Engineering PGPMOs through Gene Editing and Systems Biology: A Solution for Phytoremediation?

In light of extensive urbanization and deforestation, toxic wastes are being released into the atmosphere, causing increased air and soil pollution. Conventional methods of soil remediation are time consuming and labor and cost intensive, rendering them uneconomical to maintain sustainable agriculture. One solution is to use natural resources like plants and microbes for phytoremediation. A thorough systemic knowledge of plant-microbe interactions will allow the use of gene editing and gene manipulation techniques to increase the efficiency of plants in phytoremediation. This Opinion article focuses on gene editing techniques used in plants and microbes for phytoremediation and also emphasizes their effectiveness, advancement, and future implications for sustainable and environmentally friendly agriculture.

[1]  M. Afzal,et al.  Bacterial endophytes enhance phytostabilization in soils contaminated with uranium and lead , 2017, International journal of phytoremediation.

[2]  Sara R. Wilkinson,et al.  A pseudoknot in the 3' non-core region of the glmS ribozyme enhances self-cleavage activity. , 2005, RNA.

[3]  M. Inouye,et al.  Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems , 2016, BMC Genomics.

[4]  G. Church,et al.  Cas9 as a versatile tool for engineering biology , 2013, Nature Methods.

[5]  Zejian Guo,et al.  The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance , 2012, Journal of experimental botany.

[6]  Yanpeng Wang,et al.  Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew , 2014, Nature Biotechnology.

[7]  Thomas Macek,et al.  Polychlorinated Biphenyl Rhizoremediation by Pseudomonas fluorescens F113 Derivatives, Using a Sinorhizobium meliloti nod System To Drive bph Gene Expression , 2005, Applied and Environmental Microbiology.

[8]  D. Lelie,et al.  Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants , 2004, Nature Biotechnology.

[9]  Peel Mc,et al.  Selection of clc, cba, and fcb chlorobenzoate-catabolic genotypes from groundwater and surface waters adjacent to the Hyde park, Niagara Falls, chemical landfill. , 1999 .

[10]  Z. Vryzas The Plant as Metaorganism and Research on Next-Generation Systemic Pesticides – Prospects and Challenges , 2016, Front. Microbiol..

[11]  A. Ferré-D’Amaré,et al.  Ribozymes and riboswitches: modulation of RNA function by small molecules , 2009, Biochemistry.

[12]  B R Glick,et al.  Genetic manipulation of plant growth-promoting bacteria to enhance biocontrol of phytopathogens. , 1997, Biotechnology advances.

[13]  A. Goldman,et al.  Substrate Specificity of and Product Formation by Muconate Cycloisomerases: an Analysis of Wild-Type Enzymes and Engineered Variants , 1998, Applied and Environmental Microbiology.

[14]  Xiangzheng Deng,et al.  Laccases: Production, Expression Regulation, and Applications in Pharmaceutical Biodegradation , 2017, Front. Microbiol..

[15]  M. Daly,et al.  Hg(II) sequestration and protection by the MerR metal-binding domain (MBD). , 2006, Microbiology.

[16]  Peter Millard,et al.  Unravelling rhizosphere-microbial interactions: opportunities and limitations. , 2004, Trends in microbiology.

[17]  B. Glick,et al.  Prevalence of 1-aminocyclopropane-1-carboxylate deaminase in Rhizobium spp. , 2004, Antonie van Leeuwenhoek.

[18]  Oscar N. Ruiz,et al.  Genetic engineering to enhance mercury phytoremediation. , 2009, Current opinion in biotechnology.

[19]  T. Macek,et al.  Native Phytoremediation Potential of Urtica dioica for Removal of PCBs and Heavy Metals Can Be Improved by Genetic Manipulations Using Constitutive CaMV 35S Promoter , 2016, PloS one.

[20]  Bruce E Pivetz,et al.  Ground Water Issue: Phytoremediation of Contaminated Soil and Ground Water at Hazardous Waste Sites , 2001 .

[21]  D. Kelly,et al.  Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us? , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[22]  U. Mueller,et al.  Engineering Microbiomes to Improve Plant and Animal Health. , 2015, Trends in microbiology.

[23]  Regina A. O'Neil,et al.  Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments , 2009, The ISME Journal.

[24]  Kareem A. Mosa,et al.  Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids , 2016, Front. Plant Sci..

[25]  Nandita Singh,et al.  Transgenic plants for enhanced biodegradation and phytoremediation of organic xenobiotics. , 2009, Biotechnology advances.

