upscaling a metabolic network for micrometer&#45;sized vesicles

Kompleks Protein Ağları için Lipid Vezikül Kapsülleme Protokolü

The field of bottom-up synthetic biology focuses on constructing (minimal) cells1,2 and metabolic bioreactors for biotechnological3,4 or biomedical purposes5,6,7,8. The construction of synthetic cells provides a unique platform that allows researchers to study (membrane) proteins in well-defined conditions mimicking those of native environments, enabling the discovery of emergent properties and concealed biochemical functions of proteins and reaction networks9. As an intermediate step towards an autonomously functioning synthetic cell, modules are developed that capture essential features of living cells such as metabolic energy conservation, protein and lipid synthesis, and homeostasis. Such modules not only enhance our understanding of life but also have potential applications in the fields of medicine8 and biotechnology10.
Transmembrane proteins are at the heart of virtually any metabolic network as they transport molecules in or out of the cell, signal, and respond to the quality of the environment, and play numerous biosynthetic roles. Thus, the engineering of metabolic modules in synthetic cells requires in most cases the reconstitution of integral and/or peripheral membrane proteins into a membrane bilayer composed of specific lipids and high integrity (low permeability). The handling of these membrane proteins is challenging and requires specific knowledge and experimental skills.
Several methods have been developed to reconstitute membrane proteins within phospholipid vesicles, most often with the purpose of studying the function11,12, regulation13, kinetic properties14,15, lipid dependence15,16, and/or stability17 of a specific protein. These methods involve the rapid dilution of detergent-solubilized protein into aqueous media in the presence of lipids18, the removal of detergents by incubating detergent-solubilized protein with detergent-destabilized lipid vesicles and absorption of the detergent(s) onto polystyrene beads19, or the removal of detergents by dialysis or size-exclusion chromatography20. Organic solvents have been used to form lipid vesicles, for example, via the formation of oil-water interphases21, but the majority of integral membrane proteins are inactivated when exposed to such solvents.
In our laboratory, we mostly reconstitute membrane proteins by the detergent-absorption method to form large-unilamellar vesicles (LUVs)19. This method allows the co-reconstitution of multiple membrane proteins and the encapsulation in the vesicle lumen of enzymes, metabolites, and probes22,23. The membrane protein-containing LUVs can be converted into giant-unilamellar vesicles (GUVs) with/without encapsulation of water-soluble components, using either electroformation24 or gel-assisted swelling25 and specific conditions to preserve the integrity of the membrane proteins26.
This paper presents a protocol for the reconstitution in LUVs of an out-of-equilibrium metabolic network that regenerates ATP through the breakdown of L-arginine into L-ornithine27. The formation of ATP is coupled to the production of glycerol-3-phosphate (G3P), an important building block for phospholipid synthesis22,28. The metabolic pathway consists of two integral membrane proteins, an arginine/ornithine (ArcD) and a G3P/Pi antiporter (GlpT). In addition, three soluble enzymes (ArcA, ArcB, ArcC) are required for the recycling of ATP, and GlpK is used to convert glycerol into glycerol 3-phosphate, using the ATP from the breakdown of L-arginine, see Figure 1 for a schematic overview of the pathway. This protocol represents a good starting point for the future construction of even more complex reaction networks-for the synthesis of lipids or proteins or the division of cells. The lipid composition of the vesicles supports the activity of a wide variety of integral membrane proteins and has been optimized for the transport of diverse molecules into or out of the vesicles27,29,30.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/66627/66627fig01v2.jpg" /> 
Figure 1: Overview of the pathway for ATP production and glycerol 3-phosphate synthesis and excretion. <a href="https://www.jove.com/files/ftp_upload/66627/66627fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
In short, purified membrane proteins (solubilized in dodecyl-&#946;-D-maltoside, DDM) are added to preformed lipid vesicles that have been destabilized with Triton X-100, which allows the insertion of the proteins into the membrane. The detergent molecules are subsequently (slowly) removed by the addition of activated polystyrene beads, resulting in the formation of well-sealed proteoliposomes. Soluble components can then be added to the vesicles and encapsulated via freeze-thaw cycles, which traps the molecules in the process of membrane fusion. The obtained vesicles are highly heterogeneous and many are multilamellar. They are then extruded through a polycarbonate filter with a pore size of 400, 200, or 100 nm, which yields more uniformly sized vesicles; the smaller the pore size, the more homogeneous and unilamellar the vesicles but at the price of a smaller internal volume. Non-incorporated proteins and small molecules are removed from the external solution by size-exclusion chromatography. The proteoLUVs can be converted into micrometer size vesicles by gel-assisted swelling, and these proteoGUVs are then collected and trapped in a microfluidic chip for microscopic characterization and manipulation. Figure 2 shows a schematic overview of the full protocol.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/66627/66627fig02v2.jpg" /> 
Figure 2: Overview of the protocol for reconstituting membrane proteins and encapsulating enzymes and water-soluble components in lipid vesicles of sub-micrometer (LUVs) and micrometer size (GUVs). <a href="https://www.jove.com/files/ftp_upload/66627/66627fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The reconstitution and encapsulation protocols work well and the functionality of the proteins is retained, but the proteoLUVs and proteoGUVs are heterogeneous in size. Microfluidic approaches31,32 allow the formation of micrometer-sized vesicles that are more homogeneous in size, but functional reconstitution of membrane proteins is generally not possible because residual solvent in the bilayer inactivates the proteins. The proteoLUVs range in size from 100 to 400 nm, and at low concentrations of enzymes, the encapsulation may lead to vesicles with incomplete metabolic pathways (stochastic effects; see Figure 3). LUVs are ideal for constructing specific metabolic modules, as shown here for the production of ATP and building blocks like G3P. Such proteoLUVs can potentially be encapsulated in GUVs and serve as organelle-like compartments for the host vesicles.
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/66627/66627fig03v2.jpg" /> 
Figure 3: Number of molecules per vesicle with a diameter of 100, 200, or 400 nm. (A) When the encapsulated proteins (enzymes, probes) are in the range of 1-10 &#181;M. (B) The reconstitution is done at 1 to 1,000, 1 to 10,000, and 1 to 100,000 membrane proteins per lipid (mol/mol). We make the assumption that molecules are encapsulated at the indicated concentrations and incorporated in the membrane at these protein-to-lipid ratios. For some enzymes, we have seen that they bind to membranes, which can increase their apparent concentration in the vesicles. Abbreviation: LPR = Lipid-Protein-Ratio <a href="https://www.jove.com/files/ftp_upload/66627/66627fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Yazar Spotlight: Sentetik Hücre Mühendisliğinde Zorlukların Üstesinden Gelmek

