1
|
Gupta M, Wong M, Jawed K, Gedeon K, Barrett H, Bassalo M, Morrison C, Eqbal D, Yazdani SS, Gill RT, Huang J, Douaisi M, Dordick J, Belfort G, Koffas MA. Isobutanol production by combined in vivo and in vitro metabolic engineering. Metab Eng Commun 2022; 15:e00210. [PMID: 36325486 PMCID: PMC9619177 DOI: 10.1016/j.mec.2022.e00210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 12/12/2022] Open
Abstract
The production of the biofuel, isobutanol, in E. coli faces limitations due to alcohol toxicity, product inhibition, product recovery, and long-term industrial feasibility. Here we demonstrate an approach of combining both in vivo with in vitro metabolic engineering to produce isobutanol. The in vivo production of α-ketoisovalerate (KIV) was conducted through CRISPR mediated integration of the KIV pathway in bicistronic design (BCD) in E. coli and inhibition of competitive valine pathway using CRISPRi technology. The subsequent in vitro conversion to isobutanol was carried out with engineered enzymes for 2-ketoacid decarboxylase (KIVD) and alcohol dehydrogenase (ADH). For the in vivo production of KIV and subsequent in vitro production of isobutanol, this two-step serial approach resulted in yields of 56% and 93%, productivities of 0.62 and 0.074 g L-1 h-1, and titers of 5.6 and 1.78 g L-1, respectively. Thus, this combined biosynthetic system can be used as a modular approach for producing important metabolites, like isobutanol, without the limitations associated with in vivo production using a consolidated bioprocess.
Collapse
|
2
|
Xu G, Shi X, Gao Y, Wang J, Cheng H, Liu Y, Chen Y, Li J, Xu X, Zha J, Xia K, Linhardt RJ, Zhang X, Shi J, Koffas MA, Xu Z. Semi-rational evolution of pyruvate carboxylase from Rhizopus oryzae for elevated fumaric acid synthesis in Saccharomyces cerevisiae. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
3
|
Li H, Shi W, Li C, Zhang X, Gong J, Shi J, Koffas MA, Xu Z. Impact of ethylene glycol on DHEA dihydroxylation in Colletotrichum lini: Increasing the expression of cytochrome P450 and 6-phosphogluconate dehydrogenase and enhancing the generation of NADPH. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
4
|
Zhou S, Lyu Y, Li H, Koffas MA, Zhou J. Cover Image, Volume 116, Number 6, June 2019. Biotechnol Bioeng 2019. [DOI: 10.1002/bit.26758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
5
|
Zhou S, Lyu Y, Li H, Koffas MA, Zhou J. Fine‐tuning the (2
S
)‐naringenin synthetic pathway using an iterative high‐throughput balancing strategy. Biotechnol Bioeng 2019; 116:1392-1404. [DOI: 10.1002/bit.26941] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 12/24/2022]
|
6
|
Sarnaik A, Abernathy MH, Han X, Ouyang Y, Xia K, Chen Y, Cress B, Zhang F, Lali A, Pandit R, Linhardt RJ, Tang YJ, Koffas MA. Metabolic engineering of cyanobacteria for photoautotrophic production of heparosan, a pharmaceutical precursor of heparin. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
7
|
Zhao M, Huang D, Zhang X, Koffas MA, Zhou J, Deng Y. Metabolic engineering of Escherichia coli for producing adipic acid through the reverse adipate-degradation pathway. Metab Eng 2018; 47:254-262. [DOI: 10.1016/j.ymben.2018.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/19/2018] [Accepted: 04/01/2018] [Indexed: 12/25/2022]
|
8
|
Vaidyanathan D, Williams A, Dordick JS, Koffas MA, Linhardt RJ. Engineered heparins as new anticoagulant drugs. Bioeng Transl Med 2017; 2:17-30. [PMID: 28516163 PMCID: PMC5412866 DOI: 10.1002/btm2.10042] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/13/2016] [Accepted: 10/21/2016] [Indexed: 12/28/2022] Open
Abstract
Heparin is an anionic polysaccharide that is widely used as a clinical anticoagulant. This glycosaminoglycan is prepared from animal tissues in metric ton quantities. Animal-sourced heparin is also widely used in the preparation of low molecular weight heparins that are gaining in popularity as a result of their improved pharmacological properties. The recent contamination of pharmaceutical heparin together with concerns about increasing demand for this life saving drug and the fragility of the heparin supply chain has led the scientific community to consider other potential sources for heparin. This review examines progress toward the preparation of engineered heparins through chemical synthesis, chemoenzymatic synthesis, and metabolic engineering.
