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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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2
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Kalvapalle PB, Sridhar S, Silberg JJ, Stadler LB. Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory. Appl Environ Microbiol 2024; 90:e0236323. [PMID: 38551351 PMCID: PMC11022584 DOI: 10.1128/aem.02363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 04/18/2024] Open
Abstract
Microbial biosensors that convert environmental information into real-time visual outputs are limited in their sensing abilities in complex environments, such as soil and wastewater, due to optical inaccessibility. Biosensors that could record transient exposure to analytes within a large time window for later retrieval represent a promising approach to solve the accessibility problem. Here, we test the performance of recombinase-memory biosensors that sense a sugar (arabinose) and a microbial communication molecule (3-oxo-C12-L-homoserine lactone) over 8 days (~70 generations) following analyte exposure. These biosensors sense the analyte and trigger the expression of a recombinase enzyme which flips a segment of DNA, creating a genetic memory, and initiates fluorescent protein expression. The initial designs failed over time due to unintended DNA flipping in the absence of the analyte and loss of the flipped state after exposure to the analyte. Biosensor performance was improved by decreasing recombinase expression, removing the fluorescent protein output, and using quantitative PCR to read out stored information. Application of memory biosensors in wastewater isolates achieved memory of analyte exposure in an uncharacterized Pseudomonas isolate. By returning these engineered isolates to their native environments, recombinase-memory systems are expected to enable longer duration and in situ investigation of microbial signaling, cross-feeding, community shifts, and gene transfer beyond the reach of traditional environmental biosensors.IMPORTANCEMicrobes mediate ecological processes over timescales that can far exceed the half-lives of transient metabolites and signals that drive their collective behaviors. We investigated strategies for engineering microbes to stably record their transient exposure to a chemical over many generations through DNA rearrangements. We identify genetic architectures that improve memory biosensor performance and characterize these in wastewater isolates. Memory biosensors are expected to be useful for monitoring cell-cell signals in biofilms, detecting transient exposure to chemical pollutants, and observing microbial cross-feeding through short-lived metabolites within cryptic methane, nitrogen, and sulfur cycling processes. They will also enable in situ studies of microbial responses to ephemeral environmental changes, or other ecological processes that are currently challenging to monitor non-destructively using real-time biosensors and analytical instruments.
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Affiliation(s)
| | - Swetha Sridhar
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
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De Marchi D, Shaposhnikov R, Gobaa S, Pastorelli D, Batt G, Magni P, Pasotti L. Design and Model-Driven Analysis of Synthetic Circuits with the Staphylococcus aureus Dead-Cas9 (sadCas9) as a Programmable Transcriptional Regulator in Bacteria. ACS Synth Biol 2024; 13:763-780. [PMID: 38374729 DOI: 10.1021/acssynbio.3c00541] [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] [Indexed: 02/21/2024]
Abstract
Synthetic circuit design is crucial for engineering microbes that process environmental cues and provide biologically relevant outputs. To reliably scale-up circuit complexity, the availability of parts toolkits is central. Streptococcus pyogenes (sp)-derived CRISPR interference/dead-Cas9 (CRISPRi/spdCas9) is widely adopted for implementing programmable regulations in synthetic circuits, and alternative CRISPRi systems will further expand our toolkits of orthogonal components. Here, we showcase the potential of CRISPRi using the engineered dCas9 from Staphylococcus aureus (sadCas9), not previously used in bacterial circuits, that is attractive for its low size and high specificity. We designed a collection of ∼20 increasingly complex circuits and variants in Escherichia coli, including circuits with static function like one-/two-input logic gates (NOT, NAND), circuits with dynamic behavior like incoherent feedforward loops (iFFLs), and applied sadCas9 to fix a T7 polymerase-based cascade. Data demonstrated specific and efficient target repression (100-fold) and qualitatively successful functioning for all circuits. Other advantageous features included low sadCas9-borne cell load and orthogonality with spdCas9. However, different circuit variants showed quantitatively unexpected and previously unreported steady-state responses: the dynamic range, switch point, and slope of NOT/NAND gates changed for different output promoters, and a multiphasic behavior was observed in iFFLs, differing from the expected bell-shaped or sigmoidal curves. Model analysis explained the observed curves by complex interplays among components, due to reporter gene-borne cell load and regulator competition. Overall, CRISPRi/sadCas9 successfully expanded the available toolkit for bacterial engineering. Analysis of our circuit collection depicted the impact of generally neglected effects modulating the shape of component dose-response curves, to avoid drawing wrong conclusions on circuit functioning.
