1
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Wong CK, Lai RY, Stenzel MH. Polymersomes with micellar patches. J Colloid Interface Sci 2024; 671:449-456. [PMID: 38815380 DOI: 10.1016/j.jcis.2024.05.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/29/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Hollow block copolymer particles called polymer vesicles (polymersomes) serve as versatile containers for compartmentalization in synthetic biology and drug delivery. Recently, there has been growing interest in using polymersomes as colloidal building blocks for creating higher-order clustered structures. Most reports thus far rely on the use of DNA base-pairing interactions to "glue" polymersomes with other colloidal components. In this study, we present two alternative electrostatically driven approaches to assemble polymersomes and model colloids (micelles) into hybrid clusters. The first approach uses pH to manipulate electrostatic interactions and effectively control the clustering extent of micellar subunits on polymersomes, while the second approach relies on the hydrolysis of an acid trigger, glucono delta-lactone (GDL), to introduce temporal control over clustering. We envisage our approaches and structures reported herein will help inspire the creation of new prospects for materials science and biomedical applications.
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Affiliation(s)
- Chin Ken Wong
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, NSW, Australia.
| | - Rebecca Y Lai
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, NSW, Australia
| | - Martina H Stenzel
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, NSW, Australia.
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2
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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3
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Han T, Miao G. Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites. Molecules 2024; 29:2106. [PMID: 38731602 PMCID: PMC11085123 DOI: 10.3390/molecules29092106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/27/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.
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Affiliation(s)
- Taotao Han
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
| | - Guopeng Miao
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan 232038, China
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4
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Joshi J, Hanson AD. A pilot oral history of plant synthetic biology. PLANT PHYSIOLOGY 2024; 195:36-47. [PMID: 38163646 PMCID: PMC11060686 DOI: 10.1093/plphys/kiad585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/15/2023] [Indexed: 01/03/2024]
Abstract
The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders' personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.
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Affiliation(s)
- Jaya Joshi
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
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5
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Song YF, Bai ZY, Lai XH, Luo Z, Hogstrand C. Ip3r-Grp75-Vdac and Relevant Ca 2+ Signaling Regulate Dietary Palmitic Acid-Induced De Novo Lipogenesis by Mitochondria-Associated ER Membrane (MAM) Recruiting Seipin in Yellow Catfish. J Nutr 2024:S0022-3166(24)00224-4. [PMID: 38641205 DOI: 10.1016/j.tjnut.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/10/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND The mitochondria-associated endoplasmic reticulum membrane (MAM) is the central hub for endoplasmic reticulum and mitochondria functional communication. It plays a crucial role in hepatic lipid homeostasis. However, even though MAM has been acknowledged to be rich in enzymes that contribute to lipid biosynthesis, no study has yet investigated the exact role of MAM on hepatic neutral lipid synthesis. OBJECTIVES To address these gaps, this study investigated the systemic control mechanisms of MAM on neutral lipids synthesis by recruiting seipin, focusing on the role of the inositol trisphosphate receptor-1,4,5(Ip3r)-75 kDa glucose-regulated protein (Grp75)-voltage-dependent anion channel (Vdac) complex and their relevant Ca2+ signaling in this process. METHODS To this end, a model animal for lipid metabolism, yellow catfish (Pelteobagrus fulvidraco), were fed 6 different diets containing a range of palmitic acid (PA) concentrations from 0-150 g/kg in vivo for 10 wk. In vitro, experiments were also conducted to intercept the MAM-mediated Ca2+ signaling in isolated hepatocytes by transfecting them with si-mitochondrial calcium uniporter (mcu). Because mcu was placed in the inner mitochondrial membrane (IMM), si-mcu cannot disrupt MAM's structural integrity. RESULTS 1. Hepatocellular MAM subproteome analysis indicated excessive dietary PA intake enhanced hepatic MAM structure joined by activating Ip3r-Grp75-Vdac complexes. 2. Dietary PA intake induced hepatic neutral lipid accumulation through MAM recruiting Seipin, which activated lipid droplet biogenesis. Our findings also revealed a previously unidentified mechanism whereby MAM-recruited seipin and controlled hepatic lipid homeostasis, depending on Ip3r-Grp75-Vdac-controlled Ca2+ signaling and not only MAM's structural integrity. CONCLUSIONS These results offer a novel insight into the MAM-recruited seipin in controlling hepatic lipid synthesis in a MAM structural integrity-dependent and Ca2+ signaling-dependent manner, highlighting the critical contribution of MAM in maintaining hepatic neutral lipid homeostasis.
