1
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Sebastianelli L, Kaur H, Chen Z, Krishnamurthy R, Mansy SS. A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides. Chemistry 2024:e202400411. [PMID: 38640109 DOI: 10.1002/chem.202400411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/21/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3-(aminocarbonyl)-1-(2,3-dihydroxypropyl)pyridinium, 1-methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons from and to pyruvate within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules.
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Affiliation(s)
| | | | - Ziniu Chen
- University of Alberta, Chemistry, CANADA
| | | | - Sheref S Mansy
- University of Alberta, Chemistry, 11227 Saskatchewan Drive, Edmonton, CANADA
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2
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Rossetto D, Sebastianelli L, Oberegger S, Todorovic S, Haas H, Mansy SS. Peptide Mimics of the Cysteine-Rich Regions of HapX and SreA Bind a [2Fe-2S] Cluster In Vitro. Adv Biol (Weinh) 2024:e2300545. [PMID: 38574244 DOI: 10.1002/adbi.202300545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/07/2024] [Indexed: 04/06/2024]
Abstract
HapX and SreA are transcription factors that regulate the response of the fungus Aspergillus fumigatus to the availability of iron. During iron starvation, HapX represses genes involved in iron consuming pathways and upon a shift to iron excess, HapX activates these same genes. SreA blocks the expression of genes needed for iron uptake during periods of iron availability. Both proteins possess cysteine-rich regions (CRR) that are hypothesized to be necessary for the sensing of iron levels. However, the contribution of each of these domains to the function of the protein has remained unclear. Here, the ability of peptide analogs of each CRR is determined to bind an iron-sulfur cluster in vitro. UV-vis and resonance Raman (RR) spectroscopies reveal that each CRR is capable of coordinating a [2Fe-2S] cluster with comparable affinities. The iron-sulfur cluster coordinated to the CRR-B domain of HapX displays particularly high stability. The data are consistent with HapX and SreA mediating responses to cellular iron levels through the direct coordination of [2Fe-2S] clusters. The high stability of the CRR-B peptide may also find use as a starting point for the development of new green catalysts.
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Affiliation(s)
- Daniele Rossetto
- D-CIBIO, University of Trento, via Sommarive 9, Trento, 38123, Italy
| | - Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Simon Oberegger
- Institute of Molecular Biology, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, Oeiras, 2780-157, Portugal
| | - Hubertus Haas
- Institute of Molecular Biology, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria
| | - Sheref S Mansy
- D-CIBIO, University of Trento, via Sommarive 9, Trento, 38123, Italy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
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3
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Toparlak Ö, Sebastianelli L, Egas Ortuno V, Karki M, Xing Y, Szostak JW, Krishnamurthy R, Mansy SS. Cyclophospholipids Enable a Protocellular Life Cycle. ACS Nano 2023; 17:23772-23783. [PMID: 38038709 PMCID: PMC10722605 DOI: 10.1021/acsnano.3c07706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.
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Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
| | - Lorenzo Sebastianelli
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
| | - Veronica Egas Ortuno
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Megha Karki
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yanfeng Xing
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ramanarayanan Krishnamurthy
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
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4
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Liu Y, Liu S, Tomar A, Yen FS, Unlu G, Ropek N, Weber RA, Wang Y, Khan A, Gad M, Peng J, Terzi E, Alwaseem H, Pagano AE, Heissel S, Molina H, Allwein B, Kenny TC, Possemato RL, Zhao L, Hite RK, Vinogradova EV, Mansy SS, Birsoy K. Autoregulatory control of mitochondrial glutathione homeostasis. Science 2023; 382:820-828. [PMID: 37917749 DOI: 10.1126/science.adf4154] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Mitochondria must maintain adequate amounts of metabolites for protective and biosynthetic functions. However, how mitochondria sense the abundance of metabolites and regulate metabolic homeostasis is not well understood. In this work, we focused on glutathione (GSH), a critical redox metabolite in mitochondria, and identified a feedback mechanism that controls its abundance through the mitochondrial GSH transporter, SLC25A39. Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. Depletion of GSH dissociates AFG3L2 from SLC25A39, causing a compensatory increase in mitochondrial GSH uptake. Genetic and proteomic analyses identified a putative iron-sulfur cluster in the matrix-facing loop of SLC25A39 as essential for this regulation, coupling mitochondrial iron homeostasis to GSH import. Altogether, our work revealed a paradigm for the autoregulatory control of metabolic homeostasis in organelles.
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Affiliation(s)
- Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Shanshan Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Anju Tomar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Cellular, Computational and Integrative Biology, Università di Trento, Trento, TN, Italy
| | - Frederick S Yen
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Nathalie Ropek
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY, USA
| | - Ross A Weber
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Ying Wang
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Mark Gad
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erdem Terzi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hanan Alwaseem
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexandra E Pagano
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Benjamin Allwein
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy C Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Richard L Possemato
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ekaterina V Vinogradova
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY, USA
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
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5
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Mugoni V, Ciani Y, Quaini O, Tomasini S, Notarangelo M, Vannuccini F, Marinelli A, Leonardi E, Pontalti S, Martinelli A, Rossetto D, Pesce I, Mansy SS, Barbareschi M, Ferro A, Caffo O, Attard G, Di Vizio D, D'Agostino VG, Nardella C, Demichelis F. Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients. J Extracell Biol 2023; 2:e108. [PMID: 38046436 PMCID: PMC10688391 DOI: 10.1002/jex2.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell-free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining EV-associated RNA (EV-RNA) and cfDNA signals on n = 64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we isolated EV-enriched samples by a charge-based (CB) method and investigated EV-RNA and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV-RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi-analytes liquid biopsies' clinical implementation.
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Affiliation(s)
- Vera Mugoni
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Yari Ciani
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Orsetta Quaini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Simone Tomasini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Federico Vannuccini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Alessia Marinelli
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Elena Leonardi
- Unit of Surgical Pathology, Santa Chiara Hospital, APSSTrentoItaly
| | - Stefano Pontalti
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | - Angela Martinelli
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Daniele Rossetto
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Isabella Pesce
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Sheref S. Mansy
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | | | - Antonella Ferro
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | - Orazio Caffo
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | | | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and TherapeuticsCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | | | - Caterina Nardella
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
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6
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Nader S, Baccouche A, Connolly F, Abou-Ghanem M, Styler SA, Lewis JD, Pink D, Mansy SS. Model Atmospheric Aerosols Convert to Vesicles upon Entry into Aqueous Solution. ACS Earth Space Chem 2023; 7:252-259. [PMID: 36704180 PMCID: PMC9869892 DOI: 10.1021/acsearthspacechem.2c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Aerosols are abundant on the Earth and likely played a role in prebiotic chemistry. Aerosol particles coagulate, divide, and sample a wide variety of conditions conducive to synthesis. While much work has centered on the generation of aerosols and their chemistry, little effort has been expended on their fate after settling. Here, using a laboratory model, we show that aqueous aerosols transform into cell-sized protocellular structures upon entry into aqueous solution containing lipid. Such processes provide for a heretofore unexplored pathway for the assembly of the building blocks of life from disparate geochemical regions within cell-like vesicles with a lipid bilayer in a manner that does not lead to dilution. The efficiency of aerosol to vesicle transformation is high with prebiotically plausible lipids, such as decanoic acid and decanol, that were previously shown to be capable of forming growing and dividing vesicles. The high transformation efficiency with 10-carbon lipids in landing solutions is consistent with the surface properties and dynamics of short-chain lipids. Similar processes may be operative today as fatty acids are common constituents of both contemporary aerosols and the sea. Our work highlights a new pathway that may have facilitated the emergence of the Earth's first cells.
