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Evolution of Proliferative Model Protocells Highly Responsive to the Environment. Life (Basel) 2022; 12:life12101635. [PMID: 36295070 PMCID: PMC9605134 DOI: 10.3390/life12101635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 12/02/2022] Open
Abstract
In this review, we discuss various methods of reproducing life dynamics using a constructive approach. An increase in the structural complexity of a model protocell is accompanied by an increase in the stage of reproduction of a compartment (giant vesicle; GV) from simple reproduction to linked reproduction with the replication of information molecules (DNA), and eventually to recursive proliferation of a model protocell. An encounter between a plural protic catalyst (C) and DNA within a GV membrane containing a plural cationic lipid (V) spontaneously forms a supramolecular catalyst (C@DNA) that catalyzes the production of cationic membrane lipid V. The local formation of V causes budding deformation of the GV and equivolume divisions. The length of the DNA strand influences the frequency of proliferation, associated with the emergence of a primitive information flow that induces phenotypic plasticity in response to environmental conditions. A predominant protocell appears from the competitive proliferation of protocells containing DNA with different strand lengths, leading to an evolvable model protocell. Recently, peptides of amino acid thioesters have been used to construct peptide droplets through liquid–liquid phase separation. These droplets grew, owing to the supply of nutrients, and were divided repeatedly under a physical stimulus. This proposed chemical system demonstrates a new perspective of the origins of membraneless protocells, i.e., the “droplet world” hypothesis. Proliferative model protocells can be regarded as autonomous supramolecular machines. This concept of this review may open new horizons of “evolution” for intelligent supramolecular machines and robotics.
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Hirata Y, Matsuo M, Kurihara K, Suzuki K, Nonaka S, Sugawara T. Colocalization Analysis of Lipo-Deoxyribozyme Consisting of DNA and Protic Catalysts in a Vesicle-Based Protocellular Membrane Investigated by Confocal Microscopy. Life (Basel) 2021; 11:1364. [PMID: 34947896 PMCID: PMC8707093 DOI: 10.3390/life11121364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 12/23/2022] Open
Abstract
The linkage between the self-reproduction of compartments and the replication of DNA in a compartment is a crucial requirement for cellular life. In our giant vesicle (GV)-based model protocell, this linkage is achieved through the action of a supramolecular catalyst composed of membrane-intruded DNA and amphiphilic acid catalysts (C@DNA) in a GV membrane. In this study, we examined colocalization analysis for the formation of the supramolecular catalyst using a confocal laser scanning fluorescence microscope with high sensitivity and resolution. Red fluorescence spots emitted from DNA tagged with Texas Red (Texas Red-DNA) were observed in a GV membrane stained with phospholipid tagged with BODIPY (BODIPY-HPC). To our knowledge, this is the first direct observation of DNA embedded in a GV-based model protocellular membrane containing cationic lipids. Colocalization analysis based on a histogram of frequencies of "normalized mean deviation product" revealed that the frequencies of positively correlated [lipophilic catalyst tagged with BODIPY (BODIPY-C) and Texas Red-DNA] were significantly higher than those of [BODIPY-HPC and Texas Red-DNA]. This result demonstrates the spontaneous formation of C@DNA in the GV membrane, which serves as a lipo-deoxyribozyme for producing membrane lipids from its precursor.
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Affiliation(s)
- Yuiko Hirata
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka 259-1293, Kanagawa, Japan;
| | - Muneyuki Matsuo
- Department of Chemistry, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Hiroshima, Japan;
- Exploratory Research Center on Life and Living Systems (ExCELLS), Myodaiji, Okazaki 444-8787, Aichi, Japan; (K.K.); (S.N.)
| | - Kensuke Kurihara
- Exploratory Research Center on Life and Living Systems (ExCELLS), Myodaiji, Okazaki 444-8787, Aichi, Japan; (K.K.); (S.N.)
| | - Kentaro Suzuki
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka 259-1293, Kanagawa, Japan;
| | - Shigenori Nonaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), Myodaiji, Okazaki 444-8787, Aichi, Japan; (K.K.); (S.N.)
- National Institute for Basic Biology, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Tadashi Sugawara
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka 259-1293, Kanagawa, Japan;
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Bollella P, Edwardraja S, Guo Z, Alexandrov K, Katz E. Control of allosteric electrochemical protein switch using magnetic signals. Chem Commun (Camb) 2020; 56:9206-9209. [PMID: 32662462 DOI: 10.1039/d0cc04284f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The artificial chimeric enzyme with allosteric features was activated with a magnetic field applied at a distance.
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Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology
- The University of Queensland
- Brisbane
- Australia
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance
- ARC Centre of Excellence in Synthetic Biology
- Centre for Agriculture and the Bioeconomy
- Institute of Health and Biomedical Innovation
- Institute for Future Environments
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance
- ARC Centre of Excellence in Synthetic Biology
- Centre for Agriculture and the Bioeconomy
- Institute of Health and Biomedical Innovation
- Institute for Future Environments
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science
- Clarkson University
- Potsdam
- USA
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Matsuo M, Kan Y, Kurihara K, Jimbo T, Imai M, Toyota T, Hirata Y, Suzuki K, Sugawara T. DNA Length-dependent Division of a Giant Vesicle-based Model Protocell. Sci Rep 2019; 9:6916. [PMID: 31061467 PMCID: PMC6502804 DOI: 10.1038/s41598-019-43367-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/23/2019] [Indexed: 02/07/2023] Open
Abstract
DNA is an essential carrier of sequence-based genetic information for all life today. However, the chemical and physical properties of DNA may also affect the structure and dynamics of a vesicle-based model protocell in which it is encapsulated. To test these effects, we constructed a polyethylene glycol-grafted giant vesicle system capable of undergoing growth and division. The system incorporates a specific interaction between DNA and lipophilic catalysts as well as components of PCR. We found that vesicle division depends on the length of the encapsulated DNA, and the self-assembly of an internal supramolecular catalyst possibly leads to the direct causal relationship between DNA length and the capacity of the vesicle to self-reproduce. These results may help elucidate how nucleic acids could have functioned in the division of prebiotic protocells.
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Affiliation(s)
- Muneyuki Matsuo
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo, 153-8902, Japan.,Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Yumi Kan
- Department of Physics, Graduate School of Science, Ochanomizu University, Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Kensuke Kurihara
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), Myodaiji, Okazaki, Aichi, 444-8787, Japan.,Determent of Life and Coordination-Complex Molecular Science, Biomolecular Functions, Institute for Molecular Science, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Takehiro Jimbo
- Department of Physics, Graduate School of Science, Tohoku University, Aoba, Sendai, Miyagi, 980-8578, Japan
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Ochanomizu University, Otsuka, Bunkyo, Tokyo, 112-8610, Japan.,Department of Physics, Graduate School of Science, Tohoku University, Aoba, Sendai, Miyagi, 980-8578, Japan
| | - Taro Toyota
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo, 153-8902, Japan. .,Universal Biology Institute, The University of Tokyo, Hongo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Yuiko Hirata
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Kentaro Suzuki
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Tadashi Sugawara
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan.
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