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Affiliation(s)
- Yu-Feng Song
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan, China.
| | - Zhen-Yu Bai
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Hong Lai
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan, China
| | - Zhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Christer Hogstrand
- Diabetes and Nutritional Sciences Division, School of Medicine, King's College London, Franklin-Wilkins Building, London, United Kingdom
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6
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Zhang L, Zhou R, Liu D, Zhu M, Zhang G, Zhang L, Zhou SF, Jiang W. Multi-strategy orthogonal enhancement and analysis of aldo-keto reductase thermal stability. Int J Biol Macromol 2024; 264:130691. [PMID: 38458293 DOI: 10.1016/j.ijbiomac.2024.130691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Given their outstanding efficiency and selectivity, enzymes are integral in various domains such as drug synthesis, the food industry, and environmental management. However, the inherent instability of natural enzymes limits their widespread industrial application. In this study, we underscore the efficacy of enhancing protein thermal stability through comprehensive protein design strategies, encompassing elements such as the free energy of protein folding, internal forces within proteins, and the overall structural design. We also demonstrate the efficiency and precision of combinatorial screening in the thermal stability design of aldo-keto reductase (AKR7-2-1). In our research, three single-point mutations and five combinatorial mutations were strategically introduced into AKR7-2-1, using multiple computational techniques. Notably, the E12I/S235I mutant showed a significant increase of 25.4 °C in its melting temperature (Tm). Furthermore, the optimal mutant, E12V/S235I, maintained 80 % of its activity while realizing a 16.8 °C elevation in Tm. Remarkably, its half-life at 50 °C was increased to twenty times that of the wild type. Structural analysis indicates that this enhanced thermal stability primarily arises from reduced oscillation in the loop region and increased internal hydrogen bonding. The promising results achieved with AKR7-2-1 demonstrate that our strategy could serve as a valuable reference for enhancing the thermal stability of other industrial enzymes.
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Affiliation(s)
- Lingzhi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Rui Zhou
- Shanghai Marine Diesel Engine Research Institute, Shanghai 201108, PR China
| | - Dekai Liu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Meinan Zhu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Guangya Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Lijuan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Shu-Feng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| | - Wei Jiang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
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7
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Harder D, Ritzmann N, Ucurum Z, Müller DJ, Fotiadis D. Light Color-Controlled pH-Adjustment of Aqueous Solutions Using Engineered Proteoliposomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307524. [PMID: 38342618 PMCID: PMC11022694 DOI: 10.1002/advs.202307524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/16/2024] [Indexed: 02/13/2024]
Abstract
Controlling the pH at the microliter scale can be useful for applications in research, medicine, and industry, and therefore represents a valuable application for synthetic biology and microfluidics. The presented vesicular system translates light of different colors into specific pH changes in the surrounding solution. It works with the two light-driven proton pumps bacteriorhodopsin and blue light-absorbing proteorhodopsin Med12, that are oriented in opposite directions in the lipid membrane. A computer-controlled measuring device implements a feedback loop for automatic adjustment and maintenance of a selected pH value. A pH range spanning more than two units can be established, providing fine temporal and pH resolution. As an application example, a pH-sensitive enzyme reaction is presented where the light color controls the reaction progress. In summary, light color-controlled pH-adjustment using engineered proteoliposomes opens new possibilities to control processes at the microliter scale in different contexts, such as in synthetic biology applications.