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Affiliation(s)
- Davide De Marchi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Roman Shaposhnikov
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Samy Gobaa
- Institut Pasteur, Université Paris Cité, Biomaterials and Microfluidics Core Facility, 28 Rue du Docteur Roux, 75015 Paris, France
| | - Daniele Pastorelli
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
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Nou XA, Voigt CA. Sentinel cells programmed to respond to environmental DNA including human sequences. Nat Chem Biol 2024; 20:211-220. [PMID: 37770697 DOI: 10.1038/s41589-023-01431-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
Monitoring environmental DNA can track the presence of organisms, from viruses to animals, but requires continuous sampling of transient sequences from a complex milieu. Here we designed living sentinels using Bacillus subtilis to report the uptake of a DNA sequence after matching it to a preencoded target. Overexpression of ComK increased DNA uptake 3,000-fold, allowing for femtomolar detection in samples dominated by background DNA. This capability was demonstrated using human sequences containing single-nucleotide polymorphisms (SNPs) associated with facial features. Sequences were recorded with high efficiency and were protected from nucleases for weeks. The SNP could be determined by sequencing or in vivo using CRISPR interference to turn on reporter expression in response to a specific base. Multiple SNPs were recorded by one cell or through a consortium in which each member recorded a different sequence. Sentinel cells could surveil for specific sequences over long periods of time for applications spanning forensics, ecology and epidemiology.
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Affiliation(s)
- Xuefei Angelina Nou
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Goldman AL, Fulk EM, Momper LM, Heider C, Mulligan J, Osburn M, Masiello CA, Silberg JJ. Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface. mSystems 2024; 9:e0096623. [PMID: 38059636 PMCID: PMC10805038 DOI: 10.1128/msystems.00966-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023] Open
Abstract
Microbes can be found in abundance many kilometers underground. While microbial metabolic capabilities have been examined across different geochemical settings, it remains unclear how changes in subsurface niches affect microbial needs to sense and respond to their environment. To address this question, we examined how microbial extracellular sensor systems vary with environmental conditions across metagenomes at different Deep Mine Microbial Observatory (DeMMO) subsurface sites. Because two-component systems (TCSs) directly sense extracellular conditions and convert this information into intracellular biochemical responses, we expected that this sensor family would vary across isolated oligotrophic subterranean environments that differ in abiotic and biotic conditions. TCSs were found at all six subsurface sites, the service water control, and the surface site, with an average of 0.88 sensor histidine kinases (HKs) per 100 genes across all sites. Abundance was greater in subsurface fracture fluids compared with surface-derived fluids, and candidate phyla radiation (CPR) bacteria presented the lowest HK frequencies. Measures of microbial diversity, such as the Shannon diversity index, revealed that HK abundance is inversely correlated with microbial diversity (r2 = 0.81). Among the geochemical parameters measured, HK frequency correlated most strongly with variance in dissolved organic carbon (r2 = 0.82). Taken together, these results implicate the abiotic and biotic properties of an ecological niche as drivers of sensor needs, and they suggest that microbes in environments with large fluctuations in organic nutrients (e.g., lacustrine, terrestrial, and coastal ecosystems) may require greater TCS diversity than ecosystems with low nutrients (e.g., open ocean).IMPORTANCEThe ability to detect extracellular environmental conditions is a fundamental property of all life forms. Because microbial two-component sensor systems convert information about extracellular conditions into biochemical information that controls their behaviors, we evaluated how two-component sensor systems evolved within the deep Earth across multiple sites where abiotic and biotic properties vary. We show that these sensor systems remain abundant in microbial consortia at all subterranean sampling sites and observe correlations between sensor system abundances and abiotic (dissolved organic carbon variation) and biotic (consortia diversity) properties. These results suggest that multiple environmental properties may drive sensor protein evolution and highlight the need for further studies of metagenomic and geochemical data in parallel to understand the drivers of microbial sensor evolution.
