Recent Advances in Genetic Engineering Tools for Metabolic Engineering

Metabolic engineering has evolved exponentially due to rapid progress in the development of omics (proteomics, lipidomics and glycomics) technology and synthetic biology toolsets. Particularly, omics technologies, synthetic biology and metabolic engineering are interdependent in terms of principles of technology and their biological applications. In this article, we showcase synthetic biology toolsets currently used for the metabolic engineering of microbes and focus on some of the recent advances in the field. Specifically we have elaborated on recent progress in metabolic engineering, the associated synthetic biology toolsets, microbiome metabolic engineering (MME) and the potential industrial metabolic engineering applications. As a case study for the industrial application of metabolic engineering, we have reviewed the use of synthetic biology toolsets to bioengineer microbes and re-engineer their metabolic pathways for customised industrial applications. Some of the examples included in this article are as follows: (a) metabolic engineering of cyanobacteria, (b) metabolic engineering of Bacillus subtilis and (c) metabolic engineering in synthetic yeast for industrial applications. As a future perspective, this chapter presents a case for the broader use of synthetic biology toolsets across metabolic engineering applications.

[1]  R. Symons,et al.  Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Patrice D Cani.  Human gut microbiome: hopes, threats and promises , 2018, Gut.

[3]  Harris H. Wang,et al.  Manipulating Bacterial Communities by in situ Microbiome Engineering. , 2016, Trends in genetics : TIG.

[4]  G. F. Joyce,et al.  Directed evolution of an RNA enzyme. , 1992, Science.

[5]  Ron Milo,et al.  Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans , 2016, Cell.

[6]  Bangmao Wang,et al.  Systematic Review: Adverse Events of Fecal Microbiota Transplantation , 2016, PloS one.

[7]  Huimin Zhao,et al.  CRISPR-Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters , 2017, Nature chemical biology.

[8]  G. Hausner,et al.  Homing endonucleases: DNA scissors on a mission. , 2012, Genome.

[9]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[10]  E. Kuijper,et al.  Clinical Application and Potential of Fecal Microbiota Transplantation. , 2019, Annual review of medicine.

[11]  Gregory Stephanopoulos,et al.  Engineering microbial cell factories for biosynthesis of isoprenoid molecules: beyond lycopene. , 2007, Trends in biotechnology.

[12]  P. Salamon,et al.  Bacteriophage adhering to mucus provide a non–host-derived immunity , 2013, Proceedings of the National Academy of Sciences.

[13]  Gregory Stephanopoulos,et al.  Synthetic biology and metabolic engineering. , 2012, ACS synthetic biology.

[14]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.

[15]  James T. Morton,et al.  Impacts of the Human Gut Microbiome on Therapeutics. , 2018, Annual review of pharmacology and toxicology.

[16]  Mario R. Capecchi,et al.  Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes , 1988, Nature.

[17]  Arun S. Seetharam,et al.  Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering. , 2017, ACS synthetic biology.

[18]  T. Klaenhammer,et al.  Regulation of induced colonic inflammation by Lactobacillus acidophilus deficient in lipoteichoic acid , 2011, Proceedings of the National Academy of Sciences.

[19]  Engineering bacteria for biogenic synthesis of chalcogenide nanomaterials , 2018, bioRxiv.

[20]  J. Hassan,et al.  Development and evaluation of an experimental vaccination program using a live avirulent Salmonella typhimurium strain to protect immunized chickens against challenge with homologous and heterologous Salmonella serotypes , 1994, Infection and immunity.

[21]  N. Khan,et al.  Protocol for eukaryotic plasma membrane isolation using superparamagnetic nanoparticles , 2017, Journal of Magnetism and Magnetic Materials.

[22]  J. Lederberg,et al.  `Ome Sweet `Omics--A Genealogical Treasury of Words , 2001 .

[23]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[24]  A. C. Chang,et al.  Construction of biologically functional bacterial plasmids in vitro. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Eran Segal,et al.  Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease. , 2016, Cell host & microbe.

[26]  Drew Endy,et al.  Quantitative estimation of activity and quality for collections of functional genetic elements , 2013, Nature Methods.

[27]  Deepak B Thimiri Govinda Raj,et al.  Efficient Nanobiotechnology Method for Magnetic Lysosome Enrichment Using DMSA-SPMNP 2.0 , 2020 .

[28]  Jeff Hasty,et al.  Programmable probiotics for detection of cancer in urine , 2015, Science Translational Medicine.

[29]  G. Stephanopoulos,et al.  Network rigidity and metabolic engineering in metabolite overproduction , 1991, Science.

[30]  R. Kumar,et al.  Metabolic Engineering of Bacteria , 2011, Indian Journal of Microbiology.

[31]  Xavier Stien,et al.  Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. , 2014, The Journal of clinical investigation.

[32]  W. S. Denney,et al.  An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans , 2019, Science Translational Medicine.

[33]  Gaelen T. Hess,et al.  Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells , 2016, Nature Methods.

[34]  J. Segre,et al.  The human microbiome: our second genome. , 2012, Annual review of genomics and human genetics.

[35]  Wayne M Patrick,et al.  Error-prone PCR and effective generation of gene variant libraries for directed evolution. , 2014, Methods in molecular biology.