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Affiliation(s)
- Daniel Harder
- Institute of Biochemistry and Molecular MedicineUniversity of BernBern3012Switzerland
- National Centre of Competence in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Noah Ritzmann
- National Centre of Competence in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
- Department of Biosystems Science and EngineeringETH ZürichBasel4056Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular MedicineUniversity of BernBern3012Switzerland
| | - Daniel J. Müller
- National Centre of Competence in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
- Department of Biosystems Science and EngineeringETH ZürichBasel4056Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular MedicineUniversity of BernBern3012Switzerland
- National Centre of Competence in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
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8
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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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9
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Tang X, Chen T, Ma Y, Mao C, Hu S, Zhang R, Yan Y, Pan Q, Feng C, Zhu X. Enzyme Reaction-Assisted Programmable Transcriptional Switches for Bioactive Molecule Detection. Anal Chem 2024; 96:331-338. [PMID: 38127443 DOI: 10.1021/acs.analchem.3c04198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Bioactive molecules are highly worthwhile to recognize and explore the latent pathogenic mechanism. Conventional methods for bioactive molecule detection, including mass spectrometry and fluorescent probe imaging, are limited due to the complex processing and signal interference. Here, we designed enzyme-reaction-assisted programmable transcriptional switches for the detection of bioactive molecules. The approach is based on the use of programmable enzyme site-specific cleavage-assisted DNA triplex-based conformational switches that, upon responding to bioactive molecules, can trigger the transcription of fluorescent light-up aptamers. Thanks to the programmable nature of the sensing platform, the method can be adapted to different bioactive molecules, and we demonstrated the enzyme-small molecule catalytic reaction combination of myeloperoxidase (MPO)-hydrogen peroxide (H2O2) as a model that transcriptional switches was capable of detecting H2O2 and possessed the specificity and anti-interference ability in vitro. Furthermore, we successfully applied the switches into cells to observe the detection feasibility in vivo, and dynamically monitored changes of H2O2 in cellular oxidative stress levels. Therefore, we attempt to amalgamate the advantages of enzyme reaction with the pluripotency of programmable transcriptional switches, which can take both fields a step further, which may promote the research of biostimuli and the construction of DNA molecular devices.
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Affiliation(s)
- Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Yonggeng Ma
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Changqing Mao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Runchi Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Yilin Yan
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
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10
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Cao S, Ivanov T, Heuer J, Ferguson CTJ, Landfester K, Caire da Silva L. Dipeptide coacervates as artificial membraneless organelles for bioorthogonal catalysis. Nat Commun 2024; 15:39. [PMID: 38169470 PMCID: PMC10761997 DOI: 10.1038/s41467-023-44278-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Artificial organelles can manipulate cellular functions and introduce non-biological processes into cells. Coacervate droplets have emerged as a close analog of membraneless cellular organelles. Their biomimetic properties, such as molecular crowding and selective partitioning, make them promising components for designing cell-like materials. However, their use as artificial organelles has been limited by their complex molecular structure, limited control over internal microenvironment properties, and inherent colloidal instability. Here we report the design of dipeptide coacervates that exhibit enhanced stability, biocompatibility, and a hydrophobic microenvironment. The hydrophobic character facilitates the encapsulation of hydrophobic species, including transition metal-based catalysts, enhancing their efficiency in aqueous environments. Dipeptide coacervates carrying a metal-based catalyst are incorporated as active artificial organelles in cells and trigger an internal non-biological chemical reaction. The development of coacervates with a hydrophobic microenvironment opens an alternative avenue in the field of biomimetic materials with applications in catalysis and synthetic biology.
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Affiliation(s)
- Shoupeng Cao
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Tsvetomir Ivanov
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Julian Heuer
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Calum T J Ferguson
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany.
- Department of Chemistry, McGill University, Montreal, H3A 0B8, Canada.