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Affiliation(s)
- Serge Nader
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Alexandre Baccouche
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Fiona Connolly
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Maya Abou-Ghanem
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Sarah A. Styler
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - John D. Lewis
- Department
of Oncology, University of Alberta, Edmonton, AlbertaT6G 2E1, Canada
| | - Desmond Pink
- Nanostics
Inc., Edmonton, AlbertaT5J 4P6, Canada
| | - Sheref S. Mansy
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
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7
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Abstract
It is common to compare life with machines. Both consume fuel and release waste to run. In biology, the engine that drives the living system is referred to as metabolism. However, attempts at deciphering the origins of metabolism do not focus on this energetic relationship that sustains life but rather concentrate on nonenzymatic reactions that produce all the intermediates of an extant metabolic pathway. Such an approach is akin to studying the molecules produced from the burning of coal instead of deciphering how the released energy drives the movement of pistons and ultimately the train when investigating the mechanisms behind locomotion. Theories that do explicitly invoke geological chemical gradients to drive metabolism most frequently feature hydrothermal vent conditions, but hydrothermal vents are not the only regions of the early Earth that could have provided the fuel necessary to sustain the Earth's first (proto)cells. Here, we give examples of prior reports on protometabolism and highlight how more recent investigations of out-of-equilibrium systems may point to alternative scenarios more consistent with the majority of prebiotic chemistry data accumulated thus far. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Serge Nader
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
| | - Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
| | - Sheref S. Mansy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
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8
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Valer L, Rossetto D, Parkkila T, Sebastianelli L, Guella G, Hendricks AL, Cowan JA, Sang L, Mansy SS. Histidine Ligated Iron-Sulfur Peptides. Chembiochem 2022; 23:e202200202. [PMID: 35674331 PMCID: PMC9400863 DOI: 10.1002/cbic.202200202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/08/2022] [Indexed: 11/17/2022]
Abstract
Iron‐sulfur clusters are thought to be ancient cofactors that could have played a role in early protometabolic systems. Thus far, redox active, prebiotically plausible iron‐sulfur clusters have always contained cysteine ligands to the cluster. However, extant iron‐sulfur proteins can be found to exploit other modes of binding, including ligation by histidine residues, as seen with [2Fe‐2S] Rieske and MitoNEET proteins. Here, we investigated the ability of cysteine‐ and histidine‐containing peptides to coordinate a mononuclear Fe2+ center and a [2Fe‐2S] cluster and compare their properties with purified iron‐sulfur proteins. The iron‐sulfur peptides were characterized by UV‐vis, circular dichroism, and paramagnetic NMR spectroscopies and cyclic voltammetry. Small (≤6 amino acids) peptides can coordinate [2Fe‐2S] clusters through a combination of cysteine and histidine residues with similar reduction potentials as their corresponding proteins. Such complexes may have been important for early cell‐like systems.
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Affiliation(s)
- Luca Valer
- D-CIBIO, University of Trento, via Sommarive 9, 38123, Trento 28123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Daniele Rossetto
- D-CIBIO, University of Trento, via Sommarive 9, 38123, Trento 28123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Taylor Parkkila
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, Trento, 38123, Italy
| | - Amber L Hendricks
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH 43210, USA
| | - James A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH 43210, USA
| | - Lingzi Sang
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Sheref S Mansy
- D-CIBIO, University of Trento, via Sommarive 9, 38123, Trento 28123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
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9
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Rossetto D, Valer L, Yeh Martín N, Guella G, Hongo Y, Mansy SS. Prebiotic Environments with Mg 2+ and Thiophilic Metal Ions Increase the Thermal Stability of Cysteine and Non-cysteine Peptides. ACS Earth Space Chem 2022; 6:1221-1226. [PMID: 35620317 PMCID: PMC9126146 DOI: 10.1021/acsearthspacechem.2c00042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Wet-dry cycles driven by heating to high temperatures are frequently invoked for the prebiotic synthesis of peptides. Similarly, iron-sulfur clusters are often cited as an example of an ancient catalyst that helped prune early chemical systems into metabolic-like pathways. Because extant iron-sulfur clusters are metallocofactors of protein enzymes and nearly ubiquitous across biology, a reasonable hypothesis is that prebiotic iron-sulfur peptides formed on the early Earth. However, iron-sulfur clusters are coordinated by multiple cysteine residues, and the stability of cysteines to the heat steps of wet-dry cycles has not been determined. It, therefore, has remained unclear if the peptides needed to stabilize the formation of iron-sulfur clusters could have formed. If not, then iron-sulfur-dependent activity may have emerged later, when milder, more biological-like peptide synthesis machinery took hold. Here, we report the thermal stability of cysteine-containing peptides. We show that temperatures of 150 °C lead to the rapid degradation of cysteinyl peptides. However, the presence of Mg2+ at environmentally reasonable concentrations leads to significant protection. Thiophilic metal ions also protect against degradation at 150 °C but require concentrations not frequently observed in the environment. Nevertheless, cysteine-containing peptides are stable at lower, prebiotically plausible temperatures in seawater, carbonate lake, and ferrous lake conditions. The data are consistent with the persistence of cysteine-containing peptides on the early Earth in environments rich in metal ions. High concentrations of Mg2+ are common intra- and extra-cellularly, suggesting that the protection afforded by Mg2+ may reflect conditions that were present on the prebiotic Earth.
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Affiliation(s)
- Daniele Rossetto
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Luca Valer
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Noël Yeh Martín
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
| | - Graziano Guella
- Department
of Physics, University of Trento, Via Sommarive 14, 38123 Povo, Italy
| | - Yayoi Hongo
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Okinawa
Institute of Science and Technology Graduate University, Onna-son, Kunigami, Okinawa 904-0495, Japan
| | - Sheref S. Mansy
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
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10
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Peng H, Rossetto D, Mansy SS, Jordan MC, Roos KP, Chen IA. Treatment of Wound Infections in a Mouse Model Using Zn 2+-Releasing Phage Bound to Gold Nanorods. ACS Nano 2022; 16:4756-4774. [PMID: 35239330 PMCID: PMC8981316 DOI: 10.1021/acsnano.2c00048] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/09/2022] [Indexed: 05/20/2023]
Abstract
Infections caused by drug-resistant bacteria, particularly Gram-negative organisms, are increasingly difficult to treat using antibiotics. A potential alternative is "phage therapy", in which phages infect and lyse the bacterial host. However, phage therapy poses serious drawbacks and safety concerns, such as the risk of genetic transduction of antibiotic resistance genes, inconsistent pharmacokinetics, and unknown evolutionary potential. In contrast, metallic nanoparticles possess precise, tunable properties, including efficient conversion of electronic excitation into heat. In this work, we demonstrate that engineered phage-nanomaterial conjugates that target the Gram-negative pathogen Pseudomonas aeruginosa are highly effective as a treatment of infected wounds in mice. Photothermal heating, performed as a single treatment (15 min) or as two treatments on consecutive days, rapidly reduced the bacterial load and released Zn2+ to promote wound healing. The phage-nanomaterial treatment was significantly more effective than systemic standard-of-care antibiotics, with a >10× greater reduction in bacterial load and ∼3× faster healing as measured by wound size reduction when compared to fluoroquinolone treatment. Notably, the phage-nanomaterial was also effective against a P. aeruginosa strain resistant to polymyxins, a last-line antibiotic therapy. Unlike these antibiotics, the phage-nanomaterial showed no detectable toxicity or systemic effects in mice, consistent with the short duration and localized nature of phage-nanomaterial treatment. Our results demonstrate that phage therapy controlled by inorganic nanomaterials can be a safe and effective antimicrobial strategy in vivo.