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Affiliation(s)
| | - Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA
| | - Lily M. Momper
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Clinton Heider
- Rice University, Center for Research Computing, Houston, Texas, USA
| | - John Mulligan
- Rice University, Center for Research Computing, Houston, Texas, USA
| | - Magdalena Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Caroline A. Masiello
- Department of Biosciences, Rice University, Houston, Texas, USA
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, Texas, USA
- Department of Chemistry, Rice University, Houston, Texas, USA
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
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George DR, Danciu M, Davenport PW, Lakin MR, Chappell J, Frow EK. A bumpy road ahead for genetic biocontainment. Nat Commun 2024; 15:650. [PMID: 38245521 PMCID: PMC10799865 DOI: 10.1038/s41467-023-44531-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Affiliation(s)
- Dalton R George
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ, 85287, USA
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ, 85287, USA
| | - Mark Danciu
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Peter W Davenport
- Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Matthew R Lakin
- Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemical & Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - James Chappell
- Department of Biosciences & Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Emma K Frow
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ, 85287, USA.
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ, 85287, USA.
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Kim J, Lu LC, Gao X, Hofmockel KS, Masiello CA, Silberg JJ. Using Methyl Bromide for Interspecies Cell-Cell Signaling and As a Reporter in a Model Soil Consortium. ACS Synth Biol 2023; 12:3743-3753. [PMID: 37991716 DOI: 10.1021/acssynbio.3c00559] [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] [Indexed: 11/23/2023]
Abstract
Soil microbial communities with reduced complexity are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five-membered MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that V. beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally relevant hydration conditions. We find that methyl halide production can report on an MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. These tools will be useful for future studies that investigate how MSC responds to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.
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Affiliation(s)
- Jiwoo Kim
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Caroline A Masiello
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
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Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
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Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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Niman CM, Sukenik N, Dang T, Nwachukwu J, Thirumurthy MA, Jones AK, Naaman R, Santra K, Das TK, Paltiel Y, Baczewski LT, El-Naggar MY. Bacterial extracellular electron transfer components are spin selective. J Chem Phys 2023; 159:145101. [PMID: 37811828 DOI: 10.1063/5.0154211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/01/2023] [Indexed: 10/10/2023] Open
Abstract
Metal-reducing bacteria have adapted the ability to respire extracellular solid surfaces instead of soluble oxidants. This process requires an electron transport pathway that spans from the inner membrane, across the periplasm, through the outer membrane, and to an external surface. Multiheme cytochromes are the primary machinery for moving electrons through this pathway. Recent studies show that the chiral-induced spin selectivity (CISS) effect is observable in some of these proteins extracted from the model metal-reducing bacteria, Shewanella oneidensis MR-1. It was hypothesized that the CISS effect facilitates efficient electron transport in these proteins by coupling electron velocity to spin, thus reducing the probability of backscattering. However, these studies focused exclusively on the cell surface electron conduits, and thus, CISS has not been investigated in upstream electron transfer components such as the membrane-associated MtrA, or periplasmic proteins such as small tetraheme cytochrome (STC). By using conductive probe atomic force microscopy measurements of protein monolayers adsorbed onto ferromagnetic substrates, we show that electron transport is spin selective in both MtrA and STC. Moreover, we have determined the spin polarization of MtrA to be ∼77% and STC to be ∼35%. This disparity in spin polarizations could indicate that spin selectivity is length dependent in heme proteins, given that MtrA is approximately two times longer than STC. Most significantly, our study indicates that spin-dependent interactions affect the entire extracellular electron transport pathway.
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Affiliation(s)
- Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Nir Sukenik
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Tram Dang
- Department of Biological Sciences, University of Southern California, Los Angeles, California 91030, USA
| | - Justus Nwachukwu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Miyuki A Thirumurthy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kakali Santra
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tapan K Das
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yossi Paltiel
- Institute of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California 91030, USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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11
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Truong A, Myerscough D, Campbell I, Atkinson J, Silberg JJ. A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase. Protein Sci 2023; 32:e4746. [PMID: 37551563 PMCID: PMC10503412 DOI: 10.1002/pro.4746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Flavodoxins (Flds) mediate the flux of electrons between oxidoreductases in diverse metabolic pathways. To investigate whether Flds can support electron transfer to a sulfite reductase (SIR) that evolved to couple with a ferredoxin, we evaluated the ability of Flds to transfer electrons from a ferredoxin-NADP reductase (FNR) to a ferredoxin-dependent SIR using growth complementation of an Escherichia coli strain with a sulfur metabolism defect. We show that Flds from cyanobacteria complement this growth defect when coexpressed with an FNR and an SIR that evolved to couple with a plant ferredoxin. When we evaluated the effect of peptide insertion on Fld-mediated electron transfer, we observed a sensitivity to insertions within regions predicted to be proximal to the cofactor and partner binding sites, while a high insertion tolerance was detected within loops distal from the cofactor and within regions of helices and sheets that are proximal to those loops. Bioinformatic analysis showed that natural Fld sequence variability predicts a large fraction of the motifs that tolerate insertion of the octapeptide SGRPGSLS. These results represent the first evidence that Flds can support electron transfer to assimilatory SIRs, and they suggest that the pattern of insertion tolerance is influenced by interactions with oxidoreductase partners.