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11
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Xie X, Sun Y, Peng J, Zhang Z, Wang M, Wang Z, Lei C, Huang Y, Nie Z. Collagen Anchoring Protein-Nucleic Acid Chimeric Probe for In Situ In Vivo Mapping of a Tumor-Specific Protease. Anal Chem 2023; 95:18487-18496. [PMID: 38057291 DOI: 10.1021/acs.analchem.3c03775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
In situ analysis of biomarkers in the tumor microenvironment (TME) is important to reveal their potential roles in tumor progression and early diagnosis of tumors but remains a challenge. In this work, a bottom-up modular assembly strategy was proposed for a multifunctional protein-nucleic chimeric probe (PNCP) for in situ mapping of cancer-specific proteases. PNCP, containing a collagen anchoring module and a target proteolysis-responsive isothermal amplification sensor module, can be anchored in the collagen-rich TME and respond to the target protease in situ and generate amplified signals through rolling cycle amplification of tandem fluorescent RNAs. Taking matrix metalloproteinase 2 (MMP-2), a tumor-associated protease, as the model, the feasibility of PNCP was demonstrated for the in situ detection of MMP-2 activity in 3D tumor spheroids. Moreover, in situ in vivo mapping of MMP-2 activity was also achieved in a metastatic solid tumor model with high sensitivity, providing a useful tool for evaluating tumor metastasis and distinguishing highly aggressive forms of tumors.
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Affiliation(s)
- Xuan Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Yuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Jialong Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhenhua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Meixia Wang
- College of Biology, Hunan University, Changsha 410082, P. R. China
| | - Zeyuan Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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12
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Powers J, Jang Y. Advancing Biomimetic Functions of Synthetic Cells through Compartmentalized Cell-Free Protein Synthesis. Biomacromolecules 2023; 24:5539-5550. [PMID: 37962115 DOI: 10.1021/acs.biomac.3c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Synthetic cells are artificial constructs that mimic the structures and functions of living cells. They are attractive for studying diverse biochemical processes and elucidating the origins of life. While creating a living synthetic cell remains a grand challenge, researchers have successfully synthesized hundreds of unique synthetic cell platforms. One promising approach to developing more sophisticated synthetic cells is to integrate cell-free protein synthesis (CFPS) mechanisms into vesicle platforms. This makes it possible to create synthetic cells with complex biomimetic functions such as genetic circuits, autonomous membrane modifications, sensing and communication, and artificial organelles. This Review explores recent advances in the use of CFPS to impart advanced biomimetic structures and functions to bottom-up synthetic cell platforms. We also discuss the potential applications of synthetic cells in biomedicine as well as the future directions of synthetic cell research.
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Affiliation(s)
- Jackson Powers
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, United States
| | - Yeongseon Jang
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, United States
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13
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Zhang L, Zhou R, Fu X, Zhang G, Zhang L, Zhou SF, Jiang W. Specific coenzyme preference switching for an aldo-keto reductase that synthesizes the chiral intermediate of duloxetine. Enzyme Microb Technol 2023; 171:110326. [PMID: 37717530 DOI: 10.1016/j.enzmictec.2023.110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
The synthesis of chiral intermediates for the traditional antidepressant duloxetine has gained significant attention as the number of depressed patients continues to grow. S-N, N-Dimethyl-3-hydroxy-3-(2-thienyl)-1-propanamide (S-DHTP) is a critical intermediate in the synthesis of duloxetine, and the chemical synthesis process is complex and environmentally unfriendly. Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a major cost driver in the biocatalytic production of S-DHTP from N, N-Dimethyl-3-keto-3-(2-thienyl)-1-propanamide (DKTP). Here, we successfully modified the coenzyme preference of an aldo-keto reductase (AKR7-2-1) to use the cheaper reduced nicotinamide adenine dinucleotide (NADH) through a coenzyme preference modification approach. We utilized protein engineering to create a superior mutant, Y53F, which increased the coenzyme specificity of AKR7-2-1 by 875-fold and improved its thermal stability, enhancing its potential for industrial applications. Molecular dynamics simulations were performed to demonstrate the effect of mutations at key sites on the protein, revealing the altered coenzyme preference and increased thermal stability from structural and energetic changes. This study validates the viability of the coenzyme preference modification strategy for aldo-keto reductase, offering valuable insights for fellow researchers and guiding future investigations.