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Affiliation(s)
- Huan Peng
- Department
of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Daniele Rossetto
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- CIBIO, University of Trento, 38123 Povo, Trento, Italy
| | - Sheref S. Mansy
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- CIBIO, University of Trento, 38123 Povo, Trento, Italy
| | - Maria C. Jordan
- Department
of Physiology, David Geffen School of Medicine
at the University of California, Los Angeles, California 90095, United States
| | - Kenneth P. Roos
- Department
of Physiology, David Geffen School of Medicine
at the University of California, Los Angeles, California 90095, United States
| | - Irene A. Chen
- Department
of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
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11
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Abstract
Investigations of biology and the origins of life regularly focus on the components of the central dogma and thus the elements that compose nucleic acids and peptides. Less attention is given to the inorganic components of a biological cell, which are required for biological polymers to function. The Earth was and continues to be rich in metals, and so investigations of the emergence and evolution of life must account for the role that metal ions play. Evolution is shaped by what is present, and not all elements of the periodic table are equally accessible. The presence of metals, the solubility of their ions, and their intrinsic reactivity all impacted the composition of the cells that emerged. Geological and bioinformatic analyses clearly show that the suite of accessible metal ions changed over the history of the Earth; however, such analyses tend to be interpreted in comparison to average oceanic conditions, which do not represent well the many niche environments present on the Earth. While there is still debate concerning the sequence of events that led to extant biology, what is clear is that life as we know it requires metals, and that past and current metal-dependent events remain, at least partially, imprinted in the chemistry of the cell.
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Affiliation(s)
| | - Sheref S Mansy
- D-CIBIO, University of Trento, Povo, Italy
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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12
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Sebastianelli L, Mansy SS. Origins of life: Encapsulating Darwinian evolution. Curr Biol 2022; 32:R44-R46. [PMID: 35015996 DOI: 10.1016/j.cub.2021.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Encapsulation of RNA within model protocells promotes folding, promotes the binding of substrates, promotes catalysis, and protects against denaturation. A new study argues for an active role of lipid vesicles in the origins of life.
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Affiliation(s)
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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13
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Ha M, Nader S, Pawsey S, Struppe J, Monette M, Mansy SS, Boekhoven J, Michaelis VK. Racing toward Fast and Effective 17O Isotopic Labeling and Nuclear Magnetic Resonance Spectroscopy of N-Formyl-MLF-OH and Associated Building Blocks. J Phys Chem B 2021; 125:11916-11926. [PMID: 34694819 DOI: 10.1021/acs.jpcb.1c07397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state 1H, 13C, and 15N nuclear magnetic resonance (NMR) spectroscopy has been an essential analytical method in studying complex molecules and biomolecules for decades. While oxygen-17 (17O) NMR is an ideal and robust candidate to study hydrogen bonding within secondary and tertiary protein structures for example, it continues to elude many. We discuss an improved multiple-turnover labeling procedure to develop a fast and cost-effective method to 17O label fluoroenylmethyloxycarbonyl (Fmoc)-protected amino acid building blocks. This approach allows for inexpensive ($0.25 USD/mg) insertion of 17O labels, an important barrier to overcome for future biomolecular studies. The 17O NMR results of these building blocks and a site-specific strategy for labeled N-acetyl-MLF-OH and N-formyl-MLF-OH tripeptides are presented. We showcase growth in NMR development for maximizing sensitivity gains using emerging sensitivity enhancement techniques including population transfer, high-field dynamic nuclear polarization, and cross-polarization magic-angle spinning cryoprobes.
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Affiliation(s)
- Michelle Ha
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Serge Nader
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Shane Pawsey
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Martine Monette
- Bruker BioSpin Ltd., Bruker Corporation, 555 Steeles Avenue E, Milton, Ontario L9T 1Y6, Canada
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching 85748, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, Garching 85748, Germany
| | - Vladimir K Michaelis
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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14
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Betinol IO, Nader S, Mansy SS. Spectral decomposition of iron-sulfur clusters. Anal Biochem 2021; 629:114269. [PMID: 34089700 DOI: 10.1016/j.ab.2021.114269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The near universal availability of UV-Visible spectrophotometers makes this instrument a highly exploited tool for the inexpensive, rapid examination of iron-sulfur clusters. Yet, the analysis of iron-sulfur cluster reconstitution experiments by UV-Vis spectroscopy is notoriously difficult due to the presence of broad, ill-defined peaks. Other types of spectroscopies, such as electron paramagnetic resonance spectroscopy and Mössbauer spectroscopy, are superior in characterizing the type of cluster present and their associated electronic transitions but require expensive, less readily available equipment. Here, we describe a tool that utilizes the accessible and convenient platform of Microsoft Excel to allow for the semi-quantitative analysis of iron-sulfur clusters by UV-Vis spectroscopy. This tool, which we call Fit-FeS, could potentially be used to additionally decompose spectra of solutions containing chromophores other than iron-sulfur clusters.
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Affiliation(s)
- Isaiah O Betinol
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada.
| | - Serge Nader
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada.
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada.
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15
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Abstract
To date, multiple mechanisms have been described for the growth and division of model protocells, all of which exploit the lipid dynamics of fatty acids. In some examples, the more heterogeneous aggregate consisting of fatty acid and diacyl phospholipid or fatty acid and peptide grows at the expense of the more homogeneous aggregate containing a restricted set of lipids with similar dynamics. Imbalances between surface area and volume during growth can generate filamentous vesicles, which are typically divided by shear forces. Here, we describe another pathway for growth and division that depends simply on differences in the compositions of fatty acid membranes without additional components. Growth is driven by the thermodynamically favorable mixing of lipids between two populations, i.e., the system as a whole proceeds toward equilibrium. Division is the result of growth-induced curvature. Importantly, growth and division do not require a specific composition of lipids. For example, vesicles made from one type of lipid, e.g., short-chain fatty acids, grow and divide when fed with vesicles consisting of another type of lipid, e.g., long-chain fatty acids, and vice versa. After equilibration, additional rounds of growth and division could potentially proceed by the introduction of compositionally distinct aggregates. Since prebiotic synthesis likely gave rise to mixtures of lipids, the data are consistent with the presence of growing and dividing protocells on the prebiotic Earth.
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Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology (D-CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | - Anna Wang
- School
of Chemistry and Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology (D-CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G
2G2, Canada
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16
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Abstract
Deciphering the origins of the chemistry that supports life has frequently centered on determining prebiotically plausible paths that produce the molecules found in biology. What has been less investigated is how the energy released from the breakdown of foodstuff is coupled to the persistence of the protocell. To gain better insight into how such coupled chemistry could have emerged prebiotically, we probed the reactivity of the ribodinucleotide NAD+ with small organic molecules that were previously identified as potential constituents of protometabolism. We find that NAD+ is readily reduced nonenzymatically by α-keto acids, such as pyruvate and oxaloacetate, during oxidative decarboxylation. In the presence of FAD and a terminal electron acceptor, the consumption of α-keto acids by NAD+ initiates a plausible prebiotic electron transport chain. The observed reactivity suggests that components of the RNA world were capable of initiating the chemistry needed to capture the energy released from catabolism to drive anabolism.
