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Zhu L, Wang Y, Wu X, Wu G, Zhang G, Liu C, Zhang S. Protein design accelerates the development and application of optogenetic tools. Comput Struct Biotechnol J 2025; 27:717-732. [PMID: 40092664 PMCID: PMC11908464 DOI: 10.1016/j.csbj.2025.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 02/16/2025] [Accepted: 02/17/2025] [Indexed: 03/19/2025] Open
Abstract
Optogenetics has substantially enhanced our understanding of biological processes by enabling high-precision tracking and manipulation of individual cells. It relies on photosensitive proteins to monitor and control cellular activities, thereby paving the way for significant advancements in complex system research. Photosensitive proteins play a vital role in the development of optogenetics, facilitating the establishment of cutting-edge methods. Recent breakthroughs in protein design have opened up opportunities to develop protein-based tools that can precisely manipulate and monitor cellular activities. These advancements will significantly accelerate the development and application of optogenetic tools. This article emphasizes the pivotal role of protein design in the development of optogenetic tools, offering insights into potential future directions. We begin by providing an introduction to the historical development and fundamental principles of optogenetics, followed by an exploration of the operational mechanisms of key photosensitive domains, which includes clarifying the conformational changes they undergo in response to light, such as allosteric modulation and dimerization processes. Building on this foundation, we reveal the development of protein design tools that will enable the creation of even more sophisticated optogenetic techniques.
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Affiliation(s)
| | | | - Xiaomin Wu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Guohua Wu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Guohao Zhang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Shaowei Zhang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan 410073, China
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Stohr AM, Ma D, Chen W, Blenner M. Engineering conditional protein-protein interactions for dynamic cellular control. Biotechnol Adv 2024; 77:108457. [PMID: 39343083 DOI: 10.1016/j.biotechadv.2024.108457] [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: 06/13/2024] [Revised: 08/28/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
Conditional protein-protein interactions enable dynamic regulation of cellular activity and are an attractive approach to probe native protein interactions, improve metabolic engineering of microbial factories, and develop smart therapeutics. Conditional protein-protein interactions have been engineered to respond to various chemical, light, and nucleic acid-based stimuli. These interactions have been applied to assemble protein fragments, build protein scaffolds, and spatially organize proteins in many microbial and higher-order hosts. To foster the development of novel conditional protein-protein interactions that respond to new inputs or can be utilized in alternative settings, we provide an overview of the process of designing new engineered protein interactions while showcasing many recently developed computational tools that may accelerate protein engineering in this space.
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Affiliation(s)
- Anthony M Stohr
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Derron Ma
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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Armbruster A, Mohamed AM, Phan HT, Weber W. Lighting the way: recent developments and applications in molecular optogenetics. Curr Opin Biotechnol 2024; 87:103126. [PMID: 38554641 DOI: 10.1016/j.copbio.2024.103126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 04/02/2024]
Abstract
Molecular optogenetics utilizes genetically encoded, light-responsive protein switches to control the function of molecular processes. Over the last two years, there have been notable advances in the development of novel optogenetic switches, their utilization in elucidating intricate signaling pathways, and their progress toward practical applications in biotechnological processes, material sciences, and therapeutic applications. In this review, we discuss these areas, offer insights into recent developments, and contemplate future directions.
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Affiliation(s)
- Anja Armbruster
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Asim Me Mohamed
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Hoang T Phan
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Wilfried Weber
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; Saarland University, Department of Materials Science and Engineering, Campus D2 2, 66123 Saarbrücken, Germany.
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Novik TS, Koveshnikova EI, Kotlobay AA, Sycheva LP, Kurochkina KG, Averina OA, Belopolskaya MV, Sergiev PV, Dontsova OA, Lazarev VN, Maev IV, Kostyaeva MG, Eremeev AV, Chukina SI, Lagarkova MA. Sweet-Tasting Natural Proteins Brazzein and Monellin: Safe Sugar Substitutes for the Food Industry. Foods 2023; 12:4065. [PMID: 38002123 PMCID: PMC10670179 DOI: 10.3390/foods12224065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
This article presents the results of a comprehensive toxicity assessment of brazzein and monellin, yeast-produced recombinant sweet-tasting proteins. Excessive sugar consumption is one of the leading dietary and nutritional problems in the world, resulting in health complications such as obesity, high blood pressure, and cardiovascular disease. Although artificial small-molecule sweeteners widely replace sugar in food, their safety and long-term health effects remain debatable. Many sweet-tasting proteins, including thaumatin, miraculin, pentadin, curculin, mabinlin, brazzein, and monellin have been found in tropical plants. These proteins, such as brazzein and monellin, are thousands-fold sweeter than sucrose. Multiple reports have presented preparations of recombinant sweet-tasting proteins. A thorough and comprehensive assessment of their toxicity and safety is necessary to introduce and apply sweet-tasting proteins in the food industry. We experimentally assessed acute, subchronic, and chronic toxicity effects, as well as allergenic and mutagenic properties of recombinant brazzein and monellin. Our study was performed on three mammalian species (mice, rats, and guinea pigs). Assessment of animals' physiological, biochemical, hematological, morphological, and behavioral indices allows us to assert that monellin and brazzein are safe and nontoxic for the mammalian organism, which opens vast opportunities for their application in the food industry as sugar alternatives.