Nano ve Mikrometre Boyutlu Veziküllerde Denge Dışı Metabolik Ağların İnşası

In the Netherlands, the BaSyC consortium aims to construct synthetic cells from molecular components. The BaSyC consortium is composed of research groups ranging from molecular biology to chemistry, physics, and computational sciences. The goal of this consortium is to create a self-replicating system capable of autonomous growth to transmit information and to divide.And we currently focus on the building of molecular networks that are integrated towards more complex molecular systems. Recent developments in synthetic biology include the engineering of modules for cellular functions, integrating them into complex networks for applications in diagnostics, therapy, synthetic immunology, and adaptive materials. This progress spans groups in Europe, America, and Asia, advancing both top-down and bottom-up approaches to synthetic cell construction.Current technologies in our field include the engineering and evolutionary methods to construct and optimize metabolic networks. We use AI for molecular selection and advanced biochemical and biophysical techniques for component isolation and network formation. We also employ membrane reconstitution, physical encapsulation, and visualization via fluorescent spectroscopy and microscopy.With the integration of modules, the number of membrane proteins and enzymes increase enormously, which poses constraints on our reconstitution and encapsulation technologies. Stochastic encapsulation becomes an issue with sub-micron size vesicles, and the efficiency of forming micrometer-size vesicles decreases when multiple membrane proteins are reconstituted in the lipid membrane. In Groningen, we have developed metabolic networks for ATP productions and maintaining an out-of-equilibrium state through substrate feeding and product export.Additionally, we linked ATP recycling to the synthesis and excretion of lipid precursors, enabling secondary vesicles to produce lipids, which is a significant advancement in our field.

