Metabolic Engineering of Shikimic Acid Biosynthesis Pathway for the Production of Shikimic Acid and Its Branched Products in Microorganisms: Advances and Prospects

The shikimate pathway is a necessary pathway for the synthesis of aromatic compounds. The intermediate products of the shikimate pathway and its branching pathway have promising properties in many fields, especially in the pharmaceutical industry. Many important compounds, such as shikimic acid, quinic acid, chlorogenic acid, gallic acid, pyrogallol, catechol and so on, can be synthesized by the shikimate pathway. Among them, shikimic acid is the key raw material for the synthesis of GS4104 (Tamiflu®), an inhibitor of neuraminidase against avian influenza virus. Quininic acid is an important intermediate for synthesis of a variety of raw chemical materials and drugs. Gallic acid and catechol receive widespread attention as pharmaceutical intermediates. It is one of the hotspots to accumulate many kinds of target products by rationally modifying the shikimate pathway and its branches in recombinant strains by means of metabolic engineering. This review considers the effects of classical metabolic engineering methods, such as central carbon metabolism (CCM) pathway modification, key enzyme gene modification, blocking the downstream pathway on the shikimate pathway, as well as several expansion pathways and metabolic engineering strategies of the shikimate pathway, and expounds the synthetic biology in recent years in the application of the shikimate pathway and the future development direction.

[1]  Liming Liu,et al.  Bifunctional optogenetic switch for improving shikimic acid production in E. coli , 2022, Biotechnology for Biofuels and Bioproducts.

[2]  F. Niu,et al.  Biosensor-Guided Atmospheric and Room-Temperature Plasma Mutagenesis and Shuffling for High-Level Production of Shikimic Acid from Sucrose in Escherichia coli. , 2020, Journal of agricultural and food chemistry.

[3]  Tao Chen,et al.  Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway , 2020, Journal of Industrial Microbiology & Biotechnology.

[4]  J. Nielsen,et al.  Rewiring carbon flux in Escherichia coli using a bifunctional molecular switch. , 2020, Metabolic engineering.

[5]  M. Xian,et al.  Common problems associated with the microbial productions of aromatic compounds and corresponding metabolic engineering strategies. , 2020, Biotechnology advances.

[6]  M. Suástegui,et al.  Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products. , 2020, Metabolic engineering.

[7]  O. Kwon,et al.  Shikimic acid, a mannose bioisostere, promotes hair growth with the induction of anagen hair cycle , 2019, Scientific Reports.

[8]  Shilong Ning,et al.  Shikimic acid promotes estrogen receptor(ER)-positive breast cancer cells proliferation via activation of NF-κB signaling. , 2019, Toxicology letters.

[9]  Sang Yup Lee,et al.  Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. , 2019, Trends in biotechnology.

[10]  H. B. Reisman Economic Analysis of Fermentation Processes , 2019 .

[11]  Chen Liang,et al.  [Research progress on synthetic scaffold in metabolic engineering - a review]. , 2019, Sheng wu gong cheng xue bao = Chinese journal of biotechnology.

[12]  Hong Gao,et al.  Insight into the effect of quinic acid on biofilm formed by Staphylococcus aureus , 2019, RSC advances.

[13]  Yi-Xin Huo,et al.  CipA-mediating enzyme self-assembly to enhance the biosynthesis of pyrogallol in Escherichia coli , 2018, Applied Microbiology and Biotechnology.

[14]  Hafiz M.N. Iqbal,et al.  Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments , 2018, Applied Microbiology and Biotechnology.

[15]  Hong-bo Hu,et al.  Systematically engineering Escherichia coli for enhanced shikimate biosynthesis co‐utilizing glycerol and glucose , 2018 .

[16]  A. Escalante,et al.  Synthesis, biological activity and molecular modelling studies of shikimic acid derivatives as inhibitors of the shikimate dehydrogenase enzyme of Escherichia coli , 2018, Journal of enzyme inhibition and medicinal chemistry.