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Affiliation(s)
- Tamara S. Novik
- Scientific Research Centre Pharmbiomed, Selskohozjajstvennaja Str., 12a, Moscow 129226, Russia; (T.S.N.); (E.I.K.); (K.G.K.); (S.I.C.)
| | - Elena I. Koveshnikova
- Scientific Research Centre Pharmbiomed, Selskohozjajstvennaja Str., 12a, Moscow 129226, Russia; (T.S.N.); (E.I.K.); (K.G.K.); (S.I.C.)
| | - Anatoly A. Kotlobay
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow 119435, Russia; (A.A.K.); (V.N.L.); (A.V.E.)
| | - Lyudmila P. Sycheva
- Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Zhivopisnaya Str., 46, Moscow 123182, Russia;
| | - Karine G. Kurochkina
- Scientific Research Centre Pharmbiomed, Selskohozjajstvennaja Str., 12a, Moscow 129226, Russia; (T.S.N.); (E.I.K.); (K.G.K.); (S.I.C.)
| | - Olga A. Averina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; (O.A.A.); (P.V.S.); (O.A.D.)
| | | | - Petr V. Sergiev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; (O.A.A.); (P.V.S.); (O.A.D.)
| | - Olga A. Dontsova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; (O.A.A.); (P.V.S.); (O.A.D.)
| | - Vassili N. Lazarev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow 119435, Russia; (A.A.K.); (V.N.L.); (A.V.E.)
| | - Igor V. Maev
- Department of Propaedeutics of Internal Diseases and Gastroenterology, Moscow State University of Medicine and Dentistry, Delegatskaya St. 20/1, Moscow 103473, Russia;
| | - Margarita G. Kostyaeva
- Faculty of Medicine, Peoples Friendship University of Russia Named after Patrice Lumumba, Miklukho-Maklaya Str.6, Moscow 117198, Russia;
| | - Artem V. Eremeev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow 119435, Russia; (A.A.K.); (V.N.L.); (A.V.E.)
| | - Svetlana I. Chukina
- Scientific Research Centre Pharmbiomed, Selskohozjajstvennaja Str., 12a, Moscow 129226, Russia; (T.S.N.); (E.I.K.); (K.G.K.); (S.I.C.)
| | - Maria A. Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow 119435, Russia; (A.A.K.); (V.N.L.); (A.V.E.)
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Li K, Zheng J, Yu L, Wang B, Pan L. Exploration of the Strategy for Improving the Expression of Heterologous Sweet Protein Monellin in Aspergillus niger. J Fungi (Basel) 2023; 9:jof9050528. [PMID: 37233239 DOI: 10.3390/jof9050528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/23/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Aspergillus niger is a primary cell factory for food-grade protein (enzyme) production due to its strong protein secretion capacity and unique safety characteristics. The bottleneck issue for the current A. niger expression system is the difference in expression yield of heterologous proteins of non-fungal origin compared to those of fungal origin, which is about three orders of magnitude. The sweet protein monellin, derived from West African plants, has the potential to become a food-grade sweetener due to its high sweetness and the benefit of not containing sugar itself, but it is extremely difficult to establish a research model for heterologous expression in A. niger, owing to extremely low expression, a small molecular weight, and being undetectable with conventional protein electrophoresis. HiBiT-Tag was fused with low-expressing monellin in this work to create a research model for heterologous protein expression in A. niger at ultra-low levels. We increased monellin expression by increasing the monellin copy number, fusing monellin with the endogenous highly expressed glycosylase glaA, and eliminating extracellular protease degradation, among other strategies. In addition, we investigated the effects of overexpression of molecular chaperones, inhibiting the ERAD pathway, and enhancing the synthesis of phosphatidylinositol, phosphatidylcholine, and diglycerides in the biomembrane system. Using medium optimization, we finally obtained 0.284 mg/L of monellin in the supernatant of the shake flask. This is the first time recombinant monellin has been expressed in A. niger, with the goal of investigating ways to improve the secretory expression of heterologous proteins at ultra-low levels, which can serve as a model for the expression of other heterologous proteins in A. niger.
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Affiliation(s)
- Ke Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Junwei Zheng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Leyi Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Bin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Li Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
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