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Affiliation(s)
- Lingzhi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Rui Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Xiaoli Fu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Guangya Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Lijuan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Shu-Feng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| | - Wei Jiang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
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14
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Reverte-López M, Gavrilovic S, Merino-Salomón A, Eto H, Yagüe Relimpio A, Rivas G, Schwille P. Protein-Based Patterning to Spatially Functionalize Biomimetic Membranes. SMALL METHODS 2023; 7:e2300173. [PMID: 37350500 DOI: 10.1002/smtd.202300173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/08/2023] [Indexed: 06/24/2023]
Abstract
The bottom-up reconstitution of proteins for their modular engineering into synthetic cellular systems can reveal hidden protein functions in vitro. This is particularly evident for the bacterial Min proteins, a paradigm for self-organizing reaction-diffusion systems that displays an unexpected functionality of potential interest for bioengineering: the directional active transport of any diffusible cargo molecule on membranes. Here, the MinDE protein system is reported as a versatile surface patterning tool for the rational design of synthetically assembled 3D systems. Employing two-photon lithography, microswimmer-like structures coated with tailored lipid bilayers are fabricated and demonstrate that Min proteins can uniformly pattern bioactive molecules on their surface. Moreover, it is shown that the MinDE system can form stationary patterns inside lipid vesicles, which allow the targeting and distinctive clustering of higher-order protein structures on their inner leaflet. Given their facile use and robust function, Min proteins thus constitute a valuable molecular toolkit for spatially patterned functionalization of artificial biosystems like cell mimics and microcarriers.
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Affiliation(s)
- María Reverte-López
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Svetozar Gavrilovic
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Adrián Merino-Salomón
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Hiromune Eto
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, 3584 CT, The Netherlands
| | - Ana Yagüe Relimpio
- Department of Cellular Biophysics, Max Planck for Medical Research, 69120, Heidelberg, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28040, Spain
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
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15
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Sun Q, Shi J, Sun H, Zhu Y, Du J. Membrane and Lumen-Compartmentalized Polymersomes for Biocatalysis and Cell Mimics. Biomacromolecules 2023; 24:4587-4604. [PMID: 37842883 DOI: 10.1021/acs.biomac.3c00726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Compartmentalization is a crucial feature of a natural cell, manifested in cell membrane and inner lumen. Inspired by the cellular structure, multicompartment polymersomes (MCPs), including membrane-compartmentalized polymersomes and lumen-compartmentalized polymersomes (polymersomes-in-polymersomes), have aroused great expectations for biological applications such as biocatalysis and cell mimics in the past decades. Compared with traditional polymersomes, MCPs have advantages in encapsulating multiple enzymes separately for multistep enzymatic cascade reactions. In this review, first, the design principles and preparation methods of membrane-compartmentalized and lumen-compartmentalized polymersomes are summarized. Next, recent advances of MCPs as nanoreactors and cell mimics to mimic subcellular organelles or artificial cells are discussed. Finally, the future research directions of MCPs are prospected.