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Affiliation(s)
- Albert Truong
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Dru Myerscough
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Ian Campbell
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Joshua Atkinson
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
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12
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Liu B, Samaniego CC, Bennett MR, Franco E, Chappell J. A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. Nat Commun 2023; 14:5268. [PMID: 37644054 PMCID: PMC10465534 DOI: 10.1038/s41467-023-40785-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023] Open
Abstract
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. Toward addressing this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a design strategy to achieve tunable gene control. First, we demonstrate that STARs optimized for E. coli function across different Gram-negative species and can actuate using phage RNA polymerase, suggesting that RNA systems acting at the level of transcription are portable. Second, we explore an RNA design strategy that uses arrays of tandem and transcriptionally fused RNA regulators to precisely alter regulator concentration from 1 to 8 copies. This provides a simple means to predictably tune output gain across species and does not require access to large regulatory part libraries. Finally, we show RNA arrays can be used to achieve tunable cascading and multiplexing circuits across species, analogous to the motifs used in artificial neural networks.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - James Chappell
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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13
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Chen J, Vishweshwaraiah YL, Mailman RB, Tabdanov ED, Dokholyan NV. A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments. SCIENCE ADVANCES 2023; 9:eadg1062. [PMID: 37235645 PMCID: PMC10219599 DOI: 10.1126/sciadv.adg1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Single-protein-based devices that integrate signal sensing with logical operations to generate functional outputs offer exceptional promise for monitoring and modulating biological systems. Engineering such intelligent nanoscale computing agents is challenging, as it requires the integration of sensor domains into a functional protein via intricate allosteric networks. We incorporate a rapamycin-sensitive sensor (uniRapR) and a blue light-responsive LOV2 domain into human Src kinase, creating a protein device that functions as a noncommutative combinatorial logic circuit. In our design, rapamycin activates Src kinase, causing protein localization to focal adhesions, whereas blue light exerts the reverse effect that inactivates Src translocation. Focal adhesion maturation induced by Src activation reduces cell migration dynamics and shifts cell orientation to align along collagen nanolane fibers. Using this protein device, we reversibly control cell orientation by applying the appropriate input signals, a framework that may be useful in tissue engineering and regenerative medicine.
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Affiliation(s)
- Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | | | - Richard B. Mailman
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Erdem D. Tabdanov
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
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14
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Gotovtsev P. Microbial Cells as a Microrobots: From Drug Delivery to Advanced Biosensors. Biomimetics (Basel) 2023; 8:biomimetics8010109. [PMID: 36975339 PMCID: PMC10046805 DOI: 10.3390/biomimetics8010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The presented review focused on the microbial cell based system. This approach is based on the application of microorganisms as the main part of a robot that is responsible for the motility, cargo shipping, and in some cases, the production of useful chemicals. Living cells in such microrobots have both advantages and disadvantages. Regarding the advantages, it is necessary to mention the motility of cells, which can be natural chemotaxis or phototaxis, depending on the organism. There are approaches to make cells magnetotactic by adding nanoparticles to their surface. Today, the results of the development of such microrobots have been widely discussed. It has been shown that there is a possibility of combining different types of taxis to enhance the control level of the microrobots based on the microorganisms' cells and the efficiency of the solving task. Another advantage is the possibility of applying the whole potential of synthetic biology to make the behavior of the cells more controllable and complex. Biosynthesis of the cargo, advanced sensing, on/off switches, and other promising approaches are discussed within the context of the application for the microrobots. Thus, a synthetic biology application offers significant perspectives on microbial cell based microrobot development. Disadvantages that follow from the nature of microbial cells such as the number of external factors influence the cells, potential immune reaction, etc. They provide several limitations in the application, but do not decrease the bright perspectives of microrobots based on the cells of the microorganisms.
