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  1. Article ; Online: In Vitro

    Trettel, Daniel S / Winkler, Wade C

    Microbiology spectrum

    2023  , Page(s) e0335722

    Abstract: The shell proteins that comprise bacterial microcompartments (BMCs) can self-assemble into an array of superstructures such as nanotubes, flat sheets, and icosahedra. The physical characterization of BMCs and these superstructures typically relies on ... ...

    Abstract The shell proteins that comprise bacterial microcompartments (BMCs) can self-assemble into an array of superstructures such as nanotubes, flat sheets, and icosahedra. The physical characterization of BMCs and these superstructures typically relies on electron microscopy, which decouples samples from their solution context. We hypothesize that an investigation of fluorescently tagged BMCs and shell protein superstructures
    Language English
    Publishing date 2023-02-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.03357-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation.

    Trettel, Daniel S / Pacheco, Sara L / Laskie, Asa K / Gonzalez-Esquer, C Raul

    Frontiers in plant science

    2024  Volume 15, Page(s) 1346759

    Abstract: The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial ... ...

    Abstract The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO
    Language English
    Publishing date 2024-02-15
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2024.1346759
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Monatomic ions influence substrate permeation across bacterial microcompartment shells.

    Trettel, Daniel S / Neale, Chris / Zhao, Mingfei / Gnanakaran, S / Gonzalez-Esquer, C Raul

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 15738

    Abstract: Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for ... ...

    Abstract Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.
    MeSH term(s) Biophysics ; Biotechnology ; Chlorides ; Halogens ; Organelles
    Chemical Substances Chlorides ; Halogens
    Language English
    Publishing date 2023-09-21
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-42688-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Chemical probing provides insight into the native assembly state of a bacterial microcompartment.

    Trettel, Daniel S / Resager, William / Ueberheide, Beatrix M / Jenkins, Conor C / Winkler, Wade C

    Structure (London, England : 1993)

    2022  Volume 30, Issue 4, Page(s) 537–550.e5

    Abstract: Bacterial microcompartments (BMCs) are widespread in bacteria and are used for a variety of metabolic purposes, including catabolism of host metabolites. A suite of proteins self-assembles into the shell and cargo layers of BMCs. However, the native ... ...

    Abstract Bacterial microcompartments (BMCs) are widespread in bacteria and are used for a variety of metabolic purposes, including catabolism of host metabolites. A suite of proteins self-assembles into the shell and cargo layers of BMCs. However, the native assembly state of these large complexes remains to be elucidated. Herein, chemical probes were used to observe structural features of a native BMC. While the exterior could be demarcated with fluorophores, the interior was unexpectedly permeable, suggesting that the shell layer may be more dynamic than previously thought. This allowed access to cross-linking chemical probes, which were analyzed to uncover the protein interactome. These cross-links revealed a complex multivalent network among cargo proteins that contained encapsulation peptides and demonstrated that the shell layer follows discrete rules in its assembly. These results are consistent overall with a model in which biomolecular condensation drives interactions of cargo proteins before envelopment by shell layer proteins.
    MeSH term(s) Bacteria/metabolism ; Bacterial Proteins/chemistry ; Organelles/metabolism ; Peptides/metabolism
    Chemical Substances Bacterial Proteins ; Peptides
    Language English
    Publishing date 2022-02-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2022.02.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems.

    Pandey, Naresh / Davison, Steffi A / Krishnamurthy, Malathy / Trettel, Daniel S / Lo, Chien-Chi / Starkenburg, Shawn / Wozniak, Katherine L / Kern, Theresa L / Reardon, Sean D / Unkefer, Clifford J / Hennelly, Scott P / Dale, Taraka

    ACS synthetic biology

    2022  Volume 11, Issue 10, Page(s) 3216–3227

    Abstract: Engineered microbes can be used for producing value-added chemicals from renewable feedstocks, relieving the dependency on nonrenewable resources such as petroleum. These microbes often are composed of synthetic metabolic pathways; however, one major ... ...

    Abstract Engineered microbes can be used for producing value-added chemicals from renewable feedstocks, relieving the dependency on nonrenewable resources such as petroleum. These microbes often are composed of synthetic metabolic pathways; however, one major problem in establishing a synthetic pathway is the challenge of precisely controlling competing metabolic routes, some of which could be crucial for fitness and survival. While traditional gene deletion and/or coarse overexpression approaches do not provide precise regulation,
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Phosphoenolpyruvate/metabolism ; Pseudomonas putida/genetics ; Pseudomonas putida/metabolism ; Metabolic Engineering ; Pyruvic Acid/metabolism ; Genomics ; RNA/metabolism ; Petroleum/metabolism
    Chemical Substances Phosphoenolpyruvate (73-89-2) ; Pyruvic Acid (8558G7RUTR) ; RNA (63231-63-0) ; Petroleum
    Language English
    Publishing date 2022-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.1c00638
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A protocatechuate biosensor for

    Jha, Ramesh K / Bingen, Jeremy M / Johnson, Christopher W / Kern, Theresa L / Khanna, Payal / Trettel, Daniel S / Strauss, Charlie E M / Beckham, Gregg T / Dale, Taraka

    Metabolic engineering communications

    2018  Volume 6, Page(s) 33–38

    Abstract: Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. ... ...

    Abstract Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an
    Language English
    Publishing date 2018-03-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2821894-2
    ISSN 2214-0301 ; 2214-0301
    ISSN (online) 2214-0301
    ISSN 2214-0301
    DOI 10.1016/j.meteno.2018.03.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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