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Affiliation(s)
- Qingmei Sun
- Department of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
- Department of Polymeric Materials, School of Materials Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Junqiu Shi
- Department of Polymeric Materials, School of Materials Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Hui Sun
- State Key Laboratory of High-Efficiency Coal Utilization and Green Chemical Engineering, School of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
| | - Yunqing Zhu
- Department of Polymeric Materials, School of Materials Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Jianzhong Du
- Department of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
- Department of Polymeric Materials, School of Materials Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, 4800 Caoan Road, Shanghai 201804, China
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16
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Stano P. Chemical Systems for Wetware Artificial Life: Selected Perspectives in Synthetic Cell Research. Int J Mol Sci 2023; 24:14138. [PMID: 37762444 PMCID: PMC10532297 DOI: 10.3390/ijms241814138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The recent and important advances in bottom-up synthetic biology (SB), in particular in the field of the so-called "synthetic cells" (SCs) (or "artificial cells", or "protocells"), lead us to consider the role of wetware technologies in the "Sciences of Artificial", where they constitute the third pillar, alongside the more well-known pillars hardware (robotics) and software (Artificial Intelligence, AI). In this article, it will be highlighted how wetware approaches can help to model life and cognition from a unique perspective, complementary to robotics and AI. It is suggested that, through SB, it is possible to explore novel forms of bio-inspired technologies and systems, in particular chemical AI. Furthermore, attention is paid to the concept of semantic information and its quantification, following the strategy recently introduced by Kolchinsky and Wolpert. Semantic information, in turn, is linked to the processes of generation of "meaning", interpreted here through the lens of autonomy and cognition in artificial systems, emphasizing its role in chemical ones.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
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17
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Shono M, Honda G, Yanagisawa M, Yoshikawa K, Shioi A. Spontaneous Formation of Uniform Cell-Sized Microgels through Water/Water Phase Separation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302193. [PMID: 37224803 DOI: 10.1002/smll.202302193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/07/2023] [Indexed: 05/26/2023]
Abstract
In this study, a one-step method is discussed for producing uniform cell-sized microgels using glass capillaries filled with a binary polymer blend of polyethylene glycol (PEG) and gelatin. Upon decreasing temperature, phase separation of the PEG/gelatin blends and gelation of gelatin occur, and then the polymer blend forms linearly aligned, uniformly sized gelatin microgels in the glass capillary. When DNA is added to the polymer solution, gelatin microgels entrapping DNA are spontaneously formed, and the DNA prevents the coalescence of the microdroplets even at temperatures above the melting point. This novel method to form uniform cell-sized microgels may be applicable to other biopolymers. This method is expected to contribute to diverse materials science via biopolymer microgels and biophysics and synthetic biology through cellular models containing biopolymer gels.
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Affiliation(s)
- Mayu Shono
- Department of Chemical Engineering and Materials Science, Doshisha University, 6100321, Kyoto, Japan
| | - Gen Honda
- Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902, Japan
| | - Miho Yanagisawa
- Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902, Japan
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902, Japan
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, 113-0033, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, 6100394, Kyoto, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, 606 8501, Kyoto, Japan
| | - Akihisa Shioi
- Department of Chemical Engineering and Materials Science, Doshisha University, 6100321, Kyoto, Japan
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18
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Li Y, Liang X, Shen C, Deng K, Zeng Z, Guo B, Xu X. Bio-Responsive Macromolecular Drug and Small-Molecular Drug Conjugates: Nanoparticulate Prodrugs for Tumor Microenvironment Heterogeneity Management and Therapeutic Response Enhancement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301656. [PMID: 37144435 DOI: 10.1002/smll.202301656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Indexed: 05/06/2023]
Abstract
How to break through the poor response of current drug therapy, which often resulted from tumor microenvironment heterogeneity (TMH), remains an enormous challenge in the treatment of critical diseases. In this work, a practical solution on bio-responsive dual-drug conjugates for overcoming TMH and improving antitumor treatment, which integrates the advantages of macromolecular drugs and small-molecular drugs, is proposed. Nanoparticulate prodrugs based on small-molecular drug and macromolecular drug conjugates are designed as a robust weapon for programmable multidrug delivery at tumor-specific sites: the tumor microenvironment acid condition triggers delivery of macromolecular aptamer drugs (AX102) to manage TMH (including tumor stroma matrix, interstitial fluid pressure, vasculature network, blood perfusion, and oxygen distribution), and intracellular lysosomal acid condition activates rapid release of small-molecular drugs (doxorubicin and dactolisib) to enhance curative effects. As compared with doxorubicin chemotherapy, the tumor growth inhibition rate is enhanced by 47.94% after multiple tumor heterogeneity management. This work verifies that the nanoparticulate prodrugs facilitate TMH management and therapeutic response enhancements, as well as elucidates synergetic mechanisms for drug resistance reversal and metastasis inhibition. It is hoped that the nanoparticulate prodrugs will be an excellent demonstration of the co-delivery of small-molecular drugs and macromolecular drugs.