[26]  Norikazu Ichikawa,et al.  Rhizobitoxine Production by Bradyrhizobium elkanii Enhances Nodulation and Competitiveness onMacroptilium atropurpureum , 2000, Applied and Environmental Microbiology.

[27]  H. Blaschek,et al.  Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable "Clean" Mutant Selection in Clostridium beijerinckii as an Example. , 2016, ACS synthetic biology.

[28]  Christopher Moraes,et al.  Next generation tools to accelerate the synthetic biology process. , 2016, Integrative biology : quantitative biosciences from nano to macro.

[29]  K. Ljung,et al.  Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport-Dependent Auxin Distribution[W] , 2007, The Plant Cell Online.

[30]  E. Cahoon,et al.  Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing , 2017, Plant biotechnology journal.

[31]  Alex Toftgaard Nielsen,et al.  CRMAGE: CRISPR Optimized MAGE Recombineering , 2016, Scientific Reports.

[32]  P. Adams,et al.  Analytics for Metabolic Engineering , 2015, Front. Bioeng. Biotechnol..

[33]  S. Park,et al.  Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato , 2016, Nature Genetics.

[34]  Vincent J. Henry,et al.  OMICtools: an informative directory for multi-omic data analysis , 2014, Database J. Biol. Databases Curation.

[35]  X. Ji,et al.  Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants , 2015, Nature Plants.

[36]  G. Church,et al.  CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria , 2017, Nature.

[37]  Joshua K Young,et al.  Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA[OPEN] , 2015, Plant Physiology.

[38]  P. Rushton,et al.  Comparative Metabolome Profile between Tobacco and Soybean Grown under Water-Stressed Conditions , 2017, BioMed research international.

[39]  R. Naidu,et al.  Bioremediation approaches for organic pollutants: a critical perspective. , 2011, Environment international.

[40]  M. Mahfouz,et al.  Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance , 2016, Front. Plant Sci..

[41]  Jens Nielsen,et al.  The Impact of Systems Biology on Bioprocessing. , 2017, Trends in biotechnology.

[42]  H. Basri,et al.  A Review on Heavy Metals (As, Pb, and Hg) Uptake by Plants through Phytoremediation , 2011 .

[43]  E. Fasani,et al.  The potential of genetic engineering of plants for the remediation of soils contaminated with heavy metals. , 2018, Plant, cell & environment.

[44]  M. Rafatullah,et al.  Isolation and characterization of arsenic resistant bacteria from wastewater , 2015, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology].

[45]  Pratyoosh Shukla,et al.  Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions , 2016, Front. Plant Sci..

[46]  Yoshikazu Tanaka,et al.  Enhancement of Phosphate Absorption by Garden Plants by Genetic Engineering: A New Tool for Phytoremediation , 2013, BioMed research international.

[47]  Wenzhong Xu,et al.  Engineering arsenic tolerance and hyperaccumulation in plants for phytoremediation by a PvACR3 transgenic approach. , 2013, Environmental science & technology.

[48]  David Ando,et al.  Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering. , 2018, Methods in molecular biology.

[49]  Samiksha Singh,et al.  Heavy Metal Tolerance in Plants: Role of Transcriptomics, Proteomics, Metabolomics, and Ionomics , 2016, Front. Plant Sci..

[50]  M. Afzal,et al.  Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils. , 2013, Chemosphere.

[51]  N. Weyens,et al.  Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism , 2016, Front. Microbiol..

[52]  A. Mukherjee,et al.  Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp. , 2016, PloS one.

[53]  Xuemei Xu,et al.  Genome-Wide Analysis and Heavy Metal-Induced Expression Profiling of the HMA Gene Family in Populus trichocarpa , 2015, Front. Plant Sci..

[54]  Jin-Soo Kim,et al.  Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases , 2014, Genome research.

[55]  J. R. van der Meer,et al.  Evolution of a Pathway for Chlorobenzene Metabolism Leads to Natural Attenuation in Contaminated Groundwater , 1998, Applied and Environmental Microbiology.

[56]  Pratyoosh Shukla,et al.  Gene editing for cell engineering: trends and applications , 2017, Critical reviews in biotechnology.

[57]  Keasling,et al.  Recombinant DNA techniques for bioremediation and environmentally-friendly synthesis , 1998, Current opinion in biotechnology.

[58]  S. Banwart,et al.  Save our soils , 2011, Nature.