[17]  Bo Zhang,et al.  New Intracellular Shikimic Acid Biosensor for Monitoring Shikimate Synthesis in Corynebacterium glutamicum. , 2017, ACS synthetic biology.

[18]  Qipeng Yuan,et al.  Microbial synthesis of pyrogallol using genetically engineered Escherichia coli. , 2018, Metabolic engineering.

[19]  H. Koo,et al.  Quinic acid inhibits vascular inflammation in TNF-α-stimulated vascular smooth muscle cells. , 2017, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[20]  Qipeng Yuan,et al.  Rational engineering of p‐hydroxybenzoate hydroxylase to enable efficient gallic acid synthesis via a novel artificial biosynthetic pathway , 2017, Biotechnology and bioengineering.

[21]  Quanfeng Liang,et al.  Novel technologies combined with traditional metabolic engineering strategies facilitate the construction of shikimate-producing Escherichia coli , 2017, Microbial Cell Factories.

[22]  Ming-Yi Lee,et al.  Improvement of shikimic acid production in Escherichia coli with growth phase-dependent regulation in the biosynthetic pathway from glycerol , 2017, World journal of microbiology & biotechnology.

[23]  M. Jiang,et al.  Engineering the shikimate pathway for biosynthesis of molecules with pharmaceutical activities in E. coli. , 2016, Current opinion in biotechnology.

[24]  F. Bolivar,et al.  The Role of the ydiB Gene, Which Encodes Quinate/Shikimate Dehydrogenase, in the Production of Quinic, Dehydroshikimic and Shikimic Acids in a PTS- Strain of Escherichia coli , 2016, Journal of Molecular Microbiology and Biotechnology.

[25]  M. Inui,et al.  Metabolic engineering of Corynebacterium glutamicum for shikimate overproduction by growth-arrested cell reaction. , 2016, Metabolic engineering.

[26]  Yuguo Zheng,et al.  Application of CRISPRi in Corynebacterium glutamicum for shikimic acid production , 2016, Biotechnology Letters.

[27]  Saptarshi Ghosh,et al.  Studies on the production of shikimic acid using the aroK knockout strain of Bacillus megaterium , 2016, World Journal of Microbiology and Biotechnology.

[28]  Baoquan Zhu,et al.  Enhanced production of shikimic acid using a multi-gene co-expression system in Escherichia coli. , 2016, Chinese journal of natural medicines.

[29]  Chen Tao,et al.  Progress and application on multivariate modular metabolic engineering in metabolic engineering , 2016 .

[30]  Francisco Bolívar,et al.  Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production , 2015, Front. Bioeng. Biotechnol..

[31]  Bo Zhang,et al.  Ribosome binding site libraries and pathway modules for shikimic acid synthesis with Corynebacterium glutamicum , 2015, Microbial Cell Factories.

[32]  M. Inui,et al.  Identification and expression analysis of a gene encoding a shikimate transporter of Corynebacterium glutamicum. , 2015, Microbiology.

[33]  Z. Kmietowicz Tamiflu reduces complications of flu, new review finds , 2015, BMJ : British Medical Journal.

[34]  D. Nielsen,et al.  Rational engineering of a novel pathway for producing the aromatic compounds p-hydroxybenzoate, protocatechuate, and catechol in Escherichia coli , 2014 .

[35]  F. Bolivar,et al.  Catechol biosynthesis from glucose in Escherichia coli anthranilate-overproducer strains by heterologous expression of anthranilate 1,2-dioxygenase from Pseudomonas aeruginosa PAO1 , 2014, Microbial Cell Factories.

[36]  Marjan De Mey,et al.  Multivariate modular metabolic engineering for pathway and strain optimization. , 2014, Current opinion in biotechnology.

[37]  Joong-Hoon Ahn,et al.  Synthesis of chlorogenic acid and p-coumaroyl shikimates from glucose using engineered Escherichia coli. , 2014, Journal of microbiology and biotechnology.

