Functional interpretation of genes and elucidation of their underlying biological themes via integrated annotation and expression data; freely available |
Flux balance analysis | Systems | All relevant metabolic information of an organism (e.g., genes, enzymes, reactions) are collected, and analyzed with the aid of a mathematical model within the perspective of the entire network, and applied to make predictions and genome reconstruction | Allows tailor-made design of cell factories aimed at maximum efficiency; time-consuming; still in its infancy |
Illumina microarray technology | Sequencing | Tiny silica microbeads are housed in carefully etched microwells, and coated with multiple copies of an oligonucleotide probe targeting a specific DNA or RNA sequence; upon excitation by laser, binding of each probe to a complementary sequence in sample results in signal that conveys information to the detector | Fast and robust; no prior knowledge of gene sequences required; potent means for gene sequence and expression analysis; high cost |
Approach | Targets |
---|---|
Metal transportation | NRAMP, ZRT, IRT, ZIP, FTR, CTR, CDF, HMA, FPN, Ccc1/VIT1, PTA, AQP, MTP, PMA, V-ATPase, V-PPase, MRP, ATM/HMT, PDR, YSL, CAX, MFS |
Metal chelation | MTs, PCs, GSH, PPK, VTC, PPX, Pro (P5CS), His (HISN3), Cys (HAL2), Ser (SDC1), glycine-betaine, and organic acids |
Metal biotransformation | ChrR, arsC, CrACR2s, MerA/B/P/C/T/F, SMT, CYPs |
Oxidative stress response regulation | Trx, HSPs, carotenoids, SOD, POD, CAT, GPX, GST |
Metal stress response regulation | MTF-1, C2H2, AP2, MYB, bHLH, YABBY, bZIP, SBP, HB, WRKY13, CRR1, ABI5, GATA, CKs (IPT and CKX1), GA, ABA, BRs, JA, ET, SA, miRNAs (miR398, miR319, miR390, miR393, miR171, miR395, miR397, miR408, and miR857) |
Cell-surface bioengineering | MTs, PCs, 6x-His, CXXEE, MerR, GST, NikRm, ModE |
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Ranjbar, S.; Malcata, F.X. Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents? Molecules 2022, 27, 1473. https://doi.org/10.3390/molecules27051473
Ranjbar S, Malcata FX. Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents? Molecules. 2022; 27(5):1473. https://doi.org/10.3390/molecules27051473
Chicago/Turabian StyleRanjbar, Saeed, and Francisco Xavier Malcata. 2022. "Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents?" Molecules 27, no. 5: 1473. https://doi.org/10.3390/molecules27051473
APA StyleRanjbar, S., & Malcata, F. X. (2022). Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents? Molecules, 27(5), 1473. https://doi.org/10.3390/molecules27051473