Research Outline
AUTOMATTER; programmable Automated Materials
"ATM" refers to robots that operate autonomously.
Although they use parts similar to artificial non-natural cells (molecular devices), their fundamental operating principles (central dogma) differ. The replication and operating mechanisms they would be equipped with are different from those of organisms evolved on Earth.
A subset of ATM includes all known life forms on Earth to date, and the all ATMs are a subset of the conceptual automated machines: automata.
They are entities where actual matter accompanies the concept.
Therefore, our action experimentally creating various ATMs is equivalent to the operation of searching for life forms that exist somewhere in the vast universe.
It is inconceivable that a single thread could suffice to connect life and matter. Even if it can be called thread, it would likely be richly spread out with varying thicknesses, colors, and patterns.
Artificial cells, with their comparable size to the live cells, are expected to work as the "caretaker" at the same scale as the natural one. We are designing "channels" transporting specific molecular signals through the biomembrane. We also found that artificial cell structure itself also can be used as the one-time container for cellular delivery by using the electro-fusion method. Their biocompatibility leads the way to some application in the bioengineering field.
Watanabe, T., Sato, Y., Otaka, H., Kawamata, I., Murata, S., & Nomura, S. I. M. (2020). DNA Origami “Quick” Refolding Inside of a Micron-Sized Compartment. Molecules, 25(1), 8.→Link(OpenAccess)
Sato, Y., Komiya, K., Kawamata, I., Murata, S., & Nomura, S.-i. M. (2019). Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles. Chemical Communications., 2019, 55, 9084-9087, DOI: 10.1039/C9CC03277K. BackCoverPage →Link, →Press Release(J)(Eng)
Yusuke Sato, Yuichi Hiratsuka, Ibuki Kawamata, Satoshi Murata, Shin-ichiro M. Nomura, "Micrometer-sized molecular robot changes its shape in response to signal molecules", Science Robotics,01 Mar 2017: Vol. 2, Issue 4, aal3735. DOI: https://doi.org/10.1126/scirobotics.aal3735.
Kei Fujiwara, Miho Yanagisawa and Shin-ichiro M. Nomura, “Reconstitution of intracellular environments in vitro and in artificial cells”, BIOPHYSICS, Vol.10, pp. 43-48 (2014, Aug.) http://dx.doi.org/10.2142/biophysics.10.43.
D. Komatsu, K. Fujiwara, S.-i. M. Nomura "Construction of a remote-controlled supramolecular micro-crawler", ADVANCES IN ARTIFICIAL LIFE, (2013) DOI: http://dx.doi.org/10.7551/978-0-262-31709-2-ch031 Pages 208-209, First published 2 September 2013.
Y. Moritani, S.-i. M. Nomura, I. Morita, K. Akiyoshi “Direct integration of cell-free synthesized connexin-43 into liposomes utilizing chaperone-like function of liposomes”, FEBS Journal, 277, (2010), 3343-3352.
K. Yamaji, T. Kanai, S.-I. M. Nomura, K. Akiyoshi, M. Negishi, Y. Chen, H. Atomi, K. Yoshikawa, T. Imanaka, “Protein Synthesis in Giant Liposomes Using the In Vitro Translation System of Thermococcus kodakaraensis”, IEEE trans. Nanobiosci., 8, (2009), 325-331.
S.-i. M. Nomura, S. Kondoh, W. Asayama, A. Asada, S. Nishikawa, K. Akiyoshi, “Direct preparation of giant proteo-liposomes by in vitro membrane protein synthesis” J. Biotechnology, 133, (2008), 190-195.
S.-i. M. Nomura, K. Tsumoto, T. Hamada, K. Akiyoshi, Y. Nakatani, K. Yoshikawa, “Gene Expression within Cell-Sized Lipid Vesicles” ChemBioChem, 4, (2003), 1172-1175.
K. Tsumoto, S.-i. M. Nomura, Y. Nakatani, K. Yoshikawa, “Giant Liposome as a Biochemical Reactor: Transcription of DNA and Transportation by Laser Tweezers” Langmuir 17, (2001), 7225 –7228.
S.-i. M. Nomura, Y. Yoshikawa, K. Yoshikawa, O. Dannenmuller, S. Chasserot-Golaz, G. Ourisson, Y. Nakatani, “Towards Proto-Cells: “Primitive” Lipid Vesicles Encapsulating Giant DNA and Its Histone Complex” ChemBioChem, 6, (2001),457-459.
S.-i. Nomura, K. Yoshikawa, “Giant Phospholipid Vesicles Entrapping Giant DNA” published in Giant Vesicles Edited by P. L. Luisi and P. Walde, (John Wiley & Sons Ltd.), (2000), 313-317, at the International Workshop on Giant Vesicles (1998).
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Artificial cells cross-talking with live cells
The micrometer-sized lipid compartment is a useful microcapsule as an artificial cell's body. We can install various functional/reactive chemical soup to the capsule, such as DNAs, RNAs, proteins, catalysts, total gene expression systems, motor proteins, DNA logic gates, etc.
Some of them used for understanding and revealing the special function of micro-compartment and some used as a shape-shifting molecular robot showing an amoeba-type motion.
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Artificial cells with individual functions
The artificial cell is a molecular robot with a compatible function with a live cell, designed molecular systems as a unit of micro cellular-structures. Modern cells have indispensable structures and functions: genes, compartments, metabolism, and replication. Design, synthesis, and implement them work as a system is the key to artificial cell engineering. Another key is programmability. Every machine, including molecular robots, must work as written in the program. Through to creation of the artificial cell, our research group aims to provide potentially applicable molecular systems for medical, environmental, materials, and biotechnology.