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17
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Groaz A, Galvan S, Valer L, Rossetto D, Benedetti F, Guella G, Toparlak ÖD, Mansy SS. Cell-Free Synthesis of Dopamine and Serotonin in Two Steps with Purified Enzymes. ACTA ACUST UNITED AC 2020; 4:e2000118. [PMID: 33107224 DOI: 10.1002/adbi.202000118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/14/2020] [Indexed: 01/05/2023]
Abstract
The synthesis of serotonin and dopamine with purified enzymes is described. Both pathways start from an amino acid substrate and synthesize the monoamine neurotransmitter in two enzymatic steps. The enzymes human tryptophan hydroxylase isoform 2, Rattus norvegicus tyrosine hydroxylase, Chlamydia pneumoniae Cpn1046, and aromatic amino acid decarboxylase from Drosophila melanogaster are recombinantly expressed, purified, and shown to be functional in vitro. The hydroxylases efficiently convert L-DOPA (L-dihydroxy-phenylalanine) and 5-HTP (5-hydroxytryptophan) from L-tyrosine and L-tryptophan, respectively. A single aromatic amino acid decarboxylase is capable of converting both hydroxylated intermediates into the final neurotransmitter. The platform described here may facilitate future efforts to generate medically useful artificial cells and nanofactories.
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Affiliation(s)
- Alessandro Groaz
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | - Silvia Galvan
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | - Luca Valer
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | - Daniele Rossetto
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | | | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, Trento, 38123, Italy
| | | | - Sheref S Mansy
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr, Edmonton, AB, T6G 2G2, Canada
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18
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Toparlak ÖD, Zasso J, Bridi S, Serra MD, Macchi P, Conti L, Baudet ML, Mansy SS. Artificial cells drive neural differentiation. Sci Adv 2020; 6:eabb4920. [PMID: 32948587 PMCID: PMC7500934 DOI: 10.1126/sciadv.abb4920] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/29/2020] [Indexed: 05/02/2023]
Abstract
We report the construction of artificial cells that chemically communicate with mammalian cells under physiological conditions. The artificial cells respond to the presence of a small molecule in the environment by synthesizing and releasing a potent protein signal, brain-derived neurotrophic factor. Genetically controlled artificial cells communicate with engineered human embryonic kidney cells and murine neural stem cells. The data suggest that artificial cells are a versatile chassis for the in situ synthesis and on-demand release of chemical signals that elicit desired phenotypic changes of eukaryotic cells, including neuronal differentiation. In the future, artificial cells could be engineered to go beyond the capabilities of typical smart drug delivery vehicles by synthesizing and delivering specific therapeutic molecules tailored to distinct physiological conditions.
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Affiliation(s)
- Ö Duhan Toparlak
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Jacopo Zasso
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Simone Bridi
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Mauro Dalla Serra
- National Research Council-Institute of Biophysics & Bruno Kessler Foundation, via alla Cascata 56/C, 38123 Trento, Italy
| | - Paolo Macchi
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Luciano Conti
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Marie-Laure Baudet
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy.
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
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19
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Toparlak ÖD, Karki M, Egas Ortuno V, Krishnamurthy R, Mansy SS. Cyclophospholipids Increase Protocellular Stability to Metal Ions. Small 2020; 16:e1903381. [PMID: 31523894 DOI: 10.1002/smll.201903381] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and extant life is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here, prebiotically plausible monoacyl cyclophospholipids are shown to form robust vesicles that survive a broad range of pH and high concentrations of Mg2+ , Ca2+ , and Na+ . Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+ . These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.
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Affiliation(s)
- Ö Duhan Toparlak
- Department CIBIO, University of Trento, via Sommarive 9, 38123, Povo, Italy
| | - Megha Karki
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Veronica Egas Ortuno
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123, Povo, Italy
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20
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Yeh Martín N, Valer L, Mansy SS. Toward long-lasting artificial cells that better mimic natural living cells. Emerg Top Life Sci 2019; 3:597-607. [PMID: 33523164 PMCID: PMC7288992 DOI: 10.1042/etls20190026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/01/2023]
Abstract
Chemical communication is ubiquitous in biology, and so efforts in building convincing cellular mimics must consider how cells behave on a population level. Simple model systems have been built in the laboratory that show communication between different artificial cells and artificial cells with natural, living cells. Examples include artificial cells that depend on purely abiological components and artificial cells built from biological components and are driven by biological mechanisms. However, an artificial cell solely built to communicate chemically without carrying the machinery needed for self-preservation cannot remain active for long periods of time. What is needed is to begin integrating the pathways required for chemical communication with metabolic-like chemistry so that robust artificial systems can be built that better inform biology and aid in the generation of new technologies.
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Affiliation(s)
- Noël Yeh Martín
- Systems Biophysics, Physics Department, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 München, Germany
| | - Luca Valer
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
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21
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Schwarz-Schilling M, Dupin A, Chizzolini F, Krishnan S, Mansy SS, Simmel FC. Correction to Optimized Assembly of a Multifunctional RNA-Protein Nanostructure in a Cell-Free Gene Expression System. Nano Lett 2019; 19:4812. [PMID: 31244239 DOI: 10.1021/acs.nanolett.9b02419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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22
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Abstract
IMPACT STATEMENT Advances in the understanding of the biophysics of membranes, the nonenzymatic and enzymatic polymerization of RNA, and in the design of complex chemical reaction networks have led to a new, integrated way of viewing the shared chemistry needed to sustain life. Although a protocell capable of Darwinian evolution has yet to be built, the seemingly disparate pieces are beginning to fit together. At the very least, better cellular mimics are on the horizon that will likely teach us much about the physicochemical underpinnings of cellular life.
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23
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Bonfio C, Godino E, Corsini M, Fabrizi de Biani F, Guella G, Mansy SS. Prebiotic iron–sulfur peptide catalysts generate a pH gradient across model membranes of late protocells. Nat Catal 2018. [DOI: 10.1038/s41929-018-0116-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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24
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Schwarz-Schilling M, Dupin A, Chizzolini F, Krishnan S, Mansy SS, Simmel FC. Optimized Assembly of a Multifunctional RNA-Protein Nanostructure in a Cell-Free Gene Expression System. Nano Lett 2018; 18:2650-2657. [PMID: 29564885 DOI: 10.1021/acs.nanolett.8b00526] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins, streptavidin and two fluorescent proteins, while one binds the small molecule dye malachite green (MG). Using MG fluorescence and Förster resonance energy transfer (FRET) between the RNA-scaffolded proteins, we assess critical assembly parameters such as chemical stability, binding efficiency, and also resource sharing effects within the reaction compartment. We then optimize simultaneous expression and coassembly of the RNA-protein nanostructure within a single-compartment cell-free gene expression system. We demonstrate expression and assembly of the multicomponent nanostructures inside of emulsion droplets and their aptamer-mediated localization onto streptavidin-coated substrates, plus the successful assembly of the hybrid structures inside of bacterial cells.
