Editing Metabolic engineering (section)

== History and applications ==
[[Image:Epithelial-cells.jpg|right|thumb|135px|Cellular metabolism can be optimized for industrial use.]]

In the past, to increase the productivity of a desired [[metabolite]], a [[microorganism]] was genetically modified by chemically induced [[mutation]], and the mutant [[strain (biology)|strain]] that overexpressed the desired metabolite was then chosen.<ref name="Voit">Voit,Eberhard.,Torres,Nestor V.(2002)." Pathways Analysis and Optimization in Metabolic Engineering." Cambridge:University Press,p.ix-x</ref> However, one of the main problems with this technique was that the metabolic pathway for the production of that metabolite was not analyzed, and as a result, the constraints to production and relevant pathway enzymes to be modified were unknown.<ref name = "Voit" />

In 1990s, a new technique called metabolic engineering emerged. This technique analyzes the metabolic pathway of a [[microorganism]], and determines the constraints and their effects on the production of desired compounds. It then uses genetic engineering to relieve these constraints. Some examples of successful metabolic engineering are the following: (i) Identification of constraints to lysine production in ''[[Corynebacterium]]'' ''glutamicum'' and insertion of new genes to relieve these constraints to improve production<ref>Stephanopoulos, G. N., Aristidou, A. A., Nielsen, J. (1998). " Metabolic Engineering: Principles and Methodologies ". San Diego: Academic Press</ref> (ii) Engineering of a new [[fatty acid biosynthesis]] pathway, called reversed [[beta oxidation]] pathway, that is more efficient than the native pathway in producing fatty acids and alcohols which can potentially be catalytically converted to chemicals and fuels<ref>Dellomonaco, Clementina.(2011). '' Engineered Reversal of the beta oxidation cycle for the Synthesis of Fuels and Chemicals.'' Nature 476,355-359</ref> (iii) Improved production of [[3-deoxy-D-arabino-heptulosonate 7-phosphate|DAHP]] an aromatic metabolite produced by ''E. coli'' that is an intermediate in the production of aromatic amino acids.<ref>Patnaik, R. and Liao, J. (1994). "Engineering of Escherichia coli central metabolism for aromatic metabolite production with near theoretical yield". ''Appl. Environ. Microbiol.'' 60(11):3903-3908</ref> It was determined through metabolic flux analysis that the theoretical maximal yield of DAHP per glucose molecule utilized, was 3/7. This is because some of the carbon from glucose is lost as carbon dioxide, instead of being utilized to produce DAHP. Also, one of the metabolites (PEP, or [[phosphoenolpyruvate]]) that are used to produce DAHP, was being converted to [[pyruvate]] (PYR) to transport glucose into the cell, and therefore, was no longer available to produce DAHP. In order to relieve the shortage of PEP and increase yield, Patnaik et al. used genetic engineering on ''E. coli'' to introduce a reaction that converts PYR back to PEP. Thus, the PEP used to transport glucose into the cell is regenerated, and can be used to make DAHP. This resulted in a new theoretical maximal yield of 6/7 – double that of the native ''E. coli'' system.

At the industrial scale, metabolic engineering is becoming more convenient and cost-effective. According to the [[Biotechnology Industry Organization]], "more than 50 [[biorefinery]] facilities are being built across North America to apply metabolic engineering to produce biofuels and chemicals from renewable [[biomass]] which can help reduce greenhouse gas emissions". Potential biofuels include short-chain [[alcohols]] and alkanes (to replace [[gasoline]]), [[fatty acid methyl esters]] and [[fatty alcohols]] (to replace [[diesel fuel|diesel]]), and [[fatty acid]]-and [[isoprenoid]]-based biofuels (to replace [[diesel fuel|diesel]]).<ref>Keasling D.,Jay(2010).'' Advanced Biofuel production in microbes.'' Biotechnol.J.,5,147-162</ref>

Metabolic engineering continues to evolve in efficiency and processes aided by breakthroughs in the field of [[synthetic biology]] and progress in understanding [[Metabolite damage and its repair or pre-emption|metabolite damage and its repair or preemption]]. Early metabolic engineering experiments showed that accumulation of [[reactive intermediate]]s can limit flux in engineered pathways and be deleterious to host cells if matching damage control systems are missing or inadequate.<ref>{{Cite journal|last1=Martin|first1=Vincent J. J.|last2=Pitera|first2=Douglas J.|last3=Withers|first3=Sydnor T.|last4=Newman|first4=Jack D.|last5=Keasling|first5=Jay D.|date=2003-07-01|title=Engineering a mevalonate pathway in Escherichia coli for production of terpenoids|journal=Nature Biotechnology|volume=21|issue=7|pages=796–802|doi=10.1038/nbt833|issn=1087-0156|pmid=12778056|s2cid=17214504 }}</ref><ref>{{Cite journal|last1=Withers|first1=Sydnor T.|last2=Gottlieb|first2=Shayin S.|last3=Lieu|first3=Bonny|last4=Newman|first4=Jack D.|last5=Keasling|first5=Jay D.|date=2007-10-01|title=Identification of isopentenol biosynthetic genes from Bacillus subtilis by a screening method based on isoprenoid precursor toxicity|journal=Applied and Environmental Microbiology|volume=73|issue=19|pages=6277–6283|doi=10.1128/AEM.00861-07|issn=0099-2240|pmc=2075014|pmid=17693564}}</ref> Researchers in synthetic biology optimize genetic pathways, which in turn influence cellular metabolic outputs. Recent decreases in cost of [[DNA synthesis|synthesized DNA]] and developments in [[Synthetic biological circuit|genetic circuits]] help to influence the ability of metabolic engineering to produce desired outputs.<ref>{{Cite journal|title = Synthetic Biology and Metabolic Engineering|journal = ACS Synthetic Biology|date = 2012-11-16|pages = 514–525|volume = 1|issue = 11|doi = 10.1021/sb300094q|pmid = 23656228|first = Gregory|last = Stephanopoulos}}</ref>