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Affiliation(s)
- Yachao Li
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Changsha, Hunan, 410082, China
| | - Xiaoyu Liang
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
| | - Cheng Shen
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
| | - Kefurong Deng
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
| | - Zenan Zeng
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
| | - Beiling Guo
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
| | - Xianghui Xu
- Department of Pharmacy, College of Biology, Hunan University, Changsha, Hunan, 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Changsha, Hunan, 410082, China
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19
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Stano P, Gentili PL, Damiano L, Magarini M. A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things? Molecules 2023; 28:5564. [PMID: 37513436 PMCID: PMC10385758 DOI: 10.3390/molecules28145564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
| | - Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Luisa Damiano
- Department of Communication, Arts and Media, IULM University, 20143 Milan, Italy
| | - Maurizio Magarini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
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20
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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21
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Shimokawa N, Hamada T. Physical Concept to Explain the Regulation of Lipid Membrane Phase Separation under Isothermal Conditions. Life (Basel) 2023; 13:life13051105. [PMID: 37240749 DOI: 10.3390/life13051105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
Lateral phase separation within lipid bilayer membranes has attracted considerable attention in the fields of biophysics and cell biology. Living cells organize laterally segregated compartments, such as raft domains in an ordered phase, and regulate their dynamic structures under isothermal conditions to promote cellular functions. Model membrane systems with minimum components are powerful tools for investigating the basic phenomena of membrane phase separation. With the use of such model systems, several physicochemical characteristics of phase separation have been revealed. This review focuses on the isothermal triggering of membrane phase separation from a physical point of view. We consider the free energy of the membrane that describes lateral phase separation and explain the experimental results of model membranes to regulate domain formation under isothermal conditions. Three possible regulation factors are discussed: electrostatic interactions, chemical reactions and membrane tension. These findings may contribute to a better understanding of membrane lateral organization within living cells that function under isothermal conditions and could be useful for the development of artificial cell engineering.
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Affiliation(s)
- Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
| | - Tsutomu Hamada
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
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22
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Zhou S, Wei Y. Kaleidoscope megamolecules synthesis and application using self-assembly technology. Biotechnol Adv 2023; 65:108147. [PMID: 37023967 DOI: 10.1016/j.biotechadv.2023.108147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 02/20/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
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23
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Pavão G, Sfalcin I, Bonatto D. Biocontainment Techniques and Applications for Yeast Biotechnology. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.
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24
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Kurisu M, Katayama R, Sakuma Y, Kawakatsu T, Walde P, Imai M. Synthesising a minimal cell with artificial metabolic pathways. Commun Chem 2023; 6:56. [PMID: 36977828 PMCID: PMC10050237 DOI: 10.1038/s42004-023-00856-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
A "synthetic minimal cell" is considered here as a cell-like artificial vesicle reproduction system in which a chemical and physico-chemical transformation network is regulated by information polymers. Here we synthesise such a minimal cell consisting of three units: energy production, information polymer synthesis, and vesicle reproduction. Supplied ingredients are converted to energy currencies which trigger the synthesis of an information polymer, where the vesicle membrane plays the role of a template. The information polymer promotes membrane growth. By tuning the membrane composition and permeability to osmolytes, the growing vesicles show recursive reproduction over several generations. Our "synthetic minimal cell" greatly simplifies the scheme of contemporary living cells while keeping their essence. The chemical pathways and the vesicle reproduction pathways are well described by kinetic equations and by applying the membrane elasticity model, respectively. This study provides new insights to better understand the differences and similarities between non-living forms of matter and life.
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Affiliation(s)
- Minoru Kurisu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Ryosuke Katayama
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladmir-Prelog-Weg 5, CH-8093, Zürich, Switzerland
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan.
