Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

Mak, Wai Shun; Tran, Stephen; Marcheschi, Ryan J.; Bertolani, Steve J.; Thompson, James; Baker, David; Liao, James C.; Siegel, Justin B.

doi:10.1038/ncomms10005

Cited by 81 publications

(61 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Engineering natural enzymes (single to a few amino acid mutations) has been shown to be effective in broadening the substrate or product range or changing the enzyme kinetics, but generally the titers of the engineered enzymes are significantly reduced relative to the natural enzymes; to our knowledge, the highest titer reported for biogasoline production (e.g. short-chain alkanes or alcohols) was 728 mg · l −1 when using these mutated enzymes 9 , 11 , 31 , 32 . Type I modular PKSs have the potential to produce a very broad range of molecules by combining multiple, simple individual steps (catalyzed by protein domains) in an understandable way.…”

Section: Discussionmentioning

confidence: 94%

Short-chain ketone production by engineered polyketide synthases in Streptomyces albus

et al. 2018

View full text Add to dashboard Cite

Microbial production of fuels and commodity chemicals has been performed primarily using natural or slightly modified enzymes, which inherently limits the types of molecules that can be produced. Type I modular polyketide synthases (PKSs) are multi-domain enzymes that can produce unique and diverse molecular structures by combining particular types of catalytic domains in a specific order. This catalytic mechanism offers a wealth of engineering opportunities. Here we report engineered microbes that produce various short-chain (C5–C7) ketones using hybrid PKSs. Introduction of the genes into the chromosome of Streptomyces albus enables it to produce >1 g · l−1 of C6 and C7 ethyl ketones and several hundred mg · l−1 of C5 and C6 methyl ketones from plant biomass hydrolysates. Engine tests indicate these short-chain ketones can be added to gasoline as oxygenates to increase the octane of gasoline. Together, it demonstrates the efficient and renewable microbial production of biogasolines by hybrid enzymes.

show abstract

Section: Discussionmentioning

confidence: 94%

Short-chain ketone production by engineered polyketide synthases in Streptomyces albus

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Especially, expression of cocoa gene combinations was able to significantly alter the total fatty acid production in yeast, enabling some yeast strains to produce more CBL, indicating that the selected cocoa genes played important roles in CBL production in S. cerevisiae . As all the six cocoa genes were selected based on combining published information on the cocoa genome and a phylogenetic analysis, it is a clear example that phylogenetic analysis can be used for gene or pathway mining for metabolic engineering (Mak et al 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Increasing cocoa butter-like lipid production of Saccharomyces cerevisiae by expression of selected cocoa genes

et al. 2017

View full text Add to dashboard Cite

Cocoa butter (CB) extracted from cocoa beans mainly consists of three different kinds of triacylglycerols (TAGs), 1,3-dipalmitoyl-2-oleoyl-glycerol (POP, C16:0–C18:1–C16:0), 1-palmitoyl-3-stearoyl-2-oleoyl-glycerol (POS, C16:0–C18:1–C18:0) and 1,3-distearoyl-2-oleoyl-glycerol (SOS, C18:0–C18:1–C18:0), but CB supply is limited. Therefore, CB-like lipids (CBL, which are composed of POP, POS and SOS) are in great demand. Saccharomyces cerevisiae produces TAGs as storage lipids, which are also mainly composed of C16 and C18 fatty acids. However, POP, POS and SOS are not among the major TAG forms in yeast. TAG synthesis is mainly catalyzed by three enzymes: glycerol-3-phosphate acyltransferase (GPAT), lysophospholipid acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT). In order to produce CBL in S. cerevisiae, we selected six cocoa genes encoding GPAT, LPAT and DGAT potentially responsible for CB biosynthesis from the cocoa genome using a phylogenetic analysis approach. By expressing the selected cocoa genes in S. cerevisiae, we successfully increased total fatty acid production, TAG production and CBL production in some S. cerevisiae strains. The relative CBL content in three yeast strains harboring cocoa genes increased 190, 230 and 196% over the control strain, respectively; especially, the potential SOS content of the three yeast strains increased 254, 476 and 354% over the control strain. Moreover, one of the three yeast strains had a 2.25-fold increased TAG content and 6.7-fold higher level of CBL compared with the control strain. In summary, CBL production by S. cerevisiae were increased through expressing selected cocoa genes potentially involved in CB biosynthesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-017-0333-1) contains supplementary material, which is available to authorized users.

show abstract

“…The discovery of enzymes with new activities increases the flexibility of pathway design [28] , [63] . The combination of bioinformatics and molecular modeling can be helpful to rationally identify an enzyme catalyzing the desired reaction [64] . In addition, large sequencing data from different environments enable us to use the genetic information of ‘microbial dark matter’ [65] .…”

Section: Discussionmentioning

confidence: 99%

Modules for in vitro metabolic engineering: Pathway assembly for bio-based production of value-added chemicals

Taniguchi

Okano

Honda

2017

Synthetic and Systems Biotechnology

View full text Add to dashboard Cite

Bio-based chemical production has drawn attention regarding the realization of a sustainable society. In vitro metabolic engineering is one of the methods used for the bio-based production of value-added chemicals. This method involves the reconstitution of natural or artificial metabolic pathways by assembling purified/semi-purified enzymes in vitro. Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel, enabling easier pathway design with high modularity. Multiple modules have been designed, built, tested, and improved by different groups for different purpose. In this review, we focus on these in vitro metabolic engineering modules, especially focusing on the carbon metabolism, and present an overview of input modules, output modules, and other modules related to cofactor management.

show abstract

Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

Cited by 81 publications

References 31 publications

Short-chain ketone production by engineered polyketide synthases in Streptomyces albus

Short-chain ketone production by engineered polyketide synthases in Streptomyces albus

Increasing cocoa butter-like lipid production of Saccharomyces cerevisiae by expression of selected cocoa genes

Modules for in vitro metabolic engineering: Pathway assembly for bio-based production of value-added chemicals

Contact Info

Product

Resources

About