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Affiliation(s)
- Pavel Gotovtsev
- National Research Center "Kurchatov Institute", Biotechnology and Bioenergy Department, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141701 Moscow, Russia
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15
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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16
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Liu B, Samaniego CC, Bennett MR, Franco E, Chappell J. A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529951. [PMID: 36865180 PMCID: PMC9980294 DOI: 10.1101/2023.02.24.529951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. To address this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a novel design strategy to achieve tunable gene control. First, we demonstrate that STARs optimized for E. coli function across different Gram-negative species and can actuate using phage RNA polymerase, suggesting that RNA systems acting at the level of transcription are portable. Second, we explore a novel RNA design strategy that uses arrays of tandem and transcriptionally fused RNA regulators to precisely alter regulator concentration from 1 to 8 copies. This provides a simple means to predictably tune output gain across species and does not require access to large regulatory part libraries. Finally, we show RNA arrays can be used to achieve tunable cascading and multiplexing circuits across species, analogous to the motifs used in artificial neural networks.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, CA, USA
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, CA, USA
| | - James Chappell
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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17
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Usai F, Loi G, Scocozza F, Bellato M, Castagliuolo I, Conti M, Pasotti L. Design and biofabrication of bacterial living materials with robust and multiplexed biosensing capabilities. Mater Today Bio 2022; 18:100526. [PMID: 36632629 PMCID: PMC9826803 DOI: 10.1016/j.mtbio.2022.100526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The intertwined adoption of synthetic biology and 3D bioprinting has the potential to improve different application fields by fabricating engineered living materials (ELMs) with unnatural genetically-encoded sense & response capabilities. However, efforts are still needed to streamline the fabrication of sensing ELMs compatible with field use and improving their functional complexity. To investigate these two unmet needs, we adopted a workflow to reproducibly construct bacterial ELMs with synthetic biosensing circuits that provide red pigmentation as visible readout in response to different proof-of-concept chemical inducers. We first fabricated single-input/single-output ELMs and we demonstrated their robust performance in terms of longevity (cell viability and evolutionary stability >15 days, and long-term storage >1 month), sensing in harsh, non-sterile or nutrient-free conditions compatible with field use (soil, water, and clinical samples, including real samples from Pseudomonas aeruginosa infected patients). Then, we fabricated ELMs including multiple spatially-separated biosensor strains to engineer: level-bar materials detecting molecule concentration ranges, multi-input/multi-output devices with multiplexed sensing and information processing capabilities, and materials with cell-cell communication enabling on-demand pattern formation. Overall, we showed successful field use and multiplexed functioning of reproducibly fabricated ELMs, paving the way to a future automation of the prototyping process and boosting applications of such devices as in-situ monitoring tools or easy-to-use sensing kits.
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Affiliation(s)
- Francesca Usai
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Giada Loi
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Franca Scocozza
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Massimo Bellato
- Department of Information Engineering, University of Padua, Via Gradenigo 6b, 35131 Padua, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Michele Conti
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy,Corresponding author.
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy,Corresponding author.
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18
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Shaytan AK, Novikov RV, Vinnikov RS, Gribkova AK, Glukhov GS. From DNA-protein interactions to the genetic circuit design using CRISPR-dCas systems. Front Mol Biosci 2022; 9:1070526. [PMID: 36589238 PMCID: PMC9795063 DOI: 10.3389/fmolb.2022.1070526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023] Open
Abstract
In the last decade, the CRISPR-Cas technology has gained widespread popularity in different fields from genome editing and detecting specific DNA/RNA sequences to gene expression control. At the heart of this technology is the ability of CRISPR-Cas complexes to be programmed for targeting particular DNA loci, even when using catalytically inactive dCas-proteins. The repertoire of naturally derived and engineered dCas-proteins including fusion proteins presents a promising toolbox that can be used to construct functional synthetic genetic circuits. Rational genetic circuit design, apart from having practical relevance, is an important step towards a deeper quantitative understanding of the basic principles governing gene expression regulation and functioning of living organisms. In this minireview, we provide a succinct overview of the application of CRISPR-dCas-based systems in the emerging field of synthetic genetic circuit design. We discuss the diversity of dCas-based tools, their properties, and their application in different types of genetic circuits and outline challenges and further research directions in the field.
