Cell-free system

Cell-free systems may be divided into two primary classifications: cell extract-based, which remove components from within a whole cell for external use, and purified enzyme-based, which use purified components of the molecules known to be involved in a given process.{{Cite journal|last1=Rollin|first1=Joseph A.|last2=Tam|first2=Tsz Kin|last3=Zhang|first3=Y.-H. Percival|date=2013-06-21|title=New biotechnology paradigm: cell-free biosystems for biomanufacturing|journal=Green Chemistry|language=en|volume=15|issue=7|doi=10.1039/c3gc40625c|issn=1463-9270|page=1708}}{{Cite journal|last1=Shimizu|first1=Yoshihiro|last2=Inoue|first2=Akio|last3=Tomari|first3=Yukihide|last4=Suzuki|first4=Tsutomu|last5=Yokogawa|first5=Takashi|last6=Nishikawa|first6=Kazuya|last7=Ueda|first7=Takuya|date=2001-05-23|title=Cell-free translation reconstituted with purified components|journal=Nature Biotechnology|volume=19|issue=8|pages=751–755|doi=10.1038/90802|pmid=11479568|s2cid=22554704}} The cell extract-based type are susceptible to problems like quick degradation of components outside their host, as shown in a study by Kitaoka et al. where a cell-free translation system based on Escherichia coli (E. coli), of the cell extract-based type, had the mRNA template degrade very quickly and led to the halt of protein synthesis.{{Cite journal|last1=Kitaoka|first1=Yoshihisa|last2=Nishimura|first2=Norihiro|last3=Niwano|first3=Mitsuru|title=Cooperativity of stabilized mRNA and enhanced translation activity in the cell-free system|journal=Journal of Biotechnology|volume=48|issue=1–2|pages=1–8|doi=10.1016/0168-1656(96)01389-2|pmid=8818268|year=1996}}

The methods of preparation vary between situations of both types of cell-free systems.

Nobel Prize winner Eduard Buchner was arguably the first to present a cell-free system using yeast extracts, but since then alternative sources have been found.{{cite journal|last1=Barnett|first1=James A.|last2=Lichtenthaler|first2=Frieder W.|title=A history of research on yeasts 3: Emil Fischer, Eduard Buchner and their contemporaries, 1880-1900|journal=Yeast|date=15 March 2001|volume=18|issue=4|pages=363–388|doi=10.1002/1097-0061(20010315)18:4<363::AID-YEA677>3.0.CO;2-R|pmid=11223946|s2cid=2349735 |issn=1097-0061|doi-access=free}}{{Cite journal|last=Swartz|first=James R.|date=2012-01-01|title=Transforming biochemical engineering with cell-free biology|journal=AIChE Journal|language=en|volume=58|issue=1|pages=5–13|doi=10.1002/aic.13701|issn=1547-5905}} E. coli, wheat germ, and rabbit reticulocytes have all proven useful to create cell-free systems by extraction of their interior components.{{Cite journal|last1=Stiege|first1=Wolfgang|last2=Erdmann|first2=Volker A.|title=The potentials of the in vitro protein biosynthesis system|journal=Journal of Biotechnology|volume=41|issue=2–3|pages=81–90|doi=10.1016/0168-1656(95)00005-b|pmid=7654353|year=1995}} E. coli 30S extracts have been acquired, for example, by grinding the bacteria with alumina, followed by further cleaning.{{cite journal| author1= Matthaei H. |author2=Nirenberg | title = Characteristics and Stabilization of DNAase-Sensitive Protein Synthesis in E. coli Extracts | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 47| issue = 10 | pages = 1580–1588| year = 1962|doi=10.1073/pnas.47.10.1580 | bibcode = 1961PNAS...47.1580M | pmid=14471391 | pmc=223177|doi-access=free }} Similarly, wheat germ has been ground with acid-washed sand or powdered glass to open the cell membranes up.{{Cite book|last1=Anderson|first1=Carl W.|last2=Straus|first2=J.William|last3=Dudock|first3=Bernard S.|pages=[https://archive.org/details/recombinantdna0000unse/page/635 635–644]|doi=10.1016/0076-6879(83)01044-7|pmid=6888279|chapter=[41] Preparation of a cell-free protein-synthesizing system from wheat germ|title=Recombinant DNA Part C|volume=101|series=Methods in Enzymology|year=1983|isbn=9780121820015|chapter-url=https://archive.org/details/recombinantdna0000unse/page/635}}{{Cite journal|last1=Madin|first1=Kairat|last2=Sawasaki|first2=Tatsuya|last3=Ogasawara|first3=Tomio|last4=Endo|first4=Yaeta|date=2000-01-18|title=A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: Plants apparently contain a suicide system directed at ribosomes|journal=Proceedings of the National Academy of Sciences|language=en|volume=97|issue=2|pages=559–564|doi=10.1073/pnas.97.2.559|issn=0027-8424|pmid=10639118|pmc=15369|bibcode=2000PNAS...97..559M|doi-access=free}} Rabbit reticulocytes have been lysed in a solution of Magnesium chloride and had the extract filtered away from the membranes by centrifugation.{{Cite book|last1=Woodward|first1=William R.|last2=Ivey|first2=Joel L.|last3=Herbert|first3=Edward|pages=[https://archive.org/details/nucleicacids0000unse/page/724 724–731]|doi=10.1016/0076-6879(74)30069-9|pmid=4853925|chapter=[67a] Protein synthesis with rabbit reticulocyte preparations|title=Nucleic Acids and Protein Synthesis Part F|volume=30|series=Methods in Enzymology|year=1974|isbn=9780121818937|chapter-url=https://archive.org/details/nucleicacids0000unse/page/724}}