[38]  Wei Shen,et al.  Metabolic engineering of Escherichia coli for improving shikimate synthesis from glucose. , 2014, Bioresource technology.

[39]  Francisco Bolívar,et al.  Current perspectives on applications of shikimic and aminoshikimic acids in pharmaceutical chemistry , 2014 .

[40]  C. Yang,et al.  Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains , 2014, Microbial Cell Factories.

[41]  Jian-Zhong Liu,et al.  Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering , 2014, Microbial Cell Factories.

[42]  Francisco Bolívar,et al.  Inactivation of Pyruvate Kinase or the Phosphoenolpyruvate: Sugar Phosphotransferase System Increases Shikimic and Dehydroshikimic Acid Yields from Glucose in Bacillus subtilis , 2013, Journal of Molecular Microbiology and Biotechnology.

[43]  Jian Chen,et al.  Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from L-tyrosine. , 2013, Journal of biotechnology.

[44]  J. Otero,et al.  Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover. , 2013, Journal of the American Chemical Society.

[45]  B. Kappes,et al.  The shikimate pathway in apicomplexan parasites: implications for drug development. , 2013, Frontiers in bioscience.

[46]  Yong-Beom Park,et al.  Gallic acid, a natural polyphenolic acid, induces apoptosis and inhibits proinflammatory gene expressions in rheumatoid arthritis fibroblast-like synoviocytes. , 2013, Joint, bone, spine : revue du rhumatisme.

[47]  Qipeng Yuan,et al.  A Novel Muconic Acid Biosynthesis Approach by Shunting Tryptophan Biosynthesis via Anthranilate , 2013, Applied and Environmental Microbiology.

[48]  P. Tripathi,et al.  Expanding horizons of shikimic acid , 2013, Applied Microbiology and Biotechnology.

[49]  Joong-Hoon Ahn,et al.  Production of hydroxycinnamoyl-shikimates and chlorogenic acid in Escherichia coli: production of hydroxycinnamic acid conjugates , 2013, Microbial Cell Factories.

[50]  Saptarshi Ghosh,et al.  Production of shikimic acid. , 2012, Biotechnology advances.

[51]  Rishi Garg,et al.  Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters , 2012, Biotechnology and bioengineering.

[52]  Christoph Wittmann,et al.  Consequences of phosphoenolpyruvate:sugar phosphotranferase system and pyruvate kinase isozymes inactivation in central carbon metabolism flux distribution in Escherichia coli , 2012, Microbial Cell Factories.

[53]  Hui Wang,et al.  Deletion of the aroK gene is essential for high shikimic acid accumulation through the shikimate pathway in E. coli. , 2012, Bioresource technology.

[54]  M. Crouzet,et al.  Evidence for the involvement of the anthranilate degradation pathway in Pseudomonas aeruginosa biofilm formation , 2012, MicrobiologyOpen.

[55]  R. K. Saxena,et al.  Pandemism of swine flu and its prospective drug therapy , 2012, European Journal of Clinical Microbiology & Infectious Diseases.

[56]  Xican Li Improved pyrogallol autoxidation method: a reliable and cheap superoxide-scavenging assay suitable for all antioxidants. , 2012, Journal of agricultural and food chemistry.

[57]  Kuang-Chi Lai,et al.  Gallic acid inhibits migration and invasion in human osteosarcoma U-2 OS cells through suppressing the matrix metalloproteinase-2/-9, protein kinase B (PKB) and PKC signaling pathways. , 2012, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[58]  Xueli Zhang,et al.  Combinatorial modulation of galP and glk gene expression for improved alternative glucose utilization , 2011, Applied Microbiology and Biotechnology.

[59]  J. Keasling,et al.  Modular Engineering of l-Tyrosine Production in Escherichia coli , 2011, Applied and Environmental Microbiology.

[60]  I. Khan,et al.  Gallic acid , 2011, Acta crystallographica. Section E, Structure reports online.