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Affiliation(s)
| | - Aurore Dupin
- Physics Department E14 , Technical University Munich , 85748 Garching , Germany
| | - Fabio Chizzolini
- CIBIO , University of Trento , Via Sommarive 9 , 38123 Povo , Italy
| | - Swati Krishnan
- Physics Department E14 , Technical University Munich , 85748 Garching , Germany
| | - Sheref S Mansy
- CIBIO , University of Trento , Via Sommarive 9 , 38123 Povo , Italy
| | - Friedrich C Simmel
- Physics Department E14 , Technical University Munich , 85748 Garching , Germany
- Nanosystems Initiative Munich , 80539 Munich , Germany
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25
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Tang TYD, Cecchi D, Fracasso G, Accardi D, Coutable-Pennarun A, Mansy SS, Perriman AW, Anderson JLR, Mann S. Gene-Mediated Chemical Communication in Synthetic Protocell Communities. ACS Synth Biol 2018; 7:339-346. [PMID: 29091420 DOI: 10.1021/acssynbio.7b00306] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A gene-directed chemical communication pathway between synthetic protocell signaling transmitters (lipid vesicles) and receivers (proteinosomes) was designed, built and tested using a bottom-up modular approach comprising small molecule transcriptional control, cell-free gene expression, porin-directed efflux, substrate signaling, and enzyme cascade-mediated processing.
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Affiliation(s)
- T-Y. Dora Tang
- Max Planck Institute of Molecular Cell and Genetics, 01307 Dresden, Germany
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Dario Cecchi
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Giorgio Fracasso
- Max Planck Institute of Molecular Cell and Genetics, 01307 Dresden, Germany
| | - Davide Accardi
- Max Planck Institute of Molecular Cell and Genetics, 01307 Dresden, Germany
| | - Angelique Coutable-Pennarun
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Sheref S. Mansy
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Adam W. Perriman
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - J. L. Ross Anderson
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Stephen Mann
- Centre
for Protolife Research, School of Chemistry University, of Bristol, Bristol BS8 1TS United, Kingdom
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
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26
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Abstract
A new R tool is described that rapidly identifies, ranks, and clusters sequence patterns coordinated to metallocofactors. This tool, PdPDB, fills a void because, unlike currently available tools, PdPDB searches through sequences with metal coordination as the primary determinant and can identify patterns consisting of amino acids, nucleotides, and small molecule ligands at once. PdPDB was tested by analyzing structures that coordinate Fe2+/3+, [2Fe-2S], [4Fe-4S], Zn2+, and Mg2+ cofactors. PdPDB confirmed previously identified sequence motifs and revealed which residues are enriched (e.g., glycine) and are under-represented (e.g., glutamine) near ligands to metal centers. The data show the similarities and differences between different metal-binding sites. The patterns that coordinate metallocofactors vary, depending upon whether the metal ions play a structural or catalytic role, with catalytic metal centers exhibiting partial coordination by small molecule ligands. PdPDB 2.0.1 is freely available as a CRAN package.
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Affiliation(s)
- Luca Belmonte
- CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy
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27
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Rhoads MK, Hauk P, Terrell J, Tsao CY, Oh H, Raghavan SR, Mansy SS, Payne GF, Bentley WE. Incorporating LsrK AI-2 quorum quenching capability in a functionalized biopolymer capsule. Biotechnol Bioeng 2017; 115:278-289. [PMID: 28782813 DOI: 10.1002/bit.26397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/28/2017] [Accepted: 08/02/2017] [Indexed: 01/07/2023]
Abstract
Antibacterial resistance is an issue of increasing severity as current antibiotics are losing their effectiveness and fewer antibiotics are being developed. New methods for combating bacterial virulence are required. Modulating molecular communication among bacteria can alter phenotype, including attachment to epithelia, biofilm formation, and even toxin production. Intercepting and modulating communication networks provide a means to attenuate virulence without directly interacting with the bacteria of interest. In this work, we target communication mediated by the quorum sensing (QS) bacterial autoinducer-2, AI-2. We have assembled a capsule of biological polymers alginate and chitosan, attached an AI-2 processing kinase, LsrK, and provided substrate, ATP, for enzymatic alteration of AI-2 in culture fluids. Correspondingly, AI-2 mediated QS activity is diminished. All components of this system are "biofabricated"-they are biologically derived and their assembly is accomplished using biological means. Initially, component quantities and kinetics were tested as assembled in microtiter plates. Subsequently, the identical components and assembly means were used to create the "artificial cell" capsules. The functionalized capsules, when introduced into populations of bacteria, alter the dynamics of the AI-2 bacterial communication, attenuating QS activated phenotypes. We envision the assembly of these and other capsules or similar materials, as means to alter QS activity in a biologically compatible manner and in many environments, including in humans.
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Affiliation(s)
- Melissa K Rhoads
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, Maryland.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, Maryland.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Jessica Terrell
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, Maryland.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, Maryland.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Hyuntaek Oh
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland
| | - Srinivasa R Raghavan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland
| | - Sheref S Mansy
- CIBIO-Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, Maryland.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, Maryland.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
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28
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Affiliation(s)
- Claudia Bonfio
- CIBIO, University of Trento , via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- CIBIO, University of Trento , via Sommarive 9, 38123 Povo, Italy
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29
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Bonfio C, Valer L, Scintilla S, Shah S, Evans DJ, Jin L, Szostak JW, Sasselov DD, Sutherland JD, Mansy SS. UV-light-driven prebiotic synthesis of iron-sulfur clusters. Nat Chem 2017; 9:1229-1234. [PMID: 29168482 DOI: 10.1038/nchem.2817] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/01/2017] [Indexed: 12/17/2022]
Abstract
Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols. Iron-sulfur clusters coordinate to and are stabilized by a wide range of cysteine-containing peptides and the assembly of iron-sulfur cluster-peptide complexes can take place within model protocells in a process that parallels extant pathways. Our experiments suggest that iron-sulfur clusters may have formed easily on early Earth, facilitating the emergence of an iron-sulfur-cluster-dependent metabolism.
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Affiliation(s)
- Claudia Bonfio
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Luca Valer
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | | | - Sachin Shah
- Chemistry, School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK
| | - David J Evans
- Chemistry, School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK
| | - Lin Jin
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Dimitar D Sasselov
- Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, Massachusetts 02138, USA
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Sheref S Mansy
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
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30
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Abstract
Although RNA synthesis can be reliably controlled with different T7 transcriptional promoters during cell-free gene expression with the PURE system, protein synthesis remains largely unaffected. To better control protein levels, we investigated a series of ribosome binding sites (RBSs). Although RBS strength did strongly affect protein synthesis, the RBS sequence could explain less than half of the variability of the data. Protein expression was found to depend on other factors besides the strength of the RBS, including the GC content of the coding sequence. The complexity of protein synthesis in comparison to RNA synthesis was observed by the higher degree of variability associated with protein expression. This variability was also observed in an E. coli cell extract-based system. However, the coefficient of variation was larger with E. coli RNA polymerase than with T7 RNA polymerase, consistent with the increased complexity of E. coli RNA polymerase.
