Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels

Katsuki, 1967, Studies on the biosynthesis of ergosterol in yeast. Formation of methylated intermediates, J Biol Chem, 242, 222, 10.1016/S0021-9258(19)81452-7 Rohmer, 1993, Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate, Biochem J, 295, 517, 10.1042/bj2950517 Rohdich, 2003, The deoxyxylulose phosphate pathway of isoprenoid biosynthesis: studies on the mechanisms of the reactions catalyzed by IspG and IspH protein, P Natl Acad Sci U. S. A, 100, 1586, 10.1073/pnas.0337742100 Hornero-Mendez, 2002, Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis, FEBS Lett, 515, 133, 10.1016/S0014-5793(02)02453-5 Wang, 2007, Progress on molecular breeding and metabolic engineering of biosynthesis pathways of C30, C355, C40, C45, C50 carotenoids, Biotechnol Adv, 25, 211, 10.1016/j.biotechadv.2006.12.001 Heider, 2014, Metabolic engineering for the microbial production of carotenoids and related products with a focus on the rare C50 carotenoids, Appl Microbiol Biot, 98, 4355, 10.1007/s00253-014-5693-8 BCC-Research Ma, 2016, Microbial production strategies and applications of lycopene and other terpenoids, World J Microb Biot, 32, 10.1007/s11274-015-1975-2 Kang, 2005, Identification of genes affecting lycopene accumulation in Escherichia coli using a shot-gun method, Biotechnol Bioeng, 91, 636, 10.1002/bit.20539 Choi, 2010, In Silico Identification of gene amplification targets for improvement of lycopene production, Appl Environ Microb, 76, 3097, 10.1128/AEM.00115-10 Alper, 2005, Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli, Metab Eng, 7, 155, 10.1016/j.ymben.2004.12.003 Zhou, 2013, Lycopene production in recombinant strains of Escherichia coli is improved by knockout of the central carbon metabolism gene coding for glucose-6-phosphate dehydrogenase, Biotechnol Lett, 35, 2137, 10.1007/s10529-013-1317-0 Kim, 2001, Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production, Biotechnol Bioeng, 72, 408, 10.1002/1097-0290(20000220)72:4<408::AID-BIT1003>3.0.CO;2-H Kim, 2009, High-level production of lycopene in metabolically engineered E. coli, Process Biochem, 44, 899, 10.1016/j.procbio.2009.04.018 Rad, 2012, Type 2 IDI performs better than type 1 for improving lycopene production in metabolically engineered E. coli strains, World J Microb Biot, 28, 313, 10.1007/s11274-011-0821-4 Shen, 2015, Engineering of Escherichia coli for lycopene production through promoter engineering, Curr Pharm Biotechnol, 16, 1094, 10.2174/1389201016666150731110536 Sun, 2014, Production of lycopene by metabolically-engineered Escherichia coli, Biotechnol Lett, 36, 1515, 10.1007/s10529-014-1543-0 Zhu, 2015, Targeted engineering and scale up of lycopene overproduction in Escherichia coli, Process Biochem, 50, 341, 10.1016/j.procbio.2014.12.008 Kim, 2011, Increase of lycopene production by supplementing auxiliary carbon sources in metabolically engineered Escherichia coli, Appl Microbiol Biot, 90, 489, 10.1007/s00253-011-3091-z Tyo, 2009, Stabilized gene duplication enables long-term selection-free heterologous pathway expression, Nat Biotechnol, 27, 10.1038/nbt.1555 Chen, 2013, Chromosomal evolution of Escherichia coli for the efficient production of lycopene, Bmc Biotechnol, 13, 6, 10.1186/1472-6750-13-6 Coussement, 2017, Direct combinatorial pathway optimization, ACS Synth Biol, 6, 224, 10.1021/acssynbio.6b00122 Xie, 2015, Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering, Metab Eng, 30, 69, 10.1016/j.ymben.2015.04.009 Ozaydin, 2013, Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production, Metab Eng, 15, 174, 10.1016/j.ymben.2012.07.010 Chen, 2016, Lycopene overproduction in Saccharomyces cerevisiae through combining pathway