Our interests are... molecular robotics/artificial cell engineering for creating "Auto-Matter".
Chikako Kurokawa, Kei Fujiwara, Masamune Morita, Ibuki Kawamata, Yui Kawagishi, Atsushi Sakai, Yoshihiro Murayama, Shin-ichiro M. Nomura, Satoshi Murata, Masahiro Takinoue, and Miho Yanagisawa, "DNA cytoskeleton for stabilizing artificial cells", PNAS July 11, 2017 vol. 114 no. 28 7228-7233. doi: 10.1073/pnas.1702208114
Akira C. Saito, Toshihiko Ogura, Kei Fujiwara, Satoshi Murata, Shin-ichiro M. Nomura, "Introducing Micrometer-Sized Artificial Objects into Live Cells: A Method for Cell-Giant Unilamellar Vesicle Electrofusion", PLoS ONE 9(9): e106853 (2014, Sept.). DOI: 10.1371/journal.pone.0106853
M. Kaneda, S.-i. M. Nomura, S. Ichinose, S. Kondo, K.-i. Nakahama, K. Akiyoshi, I. Morita, “Direct formation of proteo-liposomes by in vitro synthesis and cellular cytosolic delivery with connexin-expressing liposomes”, Biomaterials, 30, (2009), 3971-3977.
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AutoMatter: programmable active matter with an automatic production system
In the biomolecular world, the complex structures are not created one by one but are assembled together by self-assembly that depends on the affinities. As is the same, in the artificial cell compartment also assembled from their component molecules automatically. Usually, one makes only several mL amounts used for experiments, but we have reported a mass production method. We aim their production of the artificial cell itself would become comparable to the growth of natural cells (right collum, lowermost).
When the swarming behavior of molecular robots works as individually programmed by a human, they shall be called “Auto-Matter”(coined word by our group). We aim to control such active matters as desired by connecting digital electronic devices and molecular devices. We are tackling the challenge of controlling molecular robots driven by motor proteins using molecular computers in situ. In the near future, molecular and electronic signals would be linked to control molecular swarms.
To be published...!
- The former version of our research outline is as follows: we never forget the initial spirits when established the group:-)
Our interests are
Creating various artificial cells (Yet Another Cell)
Reconstitution of living cells from materials (Cell Reconstruction)
Molecular robotics (Molbot)
Simulations to do YAC, CR, and Molbot.
Our main topics are the following two;
To make practical artificial cells (toward creating "Yet Another Life!")
In the nano/micro-environment, various molecules and ions collide. Artificial cells we make should live in such an environment. The artificial cells are liposomes that contain the protein expression system [1-3]. Cells require the influx and efflux of molecules through membrane proteins to maintain their metabolism and to grow. We focus on the great potentials of membrane proteins and analyze what happens by installing the membrane proteins into the artificial cells [4]. We achieved to make an artificial cell that can communicate molecules with living cells by expression of connexin proteins [5].
Recently, new types of artificial cells are being constructed by combining with the molecular robotics approach. Such artificial cells are controllable by external signals, are attachable to metals, have robots working on a membrane, and so on. Through constructions of various artificial cells, we believe we can understand “what is life“, and provide novel systems for drug delivery systems.
To know why we cannot make cells (toward Cell Reconstruction)
Cells are the ultimate machines. However, present living cells are born from “their parent(s)”, not spontaneous. Is it possible to know how to make cells from defined materials?
The goal of the project is the reconstitution of living cells from scratch. However, we know we should conquest many difficulties to achieve that. Many people discuss so far to find the way mainly by bottom-up approaches that include our artificial cell studies [1-5]. Here we propose middle-out approaches to know “why we cannot make cells”. For the aim, we are constructing mixtures of macromolecules that can mimic living cells. We believe the differences between the mimicking mixture and living cells are found through molecular biological ways (top-down) and are decreased by synthetic biological approaches (bottom-up). This is because such approaches have been performed toward knocking-out an essential chaperone (GroE) that is required for many biological systems [6-8].
We achieved to develop methods to prepare a cell extract that is “condensed to the similar concentration of macromolecules in living cells” under “additive-free” conditions [9], and to condense macromolecules in liposomes. In addition, studies on making cell extract by bottom-up approach are going on. It should be noted that we performed with a respectful mind to present living cells.
[1] Nomura SM, et al. (2001) Chembiochem 2: 457-459
[2] Nomura SM, et al. (2001) Langmuir 17: 7225-7228
[3] Nomura SM, et al. (2003) Chembiochem 4: 1172-1175
[4] Nomura SM, et al. (2008) J Biotechnol 133: 190-195
[5] Kaneda M, Nomura SM, et al. (2009) Biomaterials 30: 3971-3977
[6] Fujiwara K and Taguchi H. (2007) J Bacteriol 189:5860-5866
[7] Fujiwara K, et al. (2010) EMBO J 29:1552-1564
[8] Fujiwara K and Taguchi H. (2012) Microbiology 158:917-924
[9] Fujiwara K and Nomura SM. (2013) in press
Educations
We are very welcome to graduate students, JSPS researchers who have an interest in our researches. Please contact us by e-mail (please in English or Japanese).
Additionally, we are involved in the following two educational projects as mentors
iGEM (http://igem.org/Main_Page ...there is no team in Tohoku Univ. But if you want to start, plz ask me)
BIOMOD (http://biomod.net)
We are very welcome to be mentors for other student contests like satellite design contest (why not?), science-I (http://www.science-i.jp), and so on. Let's join us, you ambitious students!