[61]  C. Caruso,et al.  Erratum to: Modulation of Nrf2/ARE Pathway by Food Polyphenols: A Nutritional Neuroprotective Strategy for Cognitive and Neurodegenerative Disorders , 2011, Molecular Neurobiology.

[62]  Russell J. Mumper,et al.  Plant Phenolics: Extraction, Analysis and Their Antioxidant and Anticancer Properties , 2010, Molecules.

[63]  E. Papoutsakis,et al.  A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation. , 2010, Metabolic engineering.

[64]  Yuexin Liu,et al.  [Advances in mechanism of Escherichia coli carbon catabolite repression]. , 2010, Yi chuan = Hereditas.

[65]  Francisco Bolívar,et al.  Metabolic engineering for the production of shikimic acid in an evolved Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system , 2010, Microbial cell factories.

[66]  R. Gambari,et al.  Pyrogallol, an active compound from the medicinal plant Emblica officinalis, regulates expression of pro-inflammatory genes in bronchial epithelial cells. , 2008, International immunopharmacology.

[67]  E. Struys,et al.  The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: A review , 2008, Journal of Inherited Metabolic Disease.

[68]  N. Yakandawala,et al.  Metabolic engineering of Escherichia coli to enhance phenylalanine production , 2008, Applied Microbiology and Biotechnology.

[69]  Amer.,et al.  New Targets for Antibacterial Agents , 2008 .

[70]  Z. Ye,et al.  New approach to the total synthesis of (-)-zeylenone from shikimic acid. , 2006, Chemical & pharmaceutical bulletin.

[71]  S. R. Kushner,et al.  Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. , 2006, Genes & development.

[72]  Thomas A. Richards,et al.  Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements , 2006, Eukaryotic Cell.

[73]  P. Belton,et al.  Structure–activity relationship analysis of antioxidant ability and neuroprotective effect of gallic acid derivatives , 2006, Neurochemistry International.

[74]  Gunnar Lidén,et al.  Shikimic acid production by a modified strain of E. coli (W3110.shik1) under phosphate‐limited and carbon‐limited conditions , 2005, Biotechnology and bioengineering.

[75]  Guillermo Gosset,et al.  Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system , 2005, Microbial cell factories.

[76]  L. Martínez-Martínez,et al.  Nationwide Study of Escherichia coli and Klebsiella pneumoniae Producing Extended-Spectrum β-Lactamases in Spain , 2005, Antimicrobial Agents and Chemotherapy.

[77]  R. Ménard,et al.  Site-directed Mutagenesis of the Active Site Region in the Quinate/Shikimate 5-Dehydrogenase YdiB of Escherichia coli* , 2005, Journal of Biological Chemistry.

[78]  J. W. Frost,et al.  Benzene-free synthesis of catechol: interfacing microbial and chemical catalysis. , 2005, Journal of the American Chemical Society.

[79]  He Hua-qing Advances of Metabolic Engineering in Biosynthesis of Quinic Acid , 2005 .

[80]  J. Vita,et al.  Polyphenols and cardiovascular disease: effects on endothelial and platelet function. , 2005, The American journal of clinical nutrition.

[81]  P. Harrington,et al.  The synthetic development of the anti-influenza neuraminidase inhibitor oseltamivir phosphate (Tamiflu®): A challenge for synthesis & process research , 2004 .

[82]  Roel Bovenberg,et al.  Metabolic engineering for microbial production of shikimic acid. , 2003, Metabolic engineering.

[83]  Allan Matte,et al.  Structures of Shikimate Dehydrogenase AroE and Its Paralog YdiB , 2003, Journal of Biological Chemistry.

[84]  Ralph Von Daeniken,et al.  Phosphoenolpyruvate Availability and the Biosynthesis of Shikimic Acid , 2003, Biotechnology progress.

[85]  J. W. Frost,et al.  Benzene‐Free Synthesis of Adipic Acid , 2002, Biotechnology progress.