Cell-free synthetic pathway biotransformation biosystems are proposed as a new low-cost biomanufacturing platform compared to microbial fermentation used for thousands of years.{{cite journal | title=Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: Challenges and opportunities | author=Y. H. Percival Zhang | journal=Biotechnology and Bioengineering |date=March 2010 | volume=105 | issue=4 | pages=663–677 | doi=10.1002/bit.22630 | pmid=19998281| doi-access=free }} Cell-free biosystems have several advantages suitable in industrial applications:

• Very high product yields are usually accomplished without the formation of by-products or the synthesis of cell mass. For example, with a synthetic enzyme pathway, from the reaction with starch and water

:C₆H₁₀O₅ (l) + 7 H₂O (l) → 12 H₂ (g) + 6 CO₂ (g),

:nearly 12 Gaseous hydrogen has been produced per glucose unit of polysaccharides and water, three times of the theoretical yield of the best anaerobic hydrogen-producing microorganisms.{{cite journal | doi = 10.1371/journal.pone.0000456 | volume=2 | issue=5 | title=High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway | journal=PLOS ONE | pages=e456 | pmid=17520015 | pmc=1866174 | year=2007 | vauthors=Zhang YH, Evans BR, Mielenz JR, Hopkins RC, Adams MW| bibcode=2007PLoSO...2..456Z | doi-access=free }}

• In vitro biosystems can implement some biological reactions that living microbes or chemical catalysts cannot implement before. For example, beta-1,4-glucosidic bond linked cellulose can be converted to alpha-1,4-glucosidic bond linked starch by a mixture of intracellular and extracellular enzymes in a single reaction container.{{cite journal | doi = 10.1073/pnas.1302420110 | volume=110 | issue=18 | title=Enzymatic transformation of nonfood biomass to starch | journal=Proceedings of the National Academy of Sciences | pages=7182–7187 | pmid=23589840 | pmc=3645547 | vauthors=You C, Chen H, Myung S, Sathitsuksanoh N, Ma H, Zhang XZ, Li J, Zhang YH | year=2013| bibcode=2013PNAS..110.7182Y | doi-access=free }}
• Enzymatic systems, without the barrier of cellular membrane, usually have faster reaction rates than microbial systems. For instance, enzymatic fuel cells usually have much higher power outputs than microbial fuel cells.{{cite journal | doi = 10.1038/ncomms4026 | volume=5 | title=A high-energy-density sugar biobattery based on a synthetic enzymatic pathway | journal=Nature Communications | pmid=24445859 | page=3026 | vauthors=Zhu Z, Kin Tam T, Sun F, You C, Percival Zhang YH | year=2014| bibcode=2014NatCo...5.3026Z | doi-access=free | hdl=10919/87717 | hdl-access=free }}
• Enzyme cocktails can tolerate toxic compounds better than microorganisms.{{cite journal | doi = 10.1016/j.chembiol.2010.12.019 | pmid=21439482 | volume=18 | issue=3 | title=Biohydrogenation from Biomass Sugar Mediated by In Vitro Synthetic Enzymatic Pathways | journal= Chemistry & Biology| pages=372–380 | year=2011 | last1 = Wang | first1 = Yiran | last2 = Huang | first2 = Weidong | last3 = Sathitsuksanoh | first3 = Noppadon | last4 = Zhu | first4 = Zhiguang | last5 = Zhang | first5 = Y.-H. Percival| doi-access = free }}
• Enzyme mixtures usually work under broad reaction conditions, such as high temperature, low pH, the presence of organic solvents or ionic liquids.