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25
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Chen M, Liu G, Zhang M, Li Y, Hong X, Yang H. Programmatically Dynamic Microcompartmentation in Coacervate-in-Pickering Emulsion Protocell. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206437. [PMID: 36564366 DOI: 10.1002/smll.202206437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The desire for exploration of cellular functional mechanisms has substantially increased the rapid development of artificial cells. However, the construction of synthetic cells with high organizational complexity remains challenging due to the lack of facile approaches ensuring dynamic multi-compartments of cytoplasm and stability of membranes in protocells. Herein, a stable coacervate-in-Pickering emulsion protocell model comprising a membraneless coacervate phase formed by poly-l-lysine (PLys) and adenosine triphosphate (ATP) encapsulated in Pickering emulsion is put forward only through simple one-step emulsification. The dynamic distribution of intracellular components (coacervates in this protocell model) can be manipulated by changes in temperature or pH. This coacervate-in-Pickering emulsion protocell system exhibits repeatable cycle stability in response to external stimuli (at least 24 cycles for temperature and 3 cycles for pH). By encapsulating antagonistic enzymes into coacervates, glucose oxidase (GOx) and urease as an example, the control of local enzyme concentration is achieved by introducing glucose and urea to adjust the pH value in Pickering emulsion droplets. This hybrid protocell model with programmatically dynamic microcompartmentation and sufficient stability is expected to be further studied and applied in cellular biology, facilitating the development of lifelike systems with potential in practical applications.
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Affiliation(s)
- Mengqing Chen
- College of Chemistry and Molecule Sciences, Wuhan University, Wuhan, 430072, China
| | - Guoliang Liu
- College of Chemistry and Molecule Sciences, Wuhan University, Wuhan, 430072, China
| | - Ming Zhang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Yanyan Li
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Xinlin Hong
- College of Chemistry and Molecule Sciences, Wuhan University, Wuhan, 430072, China
| | - Hengquan Yang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
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Oliveira IS, Silva SG, do Vale ML, Marques EF. Model Catanionic Vesicles from Biomimetic Serine-Based Surfactants: Effect of the Combination of Chain Lengths on Vesicle Properties and Vesicle-to-Micelle Transition. MEMBRANES 2023; 13:178. [PMID: 36837681 PMCID: PMC9966114 DOI: 10.3390/membranes13020178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Mixtures of cationic and anionic surfactants often originate bilayer structures, such as vesicles and lamellar liquid crystals, that can be explored as model membranes for fundamental studies or as drug and gene nanocarriers. Here, we investigated the aggregation properties of two catanionic mixtures containing biomimetic surfactants derived from serine. The mixtures are designated as 12Ser/8-8Ser and 14Ser/10-10Ser, where mSer is a cationic, single-chained surfactant and n-nSer is an anionic, double-chained one (m and n being the C atoms in the alkyl chains). Our goal was to investigate the effects of total chain length and chain length asymmetry of the catanionic pair on the formation of catanionic vesicles, the vesicle properties and the vesicle/micelle transitions. Ocular observations, surface tension measurements, video-enhanced light microscopy, cryogenic scanning electron microscopy, dynamic and electrophoretic light scattering were used to monitor the self-assembly process and the aggregate properties. Catanionic vesicles were indeed found in both systems for molar fractions of cationic surfactant ≥0.40, always possessing positive zeta potentials (ζ = +35-50 mV), even for equimolar sample compositions. Furthermore, the 14Ser/10-10Ser vesicles were only found as single aggregates (i.e., without coexisting micelles) in a very narrow compositional range and as a bimodal population (average diameters of 80 and 300 nm). In contrast, the 12Ser/8-8Ser vesicles were found for a wider sample compositional range and as unimodal or bimodal populations, depending on the mixing ratio. The aggregate size, pH and zeta potential of the mixtures were further investigated. The unimodal 12Ser/8-8Ser vesicles (<DH> ≈ 250 nm, pH ≈ 7-8, ζ ≈ +32 mV and a cationic/anionic molar ratio of ≈2:1) are particularly promising for application as drug/gene nanocarriers. Both chain length asymmetry and total length play a key role in the aggregation features of the two systems. Molecular insights are provided by the main findings.
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Affiliation(s)
- Isabel S. Oliveira
- CIQUP, IMS (Institute of Molecular Sciences), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sandra G. Silva
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria Luísa do Vale
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Eduardo F. Marques
- CIQUP, IMS (Institute of Molecular Sciences), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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