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Affiliation(s)
- Fabio Chizzolini
- Center for Integrative Biology (CIBIO), University of Trento , via Sommarive 9, 38123 Povo TN, Italy
| | - Michele Forlin
- Center for Integrative Biology (CIBIO), University of Trento , via Sommarive 9, 38123 Povo TN, Italy
| | - Noël Yeh Martín
- Center for Integrative Biology (CIBIO), University of Trento , via Sommarive 9, 38123 Povo TN, Italy
| | - Giuliano Berloffa
- Center for Integrative Biology (CIBIO), University of Trento , via Sommarive 9, 38123 Povo TN, Italy
| | - Dario Cecchi
- Center for Integrative Biology (CIBIO), University of Trento , via Sommarive 9, 38123 Povo TN, Italy
| | - Sheref S Mansy
- Center for Integrative Biology (CIBIO), University of Trento , via Sommarive 9, 38123 Povo TN, Italy
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31
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Lentini R, Martín NY, Forlin M, Belmonte L, Fontana J, Cornella M, Martini L, Tamburini S, Bentley WE, Jousson O, Mansy SS. Two-Way Chemical Communication between Artificial and Natural Cells. ACS Cent Sci 2017; 3:117-123. [PMID: 28280778 PMCID: PMC5324081 DOI: 10.1021/acscentsci.6b00330] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Indexed: 05/02/2023]
Abstract
Artificial cells capable of both sensing and sending chemical messages to bacteria have yet to be built. Here we show that artificial cells that are able to sense and synthesize quorum signaling molecules can chemically communicate with V. fischeri, V. harveyi, E. coli, and P. aeruginosa. Activity was assessed by fluorescence, luminescence, RT-qPCR, and RNA-seq. Two potential applications for this technology were demonstrated. First, the extent to which artificial cells could imitate natural cells was quantified by a type of cellular Turing test. Artificial cells capable of sensing and in response synthesizing and releasing N-3-(oxohexanoyl)homoserine lactone showed a high degree of likeness to natural V. fischeri under specific test conditions. Second, artificial cells that sensed V. fischeri and in response degraded a quorum signaling molecule of P. aeruginosa (N-(3-oxododecanoyl)homoserine lactone) were constructed, laying the foundation for future technologies that control complex networks of natural cells.
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Affiliation(s)
- Roberta Lentini
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Noël Yeh Martín
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Michele Forlin
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Luca Belmonte
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Jason Fontana
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | | | - Laura Martini
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | | | - William E. Bentley
- Institute
for Bioscience and Biotechnology Research, University of Maryland, College
Park, Maryland 20742, United States
| | - Olivier Jousson
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Sheref S. Mansy
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
- E-mail:
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32
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Lentini R, Yeh Martín N, Mansy SS. Communicating artificial cells. Curr Opin Chem Biol 2016; 34:53-61. [DOI: 10.1016/j.cbpa.2016.06.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
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33
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Martini L, Ellington AD, Mansy SS. An in vitro selection for small molecule induced switching RNA molecules. Methods 2016; 106:51-7. [PMID: 26899430 DOI: 10.1016/j.ymeth.2016.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 10/22/2022] Open
Abstract
The selection of RNA and DNA aptamers now has a long history. However, the ability to directly select for conformational changes upon ligand binding has remained elusive. These difficulties have stymied attempts at making small molecule responsive strand displacement circuitry as well as synthetic riboswitches. Herein we present a detailed strand displacement based selection protocol to directly select for RNA molecules with switching activity. The library was based on a previously selected thiamine pyrophosphate riboswitch. The fully in vitro methodology gave sequences that showed strong strand displacement activity in the presence of thiamine pyrophosphate. Further, the selected sequences possessed riboswitch activity similar to that of natural riboswitches. The presented methodology should aid in the design of more complex, environmentally responsive strand displacement circuitry and in the selection of riboswitches responsive to toxic ligands.
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Affiliation(s)
- Laura Martini
- CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Sheref S Mansy
- CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy.
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34
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Scintilla S, Bonfio C, Belmonte L, Forlin M, Rossetto D, Li J, Cowan JA, Galliani A, Arnesano F, Assfalg M, Mansy SS. Duplications of an iron–sulphur tripeptide leads to the formation of a protoferredoxin. Chem Commun (Camb) 2016; 52:13456-13459. [DOI: 10.1039/c6cc07912a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on UV-Vis, NMR, and EPR spectroscopies and DFT and molecular dynamics calculations, a model prebiotic [2Fe–2S] tripeptide was shown to accept and donate electrons.
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Affiliation(s)
| | | | | | | | | | - Jingwei Li
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Angela Galliani
- Department of Chemistry
- University of “Bari A. Moro”
- 70125 Bari
- Italy
| | - Fabio Arnesano
- Department of Chemistry
- University of “Bari A. Moro”
- 70125 Bari
- Italy
| | - Michael Assfalg
- Department of Biotechnology
- University of Verona
- 37134 Verona
- Italy
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35
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Belmonte L, Rossetto D, Forlin M, Scintilla S, Bonfio C, Mansy SS. Cysteine containing dipeptides show a metal specificity that matches the composition of seawater. Phys Chem Chem Phys 2016; 18:20104-8. [DOI: 10.1039/c6cp00608f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cysteine containing dipeptide metal affinities do not follow the Irving–Williams series but rather follow the concentration trends found in seawater.
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36
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Martini L, Meyer AJ, Ellefson JW, Milligan JN, Forlin M, Ellington AD, Mansy SS. In Vitro Selection for Small-Molecule-Triggered Strand Displacement and Riboswitch Activity. ACS Synth Biol 2015; 4:1144-50. [PMID: 25978303 DOI: 10.1021/acssynbio.5b00054] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An in vitro selection method for ligand-responsive RNA sensors was developed that exploited strand displacement reactions. The RNA library was based on the thiamine pyrophosphate (TPP) riboswitch, and RNA sequences capable of hybridizing to a target duplex DNA in a TPP regulated manner were identified. After three rounds of selection, RNA molecules that mediated a strand exchange reaction upon TPP binding were enriched. The enriched sequences also showed riboswitch activity. Our results demonstrated that small-molecule-responsive nucleic acid sensors can be selected to control the activity of target nucleic acid circuitry.
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Affiliation(s)
- Laura Martini
- CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
| | - Adam J. Meyer
- Department
of Chemistry and Biochemistry, Institute for Cellular and Molecular
Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jared W. Ellefson
- Department
of Chemistry and Biochemistry, Institute for Cellular and Molecular
Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - John N. Milligan
- Department
of Chemistry and Biochemistry, Institute for Cellular and Molecular
Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Michele Forlin
- CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
| | - Andrew D. Ellington
- Department
of Chemistry and Biochemistry, Institute for Cellular and Molecular
Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sheref S. Mansy
- CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
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37
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Digiacomo F, Girelli G, Aor B, Marchioretti C, Pedrotti M, Perli T, Tonon E, Valentini V, Avi D, Ferrentino G, Dorigato A, Torre P, Jousson O, Mansy SS, Del Bianco C. Ethylene-producing bacteria that ripen fruit. ACS Synth Biol 2014; 3:935-8. [PMID: 25393892 DOI: 10.1021/sb5000077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ethylene is a plant hormone widely used to ripen fruit. However, the synthesis, handling, and storage of ethylene are environmentally harmful and dangerous. We engineered E. coli to produce ethylene through the activity of the ethylene-forming enzyme (EFE) from Pseudomonas syringae. EFE converts a citric acid cycle intermediate, 2-oxoglutarate, to ethylene in a single step. The production of ethylene was placed under the control of arabinose and blue light responsive regulatory systems. The resulting bacteria were capable of accelerating the ripening of tomatoes, kiwifruit, and apples.