[86]  J. W. Frost,et al.  Hydroaromatic equilibration during biosynthesis of shikimic acid. , 2001, Journal of the American Chemical Society.

[87]  J. W. Frost,et al.  Synthesis of Gallic Acid and Pyrogallol from Glucose: Replacing Natural Product Isolation with Microbial Catalysis , 2000 .

[88]  M. Federspiel Industrial Synthesis of the Key Precursor in the Synthesis of the Antiinfluenza Drug Oseltamivir Phosphate (Ro 64‐0796/002, GS‐4104‐02): Ethyl (3R,4S,5S)‐4,5‐Epoxy‐3‐(1‐ethyl‐propoxy)‐cyclohex‐1‐ene‐1‐carboxylate. , 1999 .

[89]  M. Hennig,et al.  Industrial Synthesis of the Key Precursor in the Synthesis of the Anti-Influenza Drug Oseltamivir Phosphate (Ro 64-0796/002, GS-4104-02): Ethyl (3R,4S,5S)-4,5-epoxy-3-(1-ethyl-propoxy)-cyclohex-1-ene-1-carboxylate , 1999 .

[90]  John W. Frost,et al.  SHIKIMIC ACID AND QUINIC ACID : REPLACING ISOLATION FROM PLANT SOURCES WITH RECOMBINANT MICROBIAL BIOCATALYSIS , 1999 .

[91]  A. Pittard,et al.  Cloning and analysis of the shiA gene, which encodes the shikimate transport system of escherichia coli K-12. , 1998, Gene.

[92]  J. Liao,et al.  Metabolic engineering and control analysis for production of aromatics: Role of transaldolase. , 1997, Biotechnology and bioengineering.

[93]  A. Berry,et al.  Improving production of aromatic compounds in Escherichia coli by metabolic engineering. , 1996, Trends in biotechnology.

[94]  J. Liao,et al.  Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities , 1995, Biotechnology and bioengineering.

[95]  J. W. Frost,et al.  The synthesis of quinic acid from glucose , 1995 .

[96]  J. W. Frost,et al.  Identification and removal of impediments to biocatalytic synthesis of aromatics from D-glucose: rate-limiting enzymes in the common pathway of aromatic amino acid biosynthesis , 1993 .

[97]  Stu Borman,et al.  New biosynthetic route to catechol discovered , 1992 .

[98]  G. Robinson,et al.  The production of catechols from benzene and toluene by Pseudomonas putida in glucose fed-batch culture , 1992 .

[99]  T. Chakraborty,et al.  Studies Directed Towards the Synthesis of Immunosuppressive Agent FK‐ 506: Synthesis of the Entire Top‐Half. , 1991 .

[100]  J. W. Frost,et al.  Conversion of D-glucose into catechol: the not-so-common pathway of aromatic biosynthesis , 1991 .

[101]  H. Harry Szmant,et al.  Organic Building Blocks of the Chemical Industry , 1989 .

[102]  G. Gurujeyalakshmi,et al.  Isolation of phenol-degrading Bacillus stearothermophilus and partial characterization of the phenol hydroxylase , 1989, Applied and environmental microbiology.

[103]  M. Jung Conversion of shikimic acid into 2-crotonyloxymethyl-(4R,5R,6S)-4,5,6-trihydroxycyclohex-2- ene analogous to a glyoxalase I inhibitor. , 1987, The Journal of antibiotics.

[104]  S. Marklund,et al.  Involvement of the superoxide anion radical in the autoxidation of pyrogallol and a convenient assay for superoxide dismutase. , 1974, European journal of biochemistry.

[105]  B. D. Davis,et al.  AROMATIC BIOSYNTHESIS VII , 1953 .

[106]  B. D. Davis,et al.  Aromatic biosynthesis. VII. Accumulation of two derivatives of shikimic acid by bacterial mutants. , 1953, Journal of bacteriology.