engineering with host engineering, Microb Cell Fact, 15, 113, 10.1186/s12934-016-0509-4 Matthaus, 2014, Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica, Appl Environ Microb, 80, 1660, 10.1128/AEM.03167-13 Bai, 2015, Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces, P Natl Acad Sci U. S. A, 112, 12181, 10.1073/pnas.1511027112 Yang, 2014, Biosynthesis of beta-carotene in engineered E. coli using the MEP and MVA pathways, Microb Cell Fact, 13, 160, 10.1186/s12934-014-0160-x Zhao, 2013, Engineering central metabolic modules of Escherichia coli for improving beta-carotene production, Metab Eng, 17, 42, 10.1016/j.ymben.2013.02.002 Li, 2015, Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing, Metab Eng, 31, 13, 10.1016/j.ymben.2015.06.006 Xie, 2014, Construction of a controllable beta-Carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae, Biotechnol Bioeng, 111, 125, 10.1002/bit.25002 Xie, 2015, Sequential control of biosynthetic pathways for balanced utilization of metabolic intermediates in Saccharomyces cerevisiae, Metab Eng, 28, 8, 10.1016/j.ymben.2014.11.007 Sajilata, 2008, The carotenoid pigment zeaxanthin - a review, Compr Rev Food Sci F, 7, 29, 10.1111/j.1541-4337.2007.00028.x Moeller, 2000, The potential role of dietary xanthophylls in cataract and age-related macular degeneration, J Am Coll Nutr, 19, 522s, 10.1080/07315724.2000.10718975 Nishino, 2009, Cancer prevention by carotenoids, Arch Biochem Biophys, 483, 165, 10.1016/j.abb.2008.09.011 Albrecht, 1999, Metabolic engineering of the terpenoid biosynthetic pathway of Escherichia coli for production of the carotenoids beta-carotene and zeaxanthin, Biotechnol Lett, 21, 791, 10.1023/A:1005547827380 Nishizaki, 2007, Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis, Appl Environ Microb, 73, 1355, 10.1128/AEM.02268-06 Li, 2015, Metabolic engineering of Escherichia coli to produce zeaxanthin, J Ind Microbiol Biot, 42, 627, 10.1007/s10295-014-1565-6 Shen, 2016, Dynamic control of the mevalonate pathway expression for improved zeaxanthin production in Escherichia coli and comparative proteome analysis, Metab Eng, 38, 180, 10.1016/j.ymben.2016.07.012 Scaife, 2009, Characterization of cyanobacterial beta-carotene ketolase and hydroxylase genes in Escherichia coli, and their application for astaxanthin biosynthesis, Biotechnol Bioeng, 103, 944, 10.1002/bit.22330 Liu JZ, Lu Q, Bu YF. Engineered strain with high zeaxanthin or astaxanthin ratio and its application. China patient 201710036290.9, 2017. Zelcbuch, 2013, Spanning high-dimensional expression space using ribosome-binding site combinatorics, Nucleic Acids Res, 41, e98, 10.1093/nar/gkt151 Ma, 2016, Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp ATCC 55669 for heterologous overproduction in Escherichia coli, Biotechnol J, 11, 228, 10.1002/biot.201400827 Zhou, 2015, Highly efficient biosynthesis of astaxanthin in Saccharomyces cerevisiae by integration and tuning of algal crtZ and bkt, Appl Microbiol Biot, 99, 8419, 10.1007/s00253-015-6791-y Zhou, 2017, Alleviation of metabolic bottleneck by combinatorial engineering enhanced astaxanthin synthesis in Saccharomyces cerevisiae, Enzyme Microb Tech, 100, 28, 10.1016/j.enzmictec.2017.02.006 Henke, 2016, Production of the marine carotenoid astaxanthin by metabolically engineered Corynebacterium glutamicum, Mar Drugs, 14, 124, 10.3390/md14070124 Rabinovitch-Deere, 2013, Synthetic biology and metabolic engineering approaches to produce biofuels, Chem Rev, 113, 4611, 10.1021/cr300361t Kim, 2016, Isoprene production by Escherichia coli through the exogenous mevalonate pathway with reduced formation of fermentation byproducts, Microb Cell Fact, 15, 214, 10.1186/s12934-016-0612-6 Whited, 2010, Development of