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Affiliation(s)
- Fabio Digiacomo
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Gabriele Girelli
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Bruno Aor
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Caterina Marchioretti
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Michele Pedrotti
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Thomas Perli
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Emil Tonon
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Viola Valentini
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Damiano Avi
- Atomic
and Molecular Physics Laboratory, Department of Physics, University of Trento, Via Sommarive 14, 38123 Trento, Italy
| | - Giovanna Ferrentino
- Department
of Materials Engineering and Industrial Technologies, University of Trento, Via Mesiano 77, 38123 Trento, Italy
| | - Andrea Dorigato
- Department
of Materials Engineering and Industrial Technologies, University of Trento, Via Mesiano 77, 38123 Trento, Italy
| | - Paola Torre
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Olivier Jousson
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Sheref S. Mansy
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | - Cristina Del Bianco
- Centre
for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Trento, Italy
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38
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Chizzolini F, Forlin M, Cecchi D, Mansy SS. Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter strength. ACS Synth Biol 2014; 3:363-71. [PMID: 24283192 DOI: 10.1021/sb4000977] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cell-free transcription-translation of multiple proteins typically exploits genes placed behind strong transcriptional promoters that reside on separate pieces of DNA so that protein levels can be easily controlled by changing DNA template concentration. However, such systems are not amenable to the construction of artificial cells with a synthetic genome. Herein, we evaluated the activity of a series of T7 transcriptional promoters by monitoring the fluorescence arising from a genetically encoded Spinach aptamer. Subsequently the influences of transcriptional promoter strength on fluorescent protein synthesis from one, two, and three gene operons were assessed. It was found that transcriptional promoter strength was more effective at controlling RNA synthesis than protein synthesis in vitro with the PURE system. Conversely, the gene position within the operon strongly influenced protein synthesis but not RNA synthesis.
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Affiliation(s)
- Fabio Chizzolini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
| | - Michele Forlin
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
| | - Dario Cecchi
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
| | - Sheref S. Mansy
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
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39
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Lentini R, Santero SP, Chizzolini F, Cecchi D, Fontana J, Marchioretto M, Del Bianco C, Terrell JL, Spencer AC, Martini L, Forlin M, Assfalg M, Dalla Serra M, Bentley WE, Mansy SS. Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour. Nat Commun 2014; 5:4012. [PMID: 24874202 PMCID: PMC4050265 DOI: 10.1038/ncomms5012] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 04/30/2014] [Indexed: 01/19/2023] Open
Abstract
Previous efforts to control cellular behaviour have largely relied upon various forms of genetic engineering. Once the genetic content of a living cell is modified, the behaviour of that cell typically changes as well. However, other methods of cellular control are possible. All cells sense and respond to their environment. Therefore, artificial, non-living cellular mimics could be engineered to activate or repress already existing natural sensory pathways of living cells through chemical communication. Here we describe the construction of such a system. The artificial cells expand the senses of Escherichia coli by translating a chemical message that E. coli cannot sense on its own to a molecule that activates a natural cellular response. This methodology could open new opportunities in engineering cellular behaviour without exploiting genetically modified organisms. The control of cellular behaviour largely relies on genetic engineering, but artificial cells could be designed to control cell processes through chemical communication. Here, the authors develop an artificial cell that is able to translate a chemical message into a signal that can be sensed by E. coli and activate a cellular response.
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Affiliation(s)
- Roberta Lentini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Silvia Perez Santero
- 1] CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy [2] Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Fabio Chizzolini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Dario Cecchi
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Jason Fontana
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Marta Marchioretto
- National Research Council-Institute of Biophysics & Bruno Kessler Foundation, Via alla Cascata 56/C, 38123 Trento, Italy
| | - Cristina Del Bianco
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Jessica L Terrell
- 1] Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA [2] Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Amy C Spencer
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Laura Martini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Michele Forlin
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Mauro Dalla Serra
- National Research Council-Institute of Biophysics & Bruno Kessler Foundation, Via alla Cascata 56/C, 38123 Trento, Italy
| | - William E Bentley
- 1] Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA [2] Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Sheref S Mansy
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
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40
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Torre P, Keating CD, Mansy SS. Multiphase water-in-oil emulsion droplets for cell-free transcription-translation. Langmuir 2014; 30:5695-9. [PMID: 24810327 PMCID: PMC4038361 DOI: 10.1021/la404146g] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/18/2014] [Indexed: 05/02/2023]
Abstract
The construction of genetically encoded cellular mimics in compartments containing organized synthetic cytosols is desirable for the development of artificial cells. Phase separated aqueous domains were placed within water-in-oil emulsion droplets in a manner compatible with transcription and translation machinery. Aqueous two-phase and three-phase systems (ATPS and A3PS) were assembled with dextran, poly(ethylene glycol), and Ficoll. Aqueous two-phase systems were capable of supporting the cell-free expression of protein within water droplets, whereas the aqueous three-phase-based system did not give rise to detectable protein synthesis. The expressed protein preferentially partitioned to the dextran-enriched phase. The system could serve as a foundation for building cellular mimics with liquid organelles.
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Affiliation(s)
- Paola Torre
- CIBIO, University of Trento, via delle Regole, 101, 38123 Mattarello, Italy
| | - Christine D. Keating
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sheref S. Mansy
- CIBIO, University of Trento, via delle Regole, 101, 38123 Mattarello, Italy
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41
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Abstract
We present a simple method to measure the real-time activity of riboswitches with purified components in vitro and inside of artificial cells. Typically, riboswitch activity is measured in vivo by exploiting β-galactosidase encoding constructs with a putative riboswitch sequence in the untranslated region. Additional in vitro characterization often makes use of in-line probing to explore conformational changes induced by ligand binding to the mRNA or analyses of transcript lengths in the presence and absence of ligand. However, riboswitches ultimately control protein levels and often times require accessory factors. Therefore, an in vitro system capable of monitoring protein production with fully defined components that can be supplemented with accessory factors would greatly aid riboswitch studies. Herein we present a system that is amenable to such analyses. Further, since the described system can be easily reconstituted within compartments to build artificial, cellular mimics with sensing capability, protocols are provided for building sense-response systems within water-in-oil emulsion compartments and lipid vesicles. Only standard laboratory equipment and commercially available material are exploited for the described assays, including DNA, purified transcription-translation machinery, i.e., the PURE system, and a spectrofluorometer.
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42
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Abstract
As interest shifts from individual molecules to systems of molecules, an increasing number of laboratories have sought to build from the bottom up cellular mimics that better represent the complexity of cellular life. To date there are a number of paths that could be taken to build compartmentalized cellular mimics, including the exploitation of water-in-oil emulsions, microfluidic devices, and vesicles. Each of the available options has specific advantages and disadvantages. For example, water-in-oil emulsions give high encapsulation efficiency but do not mimic well the permeability barrier of living cells. The primary advantage of the methods described herein is that they are all easy and cheap to implement. Transcription-translation machinery is encapsulated inside of phospholipid vesicles through a process that exploits common instrumentation, such as a centrifugal evaporator and an extruder. Reactions are monitored by fluorescence spectroscopy. The protocols can be adapted for recombinant protein expression, the construction of cellular mimics, the exploration of the minimum requirements for cellular life, or the assembly of genetic circuitry.
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Affiliation(s)
- Amy C Spencer
- Centre for Integrative Biology, University of Trento
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43
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Lentini R, Forlin M, Martini L, Del Bianco C, Spencer AC, Torino D, Mansy SS. Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology. ACS Synth Biol 2013; 2:482-9. [PMID: 23654270 DOI: 10.1021/sb400003y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machinery, i.e., the PUREsystem. The data were used to construct a ratiometric fluorescence assay to quantify the effect of genetic organization on in vitro expression levels. Synthetic operons with varied spacing and sequence composition between two genes that coded for fluorescent proteins were then assembled. The resulting data indicated which restriction sites and where the restriction sites should be placed in order to build genetic devices in a manner that does not interfere with protein expression. Other simple design rules were identified, such as the spacing and sequence composition influences of regions upstream and downstream of ribosome binding sites and the ability of non-AUG start codons to function in vitro.