[36]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[37]  Nicholas J Turner,et al.  Directed evolution drives the next generation of biocatalysts. , 2009, Nature chemical biology.

[38]  William E Bentley,et al.  Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models , 2017, Nature Communications.

[39]  P. Silver,et al.  Bacteriophages dynamically modulate the gut microbiota and metabolome , 2018, bioRxiv.

[40]  Timothy K Lu,et al.  Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing , 2015, bioRxiv.

[41]  S. Lynch,et al.  The Human Intestinal Microbiome in Health and Disease. , 2016, The New England journal of medicine.

[42]  Deepak B Thimiri Govinda Raj,et al.  Surface functionalization dependent subcellular localization of Superparamagnetic nanoparticle in plasma membrane and endosome , 2018, Nano Convergence.

[43]  Mohammadali Khan Mirzaei,et al.  Adapting Drug Approval Pathways for Bacteriophage-Based Therapeutics , 2016, Front. Microbiol..

[44]  J. Caporaso,et al.  Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota , 2019, Scientific Reports.

[45]  Timothy K Lu,et al.  Microbiome therapeutics - Advances and challenges. , 2016, Advanced drug delivery reviews.

[46]  P. Verheijen,et al.  Parameter identification of in vivo kinetic models: Limitations and challenges , 2013, Biotechnology journal.

[47]  Jean Paul Thiery,et al.  Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention , 2018, Nature Biomedical Engineering.

[48]  D. Relman,et al.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation , 2010, Proceedings of the National Academy of Sciences.

[49]  P. Turnbaugh,et al.  Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome , 2013, Cell.

[50]  Erin L. Doyle,et al.  Targeting DNA Double-Strand Breaks with TAL Effector Nucleases , 2010, Genetics.

[51]  M. Capecchi,et al.  Altering the genome by homologous recombination. , 1989, Science.

[52]  T. Lu,et al.  Genetically Engineered Phages: a Review of Advances over the Last Decade , 2016, Microbiology and Molecular Reviews.

[53]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[54]  L. Quadro,et al.  β-carotene-producing bacteria residing in the intestine provide vitamin A to mouse tissues in vivo. , 2014, The Journal of nutrition.

[55]  W. Fiers,et al.  Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. , 2000, Science.

[56]  Weston R. Whitaker,et al.  Gut Microbiota-Produced Tryptamine Activates an Epithelial G-Protein-Coupled Receptor to Increase Colonic Secretion. , 2018, Cell host & microbe.

[57]  Deepak B Thimiri Govinda Raj,et al.  BacMam System for Rapid Recombinant Protein Expression in Mammalian Cells. , 2019, Methods in molecular biology.

[58]  R. Schooley,et al.  Engineered bacteriophages for treatment of a patient with a disseminated drug resistant Mycobacterium abscessus , 2019, Nature Medicine.

[59]  Brian F Pfleger,et al.  Microbial production of fatty acid-derived fuels and chemicals. , 2013, Current opinion in biotechnology.

[60]  M. Moo-young,et al.  Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis , 2016, Applied and Environmental Microbiology.

[61]  F. Arnold.  Design by Directed Evolution , 1998 .

[62]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[63]  Jay D Keasling,et al.  Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. , 2015, Metabolic engineering.

[64]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[65]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[66]  R. Varma,et al.  Biofactories: engineered nanoparticles via genetically engineered organisms , 2019, Green Chemistry.

[67]  W. Schumann,et al.  The pst Operon of Bacillus subtilis Is Specifically Induced by Alkali Stress , 2003, Journal of bacteriology.

[68]  Jennifer M. Fettweis,et al.  The Integrative Human Microbiome Project , 2019, Nature.

[69]  Ian Wheeldon,et al.  Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR-Cas9-Mediated Genome Editing in Yarrowia lipolytica. , 2016, ACS synthetic biology.

[70]  K. Morris,et al.  Mobilization-competent Lentiviral Vector-mediated Sustained Transcriptional Modulation of HIV-1 Expression. , 2009, Molecular therapy : the journal of the American Society of Gene Therapy.

[71]  Christopher A. Voigt,et al.  Synthetic biology to access and expand nature's chemical diversity , 2016, Nature Reviews Microbiology.

[72]  Bahar Javdan,et al.  Systematic mapping of drug metabolism by the human gut microbiome , 2019, bioRxiv.

[73]  Chaoguang Tian,et al.  Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering , 2017, Biotechnology for Biofuels.

[74]  Dana Carroll,et al.  Origins of Programmable Nucleases for Genome Engineering. , 2016, Journal of molecular biology.

[75]  D. T. G. Raj,et al.  Application and Challenges of Synthetic Biology , 2020 .

[76]  I. Hunt von Herbing,et al.  Genetically engineered probiotic for the treatment of phenylketonuria (PKU); assessment of a novel treatment in vitro and in the PAHenu2 mouse model of PKU , 2017, PloS one.

[77]  M. Omar Din,et al.  Synchronized cycles of bacterial lysis for in vivo delivery , 2016, Nature.

[78]  S Chandrasegaran,et al.  Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[79]  J. Bailey,et al.  Toward a science of metabolic engineering , 1991, Science.