{{Main|Cell-free protein synthesis}}

In vitro biosystems can be easily controlled and accessed without membranes. Notably, in work leading to a Nobel prize the Nirenberg and Matthaei experiment used a cell-free system, of the cell extract-based type, to incorporate chosen amino acids tagged radioactively into synthesized proteins with 30S extracted from E. coli.{{cite journal| doi= 10.1073/pnas.47.10.1588|author1=Nirenberg, M.W. |author2=Matthaei, H.J. |name-list-style=amp | year = 1961 |title = The Dependence Of Cell- Free Protein Synthesis In E. coli Upon Naturally Occurring Or Synthetic Polyribonucleotides | journal = Proceedings of the National Academy of Sciences of the United States of America |volume = 47| issue = 10 | pages = 1588–1602|bibcode = 1961PNAS...47.1588N | pmid=14479932 | pmc=223178|doi-access=free }} More recent studies, such as the study done by Spirin et al. with prokaryotic and eukaryotic version of their cell-free translation system, have also synthesized proteins with increased production, incorporating techniques like continuous flow to add materials and remove products.{{Cite journal|last1=Spirin|first1=A. S.|last2=Baranov|first2=V. I.|last3=Ryabova|first3=L. A.|last4=Ovodov|first4=S. Y.|last5=Alakhov|first5=Y. B.|date=1988-11-25|title=A continuous cell-free translation system capable of producing polypeptides in high yield|journal=Science|language=en|volume=242|issue=4882|pages=1162–1164|doi=10.1126/science.3055301|issn=0036-8075|pmid=3055301|bibcode=1988Sci...242.1162S}} With such advances in yield, productivity applications have been expanded, such as the synthesis of fusion proteins to potentially serve as vaccines for B-cell lymphomas.{{Cite journal|last1=Yang|first1=Junhao|last2=Kanter|first2=Gregory|last3=Voloshin|first3=Alexei|last4=Michel-Reydellet|first4=Nathalie|last5=Velkeen|first5=Hendrik|last6=Levy|first6=Ronald|last7=Swartz|first7=James R.|date=2005-03-05|title=Rapid expression of vaccine proteins for B-cell lymphoma in a cell-free system|journal=Biotechnology and Bioengineering|language=en|volume=89|issue=5|pages=503–511|doi=10.1002/bit.20283|pmid=15669088|issn=1097-0290}} Additionally, cell-free protein synthesis is becoming a new alternative choice for fast protein synthesis.

Engineering of metabolic processes have been achieved through cell-free systems.{{cite journal |last1=Tinafar |first1=Aidan |last2=Jaenes |first2=Katariina |last3=Pardee |first3=Keith |title=Synthetic Biology Goes Cell-Free |journal=BMC Biology |date=8 August 2019 |volume=17 |issue=1 |page=64 |doi=10.1186/s12915-019-0685-x|pmid=31395057 |pmc=6688370 |doi-access=free }} Bujara et al., for example, were able to use glycolytic network extracts, consisting of enzymes from E. coli that produced dihydroxyacetone phosphate, to analyze in real-time the metabolite concentrations while altering enzyme levels, with the result of optimal production of dihydroxyacetone phosphate.{{Cite journal|last1=Bujara|first1=Matthias|last2=Schümperli|first2=Michael|last3=Pellaux|first3=René|last4=Heinemann|author4-link=Matthias Heinemann|first4=Matthias|last5=Panke|first5=Sven|title=Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis|journal=Nature Chemical Biology|volume=7|issue=5|pages=271–277|doi=10.1038/nchembio.541|pmid=21423171|year=2011|s2cid=6613252 |url=https://pure.rug.nl/ws/files/6761256/2011NatChemBiolBujara.pdf}} Further, Calhoun and Swartz were able to use a glycolytic intermediate to fuel a cell-free system, enabling relatively inexpensive ATP generation compared to reagent usage in phosphoenolpyruvate reactions.{{Cite journal|last1=Calhoun|first1=Kara A.|last2=Swartz|first2=James R.|date=2005-06-05|title=Energizing cell-free protein synthesis with glucose metabolism|journal=Biotechnology and Bioengineering|language=en|volume=90|issue=5|pages=606–613|doi=10.1002/bit.20449|pmid=15830344|issn=1097-0290|doi-access=free}}

Cell-free systems have also been used to incorporate unnatural amino acids.{{Cite journal|last1=Noren|first1=C. J.|last2=Anthony-Cahill|first2=S. J.|last3=Griffith|first3=M. C.|last4=Schultz|first4=P. G.|date=1989-04-14|title=A general method for site-specific incorporation of unnatural amino acids into proteins|journal=Science|language=en|volume=244|issue=4901|pages=182–188|doi=10.1126/science.2649980|issn=0036-8075|pmid=2649980|bibcode=1989Sci...244..182N}} Shimizu et al. were able to change a stop codon to a sense codon by omitting the RF1 release factor, indicating ability to insert desired amino acids in unnatural situations. This is of use in systems where working inside a cell is problematic, such as the process of amino acid metabolism preventing specific labelling of amino acids that would be useful in multidimensional NMR spectroscopy.{{Cite journal|last1=Kigawa|first1=Takanori|last2=Muto|first2=Yutaka|last3=Yokoyama|first3=Shigeyuki|date=1995-09-01|title=Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis|journal=Journal of Biomolecular NMR|language=en|volume=6|issue=2|pages=129–134|doi=10.1007/bf00211776|pmid=8589601|s2cid=19080000|issn=0925-2738}} Kigawa et al.were able to successfully label amino acids in a cell-free system where amino acid metabolism was no longer present, thus making such systems useful to NMR studies.

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Category:Cell biology