[59]  Kibong Kim,et al.  Destruction and detection of chemical warfare agents. , 2011, Chemical reviews.

[60]  K. Shinozaki,et al.  Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants , 2016, Scientific Reports.

[61]  Won-Yong Song,et al.  Engineering tolerance and accumulation of lead and cadmium in transgenic plants , 2003, Nature Biotechnology.

[62]  B. Singh,et al.  Harnessing plant-microbe interactions for enhancing farm productivity , 2014, Bioengineered.

[63]  J. Keasling,et al.  Uranyl Precipitation by Pseudomonas aeruginosa via Controlled Polyphosphate Metabolism , 2004, Applied and Environmental Microbiology.

[64]  T. Macek,et al.  Genetically modified plants in phytoremediation of heavy metal and metalloid soil and sediment pollution. , 2009, Biotechnology advances.

[65]  A. Sanangelantoni,et al.  Combined application of Triton X-100 and Sinorhizobium sp. Pb002 inoculum for the improvement of lead phytoextraction by Brassica juncea in EDTA amended soil. , 2006, Chemosphere.

[66]  L. Alvarez-Cohen,et al.  Kinetics of 1,4-dioxane biodegradation by monooxygenase-expressing bacteria. , 2006, Environmental science & technology.

[67]  Xia Yang,et al.  Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration , 2016, BMC Genomics.

[68]  T. Chai,et al.  Cd-induced changes in leaf proteome of the hyperaccumulator plant Phytolacca americana. , 2011, Chemosphere.

[69]  Yaoguang Liu,et al.  Enhanced Rice Blast Resistance by CRISPR/Cas9-Targeted Mutagenesis of the ERF Transcription Factor Gene OsERF922 , 2016, PloS one.

[70]  Harkesh B. Singh,et al.  Plant-microbe interactions: novel applications for exploitation in multipurpose remediation technologies. , 2012, Trends in biotechnology.

[71]  D. Schofield,et al.  Generation of a mutagenized organophosphorus hydrolase for the biodegradation of the organophosphate pesticides malathion and demeton‐S , 2010, Journal of applied microbiology.

[72]  Jianmin Zhao,et al.  An Integrated Proteomic and Metabolomic Study on the Chronic Effects of Mercury in Suaeda salsa under an Environmentally Relevant Salinity , 2013, PloS one.

[73]  M. Spalding,et al.  High-efficiency TALEN-based gene editing produces disease-resistant rice , 2012, Nature Biotechnology.

[74]  S. Siripornadulsil,et al.  Changes in the proteome of the cadmium-tolerant bacteria Cupriavidus taiwanensis KKU2500-3 in response to cadmium toxicity. , 2014, Canadian journal of microbiology.

[75]  Ana Segura,et al.  New family of biosensors for monitoring BTX in aquatic and edaphic environments , 2016, Microbial biotechnology.

[76]  Shana Topp,et al.  Emerging applications of riboswitches in chemical biology. , 2010, ACS chemical biology.

[77]  D. Bouchez,et al.  Expression of a truncated tobacco NtCBP4 channel in transgenic plants and disruption of the homologous Arabidopsis CNGC1 gene confer Pb2+ tolerance. , 2000, The Plant journal : for cell and molecular biology.

[78]  Beatrix Suess,et al.  Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators , 2012, FEBS letters.

[79]  H. Nguyen,et al.  Integrating omic approaches for abiotic stress tolerance in soybean , 2014, Front. Plant Sci..

[80]  K. Pagilla,et al.  Recent applications of Vitreoscilla hemoglobin technology in bioproduct synthesis and bioremediation , 2015, Applied Microbiology and Biotechnology.

[81]  A. Steinbüchel,et al.  Biodegradation of the Organic Disulfide 4,4′-Dithiodibutyric Acid by Rhodococcus spp , 2015, Applied and Environmental Microbiology.

[82]  R. Donn,et al.  Network analysis: a new approach to study endocrine disorders. , 2013, Journal of molecular endocrinology.

[83]  J. Schnoor,et al.  Phytoremediation of polychlorinated biphenyls: new trends and promises. , 2010, Environmental science & technology.

[84]  R. Breaker,et al.  Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. , 2015, Molecular cell.

[85]  T. Wood,et al.  Toluene 3-Monooxygenase of Ralstonia pickettii PKO1 Is a para-Hydroxylating Enzyme , 2004, Journal of bacteriology.