Mikrometre Boyutlu Veziküller için Metabolik Bir Ağın Yükseltilmesi

Başlamak için, kesilmiş 200 mikrolitrelik bir pipet ucunun altını önceden yapılmış bir mikroakışkan yakalama cihazına yerleştirin. Çipin giriş haznesine 400 mikrolitre beta kazein çözeltisi enjekte etmek için 0,2 mikrometre filtreli bir şırınga kullanarak pipetleyin. Çipi altı dakika boyunca 900 G'de santrifüjleyin.Sıvı seviyesi artık hem girişte hem de çıkışta eşit olmalıdır. İki objektif slaytta ara parçanın bir taslağını çizin. Slaytları hidrofilik hale getirmek için bir dakika boyunca yüksek oksijenli plazma ile temizleyin.Tamamen agaroz ile kaplanana kadar slaydın üzerine düşük jelleşme sıcaklığındaki agarozu ekleyin. Daha sonra slaytı 90 derecelik bir açıyla eğin ve fazla agarozu bir doku üzerine boşaltın. Slaytları 30 dakika boyunca 50 santigrat dereceye yerleştirin.Bir milimetrelik bir prob ile donatılmış bir el tipi prob sonikatörü ile hazırlanan proteolipozomları sonikleştirin. Sonikasyonu beş kez tekrarlamadan önce proteo SUV'ları 30 saniye boyunca buz üzerinde tutun. 100 mikrolitrelik bir şırınga ile, hazırlanmış bir agaroz jeli üzerine 0,5 mikrolitrelik proteo SUV damlacıkları bırakın.Damlacıkları kurutmak için yaklaşık 10 dakika nitrojen akışı kullanın. Bir şırınga ve iğne ile, şişme solüsyonunu yan taraftaki küçük bir delikten hazırlanmış bir odaya pipetleyin ve veziküllerin en az 30 dakika boyunca 22 santigrat derecede şişmesine izin verin. GUV'leri jelden toplamak için hazneyi katı bir yüzeye hafifçe vurun.GUV'leri mikroskopi için yakalamak için, bir mikroskop üzerine pasifleştirilmiş bir mikroakışkan çip monte edin. Kusurları kontrol ettikten sonra, boruyu bükülmüş bir iğne ile rezervuar çıkışına bağlayın. Diğer ucunu bir mililitrelik bir şırıngaya bağladıktan sonra, şırıngayı dakikada maksimum 10 mikrolitre akış hızına sahip bir pompaya monte edin.Rezervuarın yıkama tamponunu yeni ortamla değiştirin. En az 80 mikrolitre tampon P ile yıkayın. Fazla tamponu çıkardıktan sonra proteo GUV'leri hazneye ekleyin. Çip içinde yeterli GUV sıkışana kadar çipi zaman içinde izleyin.Fazla GUV solüsyonunu pipetleyin. Ardından, yıkama tamponunu P dakikada 0,1 ila bir mikrolitre akış hızında ekleyin. Son olarak, tuzakları yeterli miktarda vezikül ile lokalize edin.Ayarları mikroskoba uyguladıktan sonra, hazneye dakikada 0,5 mikrolitre akış hızında tampon R ekleyin. Kurutulmuş proteo LUV'lerin düşük jelleşme sıcaklığındaki agaroz jel üzerinde rehidrasyonu, mikrometre boyutunda veziküllerin oluşumuna neden oldu. GUV'lar hasat edildi ve bir beta kazein pasifleştirilmiş mikroakışkan cihaz içinde hapsedildi.

upscaling-a-metabolic-network-for-micrometersized-vesicles

Research

JoVE Journal

Biochemistry

Upscaling a Metabolic Network for Micrometer&#45;Sized Vesicles

Construction of Out&#45;of&#45;Equilibrium Metabolic Networks in Nano&#45; and Micrometer&#45;Sized Vesicles

We present a method to incorporate into vesicles complex protein networks, involving integral membrane proteins, enzymes, and fluorescence-based sensors, ...

Biyokimya

Reconstitution of Purified Membrane Proteins into Preformed Liposomes

Saflaştırılmış Membran Proteinlerinin Önceden Şekillendirilmiş Lipozomlara Yeniden Sulandırılması

Encapsulation of a Metabolic Network for ATP Recycling and Glycerol 3&#45;P Synthesis in Submicron&#45;Size Vesicles

Mikron Altı Boyutlu Veziküllerde ATP Geri Dönüşümü ve Gliserol 3-P Sentezi için Bir Metabolik Ağın Kapsüllenmesi