Collapse
|
9
|
He L, Xiu Y, Jones JA, Baidoo EE, Keasling JD, Tang YJ, Koffas MA. Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions. Metab Eng 2017; 39:247-256. [DOI: 10.1016/j.ymben.2016.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/12/2016] [Accepted: 12/20/2016] [Indexed: 11/30/2022]
|
10
|
Guleria S, Zhou J, Koffas MA. Nutraceuticals (Vitamin C, Carotenoids, Resveratrol). Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|
11
|
Shirke AN, Su A, Jones JA, Butterfoss GL, Koffas MA, Kim JR, Gross RA. Comparative thermal inactivation analysis ofAspergillus oryzaeandThiellavia terrestriscutinase: Role of glycosylation. Biotechnol Bioeng 2016; 114:63-73. [DOI: 10.1002/bit.26052] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 07/01/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022]
|
12
|
Pandey RP, Parajuli P, Koffas MA, Sohng JK. Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology. Biotechnol Adv 2016; 34:634-662. [DOI: 10.1016/j.biotechadv.2016.02.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 12/18/2022]
|
13
|
Wu G, Yan Q, Jones JA, Tang YJ, Fong SS, Koffas MA. Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications. Trends Biotechnol 2016; 34:652-664. [DOI: 10.1016/j.tibtech.2016.02.010] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 01/23/2023]
|
14
|
Bhan N, Xu P, Khalidi O, Koffas MA. Redirecting carbon flux into malonyl-CoA to improve resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2012.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
15
|
Xu P, Gu Q, Wang W, Wong L, Bower AG, Collins CH, Koffas MA. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun 2013; 4:1409. [DOI: 10.1038/ncomms2425] [Citation(s) in RCA: 360] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/21/2012] [Indexed: 01/10/2023] Open
|
16
|
Lim CG, A.G. Koffas M. Bioavailability and Recent Advances in the Bioactivity of Flavonoid and Stilbene Compounds. CURR ORG CHEM 2010. [DOI: 10.2174/138527210792927654] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
17
|
Leonard E, Yan Y, Chemler J, Matern U, Martens S, Koffas MA. Characterization of dihydroflavonol 4-reductases for recombinant plant pigment biosynthesis applications. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701685635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
18
|
Koffas MA, Ramamoorthi R, Pine WA, Sinskey AJ, Stephanopoulos G. Sequence of the Corynebacterium glutamicum pyruvate carboxylase gene. Appl Microbiol Biotechnol 1998; 50:346-52. [PMID: 9802220 DOI: 10.1007/s002530051302] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyruvate carboxylase is an important anaplerotic enzyme replenishing oxaloacetate consumed for biosynthesis during growth, or lysine and glutamic acid production in industrial fermentations. We used regions of homology from pyruvate carboxylase sequences of 12 different species (corresponding to the ATP- and pyruvate-binding sites), to design polymerase chain reaction (PCR) primers for amplifying a fragment of the pyruvate carboxylase (pc) gene from C. glutamicum genomic DNA. This 850-base-pair fragment was used to probe a C. glutamicum cosmid library and four candidate pc cosmids were identified. The fragment was sequenced and the sequence of the complete gene was obtained by several rounds of primer synthesis, PCR on one of the positive cosmids, and sequencing. The C. glutamicum pc sequence shows 64% homology with the pc gene of Mycobacterium tuberculosis and 44% homology with the human pc gene. Regions of ATP, pyruvate and biotin binding have also been identified.
Collapse
|