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      Engineering Cyborg Bacteria Through Intracellular Hydrogelation

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          Abstract

          Natural and artificial cells are two common chassis in synthetic biology. Natural cells can perform complex tasks through synthetic genetic constructs, but their autonomous replication often causes safety concerns for biomedical applications. In contrast, artificial cells based on nonreplicating materials, albeit possessing reduced biochemical complexity, provide more defined and controllable functions. Here, for the first time, the authors create hybrid material‐cell entities termed Cyborg Cells. To create Cyborg Cells, a synthetic polymer network is assembled inside each bacterium, rendering them incapable of dividing. Cyborg Cells preserve essential functions, including cellular metabolism, motility, protein synthesis, and compatibility with genetic circuits. Cyborg Cells also acquire new abilities to resist stressors that otherwise kill natural cells. Finally, the authors demonstrate the therapeutic potential by showing invasion into cancer cells. This work establishes a new paradigm in cellular bioengineering by exploiting a combination of intracellular man‐made polymers and their interaction with the protein networks of living cells.

          Abstract

          Synthetic biology has made major strides toward creating programmable bio‐micromachines. Despite these efforts, current living synthetic cells are created primarily using genetic approaches, and they autonomously divide. Here, the authors show how assembling a man‐made polymer matrix inside bacteria creates semi‐living entities termed Cyborg Cells. The Cyborg Cells are programmable, do not divide, preserve essential cellular activities, and gain nonnative abilities.

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          Most cited references50

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          Engineering Cellular Metabolism.

          Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds, and pharmaceuticals. However, making cells into efficient factories is challenging because cells have evolved robust metabolic networks with hard-wired, tightly regulated lines of communication between molecular pathways that resist efforts to divert resources. Here, we will review the current status and challenges of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation.
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            Synchronized cycles of bacterial lysis for in vivo delivery

            The pervasive view of bacteria as strictly pathogenic has given way to an appreciation of the widespread prevalence of beneficial microbes within the human body 1–3 . Given this milieu, it is perhaps inevitable that some bacteria would evolve to preferentially grow in environments that harbor disease and thus provide a natural platform for the development of engineered therapies 4–6 . Such therapies could benefit from bacteria that are programmed to limit bacterial growth while continually producing and releasing cytotoxic agents in situ 7–10 . Here, we engineer a clinically relevant bacterium to lyse synchronously at a threshold population density and to release genetically encoded cargo. Following quorum lysis, a small number of surviving bacteria reseed the growing population, thus leading to pulsatile delivery cycles. We use microfluidic devices to characterize the engineered lysis strain and we demonstrate its potential as a drug delivery platform via co-culture with human cancer cells in vitro. As a proof of principle, we track the bacterial population dynamics in ectopic syngeneic colorectal tumors in mice. The lysis strain exhibits pulsatile population dynamics in vivo, with mean bacterial luminescence that remained two orders of magnitude lower than an unmodified strain. Finally, guided by previous findings that certain bacteria can enhance the efficacy of standard therapies 11 , we orally administer the lysis strain, alone or in combination with a clinical chemotherapeutic, to a syngeneic transplantation model of hepatic colorectal metastases. We find that the combination of both circuit-engineered bacteria and chemotherapy leads to a notable reduction of tumor activity along with a marked survival benefit over either therapy alone. Our approach establishes a methodology for leveraging the tools of synthetic biology to exploit the natural propensity for certain bacteria to colonize disease sites.
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              Alkaline pH homeostasis in bacteria: new insights.

              The capacity of bacteria to survive and grow at alkaline pH values is of widespread importance in the epidemiology of pathogenic bacteria, in remediation and industrial settings, as well as in marine, plant-associated and extremely alkaline ecological niches. Alkali-tolerance and alkaliphily, in turn, strongly depend upon mechanisms for alkaline pH homeostasis, as shown in pH shift experiments and growth experiments in chemostats at different external pH values. Transcriptome and proteome analyses have recently complemented physiological and genetic studies, revealing numerous adaptations that contribute to alkaline pH homeostasis. These include elevated levels of transporters and enzymes that promote proton capture and retention (e.g., the ATP synthase and monovalent cation/proton antiporters), metabolic changes that lead to increased acid production, and changes in the cell surface layers that contribute to cytoplasmic proton retention. Targeted studies over the past decade have followed up the long-recognized importance of monovalent cations in active pH homeostasis. These studies show the centrality of monovalent cation/proton antiporters in this process while microbial genomics provides information about the constellation of such antiporters in individual strains. A comprehensive phylogenetic analysis of both eukaryotic and prokaryotic genome databases has identified orthologs from bacteria to humans that allow better understanding of the specific functions and physiological roles of the antiporters. Detailed information about the properties of multiple antiporters in individual strains is starting to explain how specific monovalent cation/proton antiporters play dominant roles in alkaline pH homeostasis in cells that have several additional antiporters catalyzing ostensibly similar reactions. New insights into the pH-dependent Na(+)/H(+) antiporter NhaA that plays an important role in Escherichia coli have recently emerged from the determination of the structure of NhaA. This review highlights the approaches, major findings and unresolved problems in alkaline pH homeostasis, focusing on the small number of well-characterized alkali-tolerant and extremely alkaliphilic bacteria.
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                Author and article information

                Contributors
                chu@ibms.sinica.edu.tw
                cmtan@ucdavis.edu
                Journal
                Adv Sci (Weinh)
                Adv Sci (Weinh)
                10.1002/(ISSN)2198-3844
                ADVS
                Advanced Science
                John Wiley and Sons Inc. (Hoboken )
                2198-3844
                11 January 2023
                March 2023
                : 10
                : 9 ( doiID: 10.1002/advs.v10.9 )
                : 2204175
                Affiliations
                [ 1 ] Department of Biomedical Engineering University of California Davis CA 95616 USA
                [ 2 ] Institute of Biomedical Sciences Academia Sinica Taipei 11529 Taiwan
                [ 3 ] Department of Surgery University of California Davis School of Medicine Sacramento CA 95817 USA
                Author notes
                Author information
                https://orcid.org/0000-0002-9686-7375
                https://orcid.org/0000-0003-1049-1192
                Article
                ADVS4949
                10.1002/advs.202204175
                10037956
                36628538
                d9e2f17d-430f-4ae9-b5a4-a2f8f2577a61
                © 2023 The Authors. Advanced Science published by Wiley‐VCH GmbH

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 November 2022
                : 20 July 2022
                Page count
                Figures: 6, Tables: 0, Pages: 11, Words: 7319
                Funding
                Funded by: CONACYT UC‐MEXUS Doctoral Fellowship to L.E.C‐L.
                Funded by: National Institutes of Health , doi 10.13039/100000002;
                Award ID: 1R35GM142788
                Award ID: 5R21EB025938
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                March 24, 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.6 mode:remove_FC converted:24.03.2023

                cellular chassis,hybrid material,hydrogel,nonreplicating bacteria,nonculturable cells,synthetic biology

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