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Affiliation(s)
- A. K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: A. K. Shaytan,
| | - R. V. Novikov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - R. S. Vinnikov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - A. K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - G. S. Glukhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen, China
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19
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Feedforward growth rate control mitigates gene activation burden. Nat Commun 2022; 13:7054. [PMID: 36396941 PMCID: PMC9672102 DOI: 10.1038/s41467-022-34647-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
Heterologous gene activation causes non-physiological burden on cellular resources that cells are unable to adjust to. Here, we introduce a feedforward controller that actuates growth rate upon activation of a gene of interest (GOI) to compensate for such a burden. The controller achieves this by activating a modified SpoT enzyme (SpoTH) with sole hydrolysis activity, which lowers ppGpp level and thus increases growth rate. An inducible RelA+ expression cassette further allows to precisely set the basal level of ppGpp, and thus nominal growth rate, in any bacterial strain. Without the controller, activation of the GOI decreased growth rate by more than 50%. With the controller, we could activate the GOI to the same level without growth rate defect. A cell strain armed with the controller in co-culture enabled persistent population-level activation of a GOI, which could not be achieved by a strain devoid of the controller. The feedforward controller is a tunable, modular, and portable tool that allows dynamic gene activation without growth rate defects for bacterial synthetic biology applications.
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20
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Atkinson JT, Su L, Zhang X, Bennett GN, Silberg JJ, Ajo-Franklin CM. Real-time bioelectronic sensing of environmental contaminants. Nature 2022; 611:548-553. [DOI: 10.1038/s41586-022-05356-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2022] [Indexed: 11/07/2022]
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21
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2022; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore,Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore,Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore,Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore,Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore,Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore,Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore,Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore,E-mail:
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22
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Sridhar S, Ajo-Franklin CM, Masiello CA. A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology. ACS Synth Biol 2022; 11:2909-2916. [PMID: 35961652 PMCID: PMC9486965 DOI: 10.1021/acssynbio.2c00079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial biosensors sense and report exposures to stimuli, thereby facilitating our understanding of environmental processes. Successful design and deployment of biosensors hinge on the persistence of the microbial host of the genetic circuit, termed the chassis. However, model chassis organisms may persist poorly in environmental conditions. In contrast, non-model organisms persist better in environmental conditions but are limited by other challenges, such as genetic intractability and part unavailability. Here we identify ecological, metabolic, and genetic constraints for chassis development and propose a conceptual framework for the systematic selection of environmental biosensor chassis. We identify key challenges with using current model chassis and delineate major points of conflict in choosing the most suitable organisms as chassis for environmental biosensing. This framework provides a way forward in the selection of biosensor chassis for environmental synthetic biology.
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Affiliation(s)
- Swetha Sridhar
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United
States,Tel: 713-348-2565.
| | - Caroline M. Ajo-Franklin
- Department
of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Caroline A. Masiello
- Department
of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States,Department
of Earth, Environmental, and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United
States
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23
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Abstract
Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~105-fold by mineralogy and ~103-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. IMPORTANCE Understanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameter's effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) microbes. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.
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24
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Fulk EM, Gao X, Lu LC, Redeker KR, Masiello CA, Silberg JJ. Nondestructive Chemical Sensing within Bulk Soil Using 1000 Biosensors Per Gram of Matrix. ACS Synth Biol 2022; 11:2372-2383. [PMID: 35715210 DOI: 10.1021/acssynbio.2c00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram of soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram of soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with decreased perturbation of the soil environment compared to previously reported approaches, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.
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Affiliation(s)
- Emily M Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Kelly R Redeker
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Caroline A Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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25
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Wang T, Lu Y. Advances, Challenges and Future Trends of Cell-Free Transcription-Translation Biosensors. BIOSENSORS 2022; 12:bios12050318. [PMID: 35624619 PMCID: PMC9138237 DOI: 10.3390/bios12050318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/16/2022]
Abstract
In recent years, the application of cell-free protein synthesis systems in biosensing has been developing rapidly. Cell-free synthetic biology, with its advantages of high biosafety, fast material transport, and high sensitivity, has overcome many defects of cell-based biosensors and provided an abiotic substitute for biosensors. In addition, the application of freeze-drying technology has improved the stability of such systems, making it possible to realize point-of-care application of field detection and broadening the application prospects of cell-free biosensors. However, despite these advancements, challenges such as the risk of sample interference due to the lack of physical barriers, maintenance of activity during storage, and poor robustness still need to be addressed before the full potential of cell-free biosensors can be realized on a larger scale. In this review, current strategies and research results for improving the performance of cell-free biosensors are summarized, including a comprehensive discussion of the existing challenges, future trends, and potential investments needed for improvement.