a gas-phase bioprocess for isoprene monomer production using metabolic pathway engineering, Ind Biotechnol, 6, 152, 10.1089/ind.2010.6.152 Yang, 2016, Synergy between methylerythritol phosphate pathway and mevalonate pathway for isoprene production in Escherichia coli, Metab Eng, 37, 79, 10.1016/j.ymben.2016.05.003 Lv, 2016, Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae, Nat Commun, 7, 12851, 10.1038/ncomms12851 Wang, 2017, Combining Gal4p-mediated expression enhancement and directed evolution of isoprene synthase to improve isoprene production in Saccharomyces cerevisiae, Metab Eng, 39, 257, 10.1016/j.ymben.2016.12.011 Gupta, 2015, Metabolic engineering for isoprenoid-based biofuel production, J Appl Microbiol, 119, 605, 10.1111/jam.12871 Zheng, 2013, Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels, Biotechnol Biofuels, 6, 57, 10.1186/1754-6834-6-57 Foo, 2014, Improving microbial biogasoline production in Escherichia coli using tolerance engineering, Mbio, 5, 10.1128/mBio.01932-14 Kang, 2016, Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production, Metab Eng, 34, 25, 10.1016/j.ymben.2015.12.002 George, 2015, Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli, Sci Rep-Uk, 5, 11128, 10.1038/srep11128 Kim, 2015, Microbial synthesis of myrcene by metabolically engineered Escherichia coil, J Agric Food Chem, 63, 4606, 10.1021/acs.jafc.5b01334 Zhang, 2014, Microbial production of sabinene-a new terpene-based precursor of advanced biofuel, Microb Cell Fact, 13, 20, 10.1186/1475-2859-13-20 Yang, 2013, Metabolic engineering of Escherichia coli for the biosynthesis of alpha-pinene, Biotechnol Biofuels, 6, 60, 10.1186/1754-6834-6-60 Sarria, 2014, Microbial synthesis of pinene, ACS Synth Biol, 3, 466, 10.1021/sb4001382 Tashiro, 2016, Bacterial production of pinene by a laboratory-evolved pinene-synthase, ACS Synth Biol, 5, 1011, 10.1021/acssynbio.6b00140 Alonso-Gutierrez, 2013, Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production, Metab Eng, 19, 33, 10.1016/j.ymben.2013.05.004 Dunlop, 2011, Engineering microbes for tolerance to next-generation biofuels, Biotechnol Biofuels, 4, 32, 10.1186/1754-6834-4-32 Dunlop, 2011, Engineering microbial biofuel tolerance and export using efflux pumps, Mol Syst Biol, 7, 487, 10.1038/msb.2011.21 Mingardon, 2015, Improving olefin tolerance and production in E. coli using native and evolved AcrB, Biotechnol Bioeng, 112, 879, 10.1002/bit.25511 Wang, 2011, Metabolic engineering of Escherichia coli for alpha-farnesene production, Metab Eng, 13, 648, 10.1016/j.ymben.2011.08.001 Zhu, 2014, In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli, Biotechnol Bioeng, 111, 1396, 10.1002/bit.25198 Meadows, 2016, Rewriting yeast central carbon metabolism for industrial isoprenoid production, Nature, 537, 10.1038/nature19769 Peralta-Yahya, 2011, Identification and microbial production of a terpene-based advanced biofuel, Nat Commun, 2, 483, 10.1038/ncomms1494 Kirby, 2015, Enhancing terpene yield from sugars via novel routes to 1-Deoxy-D-Xylulose 5-Phosphate, Appl Environ Microb, 81, 130, 10.1128/AEM.02920-14 Ozaydin, 2013, Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production, Metab Eng, 15, 174, 10.1016/j.ymben.2012.07.010 Wang, 2010, Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway, Biotechnol Bioeng, 107, 421, 10.1002/bit.22831 Wang, 2016, Farnesol production in Escherichia coli through the construction of a farnesol biosynthesis pathway - application of PgpB and YbjG phosphatases, Biotechnol J, 11, 1291, 10.1002/biot.201600250 Ohto, 2009, Overexpression of the gene encoding HMG-CoA reductase in Saccharomyces cerevisiae for production of prenyl alcohols, Appl Microbiol Biot, 82, 837, 10.1007/s00253-008-1807-5