encapsulation of a metabolic network for atp recycling and glycerol 3&#45;p synthesis in submicron&#45;size vesicles

복잡한 단백질 네트워크를 위한 지질 소포 캡슐화 프로토콜

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>

저자 스포트라이트: 합성 세포 공학의 과제 해결

나노미터 및 마이크로미터 크기의 소포에서 평형을 벗어난 대사 네트워크 구축

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.

서브미크론 크기 소포에서 ATP 재활용 및 글리세롤 3-P 합성을 위한 대사 네트워크 캡슐화

먼저 92.7마이크로리터의 버퍼 A를 빈 1.5밀리리터 튜브에 피펫팅합니다. 그런 다음 DTT, ADP 나트륨, 염화 마그네슘, L-오르니틴 및 효소를 추가합니다. 용액을 부드럽게 혼합한 후 미리 형성된 프로테올리포좀 66.6마이크로리터 위에 첨가합니다.혼합물을 액체 질소에 급속 얼린 다음 약 섭씨 10도의 얼음 욕조에서 해동합니다. 캡슐화 혼합물을 압출기에 13회 통과시켜 완충액 A, DTT, ADP 나트륨 및 L-오르니틴으로 사전 평형을 이루고 압출된 용액을 1.5밀리리터 튜브에 수집합니다. ATP, 피펫 완충액 K, 프로테오올리포솜 및 이오노포어의 합성을 측정하기 위해 작은 창이 있는 검은색 석영 큐벳에 넣습니다.형광계에서 샘플을 섭씨 30도로 예열합니다. 이제 perceval HR의 여기 스펙트럼을 획득하십시오. 프로브 신호가 일정하면 L-아르기닌과 글리세롤을 과도하게 첨가하여 대사 네트워크를 시작하고 시간 경과에 따른 반응을 추적합니다. 프로테올리포좀에 L-아르기닌을 추가하면 500 및 430 나노미터 여기(excitation)에서 perceval HR 형광 비율이 급격히 증가했습니다.

encapsulation-metabolic-network-for-atp-recycling-glycerol-3-p

Research

JoVE Journal

Biochemistry

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

75 조회수.  University of Groningen. 먼저 92.7마이크로리터의 버퍼 A를 빈 1.5밀리리터 튜브에 피펫팅합니다. 그런 다음 DTT, ADP 나트륨, 염화 마그네슘, L-오르니틴 및 효소를 추가합니다. 용액을 부드럽게 혼합한 후 미리 형성된 프로테올리포좀 66.6마이크로리터 위에 첨가합니다.혼합물을 액체 질소에 급속 얼린 다음 약 섭씨 10도의 얼음 욕조에서 해동합니다. 캡슐화 혼합물을 압출기에 13회 통과시켜 완충액...

비디오: 서브미크론 크기 소포에서 ATP 재활용 및 글리세롤 3-P 합성을 위한 대사 네트워크 캡슐화

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, using purified components. This method is relevant for the design and construction of bioreactors and the study of complex out-of-equilibrium metabolic reaction networks. We start by reconstituting (multiple) membrane proteins into large unilamellar vesicles (LUVs) according to a previously developed protocol. We then encapsulate a mixture of purified enzymes, metabolites, and fluorescence-based sensors (fluorescent proteins or dyes) via freeze-thaw-extrusion and remove non-incorporated components by centrifugation and/or size-exclusion chromatography. The performance of the metabolic networks is measured in real time by monitoring the ATP/ADP ratio, metabolite concentration, internal pH, or other parameters by fluorescence readout. Our membrane protein-containing vesicles of 100-400 nm diameter can be converted into giant-unilamellar vesicles (GUVs), using existing but optimized procedures. The approach enables the inclusion of soluble components (enzymes, metabolites, sensors) into micrometer-size vesicles, thus upscaling the volume of the bioreactors by orders of magnitude. The metabolic network containing GUVs are&#160;trapped in microfluidic devices for analysis by optical microscopy.

We present a protocol for reconstituting membrane proteins and encapsulating enzymes and other water-soluble components in lipid vesicles of sub-micrometer and micrometer size.

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