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26
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Vaiana CA, Kim H, Cottet J, Oai K, Ge Z, Conforti K, King AM, Meyer AJ, Chen H, Voigt CA, Buie CR. Characterizing chemical signaling between engineered "microbial sentinels" in porous microplates. Mol Syst Biol 2022; 18:e10785. [PMID: 35315586 PMCID: PMC8938921 DOI: 10.15252/msb.202110785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Living materials combine a material scaffold, that is often porous, with engineered cells that perform sensing, computing, and biosynthetic tasks. Designing such systems is difficult because little is known regarding signaling transport parameters in the material. Here, the development of a porous microplate is presented. Hydrogel barriers between wells have a porosity of 60% and a tortuosity factor of 1.6, allowing molecular diffusion between wells. The permeability of dyes, antibiotics, inducers, and quorum signals between wells were characterized. A “sentinel” strain was constructed by introducing orthogonal sensors into the genome of Escherichia coli MG1655 for IPTG, anhydrotetracycline, L‐arabinose, and four quorum signals. The strain’s response to inducer diffusion through the wells was quantified up to 14 mm, and quorum and antibacterial signaling were measured over 16 h. Signaling distance is dictated by hydrogel adsorption, quantified using a linear finite element model that yields adsorption coefficients from 0 to 0.1 mol m−3. Parameters derived herein will aid the design of living materials for pathogen remediation, computation, and self‐organizing biofilms.
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Affiliation(s)
- Christopher A Vaiana
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hyungseok Kim
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Cottet
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keiko Oai
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhifei Ge
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kameron Conforti
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haorong Chen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cullen R Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Evans S, Allison S, Hawkes C. Microbes, memory, and moisture: predicting microbial moisture responses and their impact on carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Evans
- W.K. Kellogg Biological Station, Ecology and Evolutionary Biology Program Department of Integrative Biology Michigan State University Hickory Corners MI 49083 USA
| | - Steve Allison
- Department of Ecology and Evolutionary Biology Department of Earth System Science University of California Irvine California 92697 USA
| | - Christine Hawkes
- Department of Plant and Microbial Biology North Carolina State University Raleigh NC 27607 USA
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Wan X, Saltepe B, Yu L, Wang B. Programming living sensors for environment, health and biomanufacturing. Microb Biotechnol 2021; 14:2334-2342. [PMID: 33960658 PMCID: PMC8601174 DOI: 10.1111/1751-7915.13820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 01/10/2023] Open
Abstract
Synthetic biology offers new tools and capabilities of engineering cells with desired functions for example as new biosensing platforms leveraging engineered microbes. In the last two decades, bacterial cells have been programmed to sense and respond to various input cues for versatile purposes including environmental monitoring, disease diagnosis and adaptive biomanufacturing. Despite demonstrated proof-of-concept success in the laboratory, the real-world applications of microbial sensors have been restricted due to certain technical and societal limitations. Yet, most limitations can be addressed by new technological developments in synthetic biology such as circuit design, biocontainment and machine learning. Here, we summarize the latest advances in synthetic biology and discuss how they could accelerate the development, enhance the performance and address the present limitations of microbial sensors to facilitate their use in the field. We view that programmable living sensors are promising sensing platforms to achieve sustainable, affordable and easy-to-use on-site detection in diverse settings.
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Affiliation(s)
- Xinyi Wan
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Behide Saltepe
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
| | - Luyang Yu
- The Provincial International Science and Technology Cooperation Base for Engineering BiologyInternational CampusZhejiang UniversityHaining314400China
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | - Baojun Wang
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
- The Provincial International Science and Technology Cooperation Base for Engineering BiologyInternational CampusZhejiang UniversityHaining314400China
- College of Life SciencesZhejiang UniversityHangzhou310058China
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