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Müller GA. The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms. Bioengineering (Basel) 2025; 12:532. [PMID: 40428151 PMCID: PMC12109375 DOI: 10.3390/bioengineering12050532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2025] [Revised: 05/05/2025] [Accepted: 05/07/2025] [Indexed: 05/29/2025] Open
Abstract
So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a "fit" between donor and acceptor proteomes and structures. "Fitting" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) "Blending" or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's "gemmules" to "stirps", cytoplasmic and "plasmon" inheritance, "rhizene agency", "communicology", "transdisciplinary membranology" to up to Kirschner's "facilitated variation".
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Affiliation(s)
- Günter A. Müller
- Biology and Technology Studies Institute Munich (BITSIM), 80939 Munich, Germany; ; Tel.: +49-151-25216987
- Institute of Media Sociology, Department of Cultural Sciences, University of Paderborn, 33104 Paderborn, Germany
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Postnikov EB, Singh AP, Sychev AV, Lavrova AI, Singh VK. A stochastic model for the bacterial growth exhibiting staged growth, desynchronization, saturation and persistence. Math Biosci 2024; 378:109322. [PMID: 39490581 DOI: 10.1016/j.mbs.2024.109322] [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: 07/03/2024] [Revised: 10/03/2024] [Accepted: 10/19/2024] [Indexed: 11/05/2024]
Abstract
We consider a model of population growth based on the stochastic variation of the population size-controlled duplication of bacterial cells. It is shown that the proper choice of the control function allows for reproducing a variety of regimes: a logistic growth with saturation, a hindered growth typical for persistent bacterial systems, and a linear population growth detected for some mycobacterial populations. When supplied with the rectangular function having the width equal to the generation time, this approach represents the solution generalizing Rubinow's age-maturity model reproducing systems with desynchronization and saturation. The model's plausibility is confirmed by the direct comparison with real data for the growth of M. tuberculosis populations obtained with the BACTEC MGIT system under different conditions of growth synchronization.
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Affiliation(s)
- Eugene B Postnikov
- Department of Theoretical Physics, Kursk State University, Radishcheva st. 33, Kursk, 305000, Russia.
| | - Anant Pratap Singh
- Department of Mathematical Sciences, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Alexander V Sychev
- Research Center for Condensed Matter Physics, Kursk State University, Radishcheva st. 33, Kursk, 305000, Russia
| | - Anastasia I Lavrova
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Ligovskiy av. 2-4, Saint-Petersburg, 194064, Russia; Sophya Kovalevskaya North-West Mathematical Research Center, Immanuel Kant Baltic Federal University, Nevskogo st. 14, Kaliningrad, 236041, Russia
| | - Vineet Kumar Singh
- Department of Mathematical Sciences, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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Bioethanol production by reusable Saccharomyces cerevisiae immobilized in a macroporous monolithic hydrogel matrices. J Biotechnol 2016; 233:56-65. [DOI: 10.1016/j.jbiotec.2016.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 07/02/2016] [Accepted: 07/07/2016] [Indexed: 11/24/2022]
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Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol 2015; 11:784. [PMID: 25678603 PMCID: PMC4358657 DOI: 10.15252/msb.20145697] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector's total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies.
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Affiliation(s)
- Sheng Hui
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Josh M Silverman
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephen S Chen
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - David W Erickson
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Markus Basan
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Jilong Wang
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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Symposium: The Drug Resistance of Micro-Organisms. Proc R Soc Med 1952. [DOI: 10.1177/003591575204500514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Murrell WG, Vincent JM. The esters of 4-hydroxybenzoic acid and related compounds. IV. The bacteriostatic action of n-alkyl 4-hydroxybenzoates. ACTA ACUST UNITED AC 1950. [DOI: 10.1002/jctb.5000690407] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Thatcher F, Maclean JT. Synergistic action between the sulfonamides, certain dyes, and streptomycin against gram-negative bacteria; preliminary report. J Urol 1947; 57:902-31. [PMID: 20295868 DOI: 10.1016/s0022-5347(17)69727-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- F.S. Thatcher
- From the Department of Bacteriology, Macdonald College, McGill University and the Departments of Urology, Montreal Military Hospital and Royal Victoria Hospital, Montreal
| | - John T. Maclean
- From the Department of Bacteriology, Macdonald College, McGill University and the Departments of Urology, Montreal Military Hospital and Royal Victoria Hospital, Montreal
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