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Affiliation(s)
- Roberta Lentini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Michele Forlin
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Laura Martini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Cristina Del Bianco
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Amy C. Spencer
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Domenica Torino
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Sheref S. Mansy
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
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44
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Abstract
Several laboratories are pursuing the synthesis of cellular systems from different directions, including those that begin with simple chemicals to those that exploit existing cells. The methods that begin with nonliving components tend to focus on mimicking specific features of life, such as genomic replication, protein synthesis, sensory systems, and compartment formation, growth, and division. Conversely, the more prevalent synthetic biology approaches begin with something that is already alive and seek to impart new behavior on existing cells. Here we discuss advances in building cell-like systems that mimic key features of life with defined components.
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Affiliation(s)
| | | | - Sheref S. Mansy
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy
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Abstract
Prebiotic soup experiments have shown that the molecular building blocks of life can be built under prebiotically plausible conditions. From this starting point, researchers have launched continued studies of polymerization and explorations of the breadth of RNA function. Recently, effort has intensified to examine experimentally another stage of the origins of life: the assembly of the molecular parts into model protocells intended to represent the first primitive, cell-like systems to emerge on Earth. Although it may not be possible to recreate the precise sequence of events that led to cellular life, laboratory experiments have begun to show what was and was not possible. Prebiotically plausible lipid vesicles form easily and have many properties that are conducive to cellular function. In addition to protecting nascent replicating genetic systems from parasitic sequences, vesicles facilitate evolution. The data thus far suggest that prebiotically plausible vesicles could have grown, divided, and promoted competition between distinct chemical systems. Most protocellular studies to date have probed the role of self-replication, one feature of extant life in the emergence of the first cellular system. Undoubtedly replicating systems were crucial for protocellular evolution, but other features of life must have been important as well. For example, life does not exist in isolation. A living system must cope with and adapt to environmental fluctuations to survive. The protocell must have generated some of these fluctuations because cellular activity necessarily modifies its surroundings by selectively absorbing nutrients and releasing unwanted molecules. It seems likely that life would have faced this challenge early and either emerged in dynamic locales that continuously regenerated conditions conducive to life or exploited mechanisms to physically move to new areas not depleted in resources. Further studies that explore non-replication-based aspects of the origins of life could reveal a more complete picture of the transition from prebiotic chemistry to early life.
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Forlin M, Lentini R, Mansy SS. Cellular imitations. Curr Opin Chem Biol 2012; 16:586-92. [DOI: 10.1016/j.cbpa.2012.10.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 09/04/2012] [Accepted: 10/12/2012] [Indexed: 01/26/2023]
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Abstract
Background Bacterial and viral DNA replication was previously reconstituted in vitro from component parts [1-4]. Significant advances in building minimal cell-like structures also have been made recently [5-7]. Combining the two approaches would further attempts to build a minimal cell-like structure capable of undergoing evolution by combining membrane encapsulation and genome replication. Towards this end, we attempted to use purified genomic replication protein components from thermophilic bacterial sources to copy strands of DNA isothermally within lipid vesicles. Findings Bacterial replication components (such as helicases and DNA polymerases) are compatible with methods for the generation of lipid vesicles. Encapsulation inside phospholipid vesicles does not inhibit the activity of bacterial DNA genome replication machinery. Further the described system is efficient at isothermally amplifying short segments of DNA within phospholipid vesicles. Conclusions Herein we show that bacterial isothermal DNA replication machinery is functional inside of phospholipid vesicles, suggesting that replicating cellular mimics can be built from purified bacterial components.
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Affiliation(s)
- Domenica Torino
- Centre for Integrative Biology, University of Trento, Via delle Regole, 101 Mattarello, Italy.
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Wu SP, Bellei M, Mansy SS, Battistuzzi G, Sola M, Cowan JA. Redox chemistry of the Schizosaccharomyces pombe ferredoxin electron-transfer domain and influence of Cys to Ser substitutions. J Inorg Biochem 2011; 105:806-11. [PMID: 21497579 DOI: 10.1016/j.jinorgbio.2011.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/29/2011] [Accepted: 03/10/2011] [Indexed: 11/26/2022]
Abstract
Schizosaccharomyces pombe (Sp) ferredoxin contains a C-terminal electron transfer protein ferredoxin domain (etp(Fd)) that is homologous to adrenodoxin. The ferredoxin has been characterized by spectroelectrochemical methods, and Mössbauer, UV-Vis and circular dichroism spectroscopies. The Mössbauer spectrum is consistent with a standard diferric [2Fe-2S](2+) cluster. While showing sequence homology to vertebrate ferredoxins, the E°' and the reduction thermodynamics for etp(Fd) (-0.392 V) are similar to plant-type ferredoxins. Relatively stable Cys to Ser derivatives were made for each of the four bound Cys residues and variations in the visible spectrum in the 380-450 nm range were observed that are characteristic of oxygen ligated clusters, including members of the [2Fe-2S] cluster IscU/ISU scaffold proteins. Circular dichroism spectra were similar and consistent with no significant structural change accompanying these mutations. All derivatives were active in an NADPH-Fd reductase cytochrome c assay. The binding affinity of Fd to the reductase was similar, however, V(max) reflecting rate limiting electron transfer was found to decrease ~13-fold. The data are consistent with relatively minor perturbations of both the electronic properties of the cluster following substitution of the Fe-bond S atom with O, and the electronic coupling of the cluster to the protein.
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Affiliation(s)
- Shu-pao Wu
- Evans Laboratory of Chemistry, Ohio State University, Columbus, OH 43210, USA
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Bellei M, Battistuzzi G, Wu SP, Mansy SS, Cowan JA, Sola M. Control of reduction thermodynamics in [2Fe-2S] ferredoxins Entropy-enthalpy compensation and the influence of surface mutations. J Inorg Biochem 2010; 104:691-6. [PMID: 20362339 DOI: 10.1016/j.jinorgbio.2010.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/04/2010] [Accepted: 03/04/2010] [Indexed: 11/27/2022]
Abstract
The reaction thermodynamics for the one-electron reduction of the [2Fe-2S] cluster of both human ferredoxin and various surface point mutants, in which each of the negatively charged residues Asp72, Glu73, Asp76, and Asp79 were converted to Ala, have been determined by variable temperature spectroelectrochemical measurements. The above are conserved residues that have been implicated in interactions between the vertebrate-type ferredoxins and their redox partners. In all cases, and similar to other 2Fe-ferredoxins, the reduction potentials are negative as a result of both an enthalpic and entropic stabilization of the oxidized state. Although all Hs Fd mutants, with the exception of Asp72Ala, show slightly higher E degrees ' values than that of wild type Hs Fd, according to expectations for a purely electrostatic model, they exhibit changes in the H degrees '(rc) values that are electrostatically counter-intuitive. The observation of enthalpy-entropy compensation within the protein series indicates that the mutation-induced changes in H degrees '(rc) and S degrees '(rc) are dominated by reduction-induced solvent reorganization effects. Protein-based entropic effects are likely to be responsible for the low E degrees ' value of D72A.
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Affiliation(s)
- Marzia Bellei
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi, 183, 41100 Modena, Italy
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