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Dutcher CA, Andreas MP, Giessen TW. A two-component quasi-icosahedral protein nanocompartment with variable shell composition and irregular tiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591138. [PMID: 38712103 PMCID: PMC11071501 DOI: 10.1101/2024.04.25.591138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral HK97-fold. Here, we report the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus. We show the differential assembly behavior of the two shell components and demonstrate their ability to co-assemble into mixed shells with variable shell composition. We determined the structures of both shell proteins using cryo-electron microscopy. Using 3D-classification and crosslinking studies, we highlight the irregular tiling of mixed shells. Our work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.
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Affiliation(s)
- Cassandra A. Dutcher
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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2
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Shinde YD, Chowdhury C. Potential utility of bacterial protein nanoreactor for sustainable in-situ biocatalysis in wide range of bioprocess conditions. Enzyme Microb Technol 2024; 173:110354. [PMID: 37988973 DOI: 10.1016/j.enzmictec.2023.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/30/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles that natively encapsulates the enzymes, substrates, and cofactors within a protein shell. They optimize the reaction rates by enriching the substrate in the vicinity of enzymes to increase the yields of the product and mitigate the outward diffusion of the toxic or volatile intermediates. The shell protein subunits of MCP shell are selectively permeable and have specialized pores for the selective inward diffusion of substrates and products release. Given their attributes, MCPs have been recently explored as potential candidates as subcellular nano-bioreactor for the enhanced production of industrially important molecules by exercising pathway encapsulation. In the current study, MCPs have been shown to sustain enzyme activity for extended periods, emphasizing their durability against a range of physical challenges such as temperature, pH and organic solvents. The significance of an intact shell in conferring maximum protection is highlighted by analyzing the differences in enzyme activities inside the intact and broken shell. Moreover, a minimal synthetic shell was designed with recruitment of a heterologous enzyme cargo to demonstrate the improved durability of the enzyme. The encapsulated enzyme was shown to be more stable than its free counterpart under the aforementioned conditions. Bacterial MCP-mediated encapsulation can serve as a potential strategy to shield the enzymes used under extreme conditions by maintaining the internal microenvironment and enhancing their cycle life, thereby opening new means for stabilizing, and reutilizing the enzymes in several bioprocess industries.
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Affiliation(s)
- Yashodhara D Shinde
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India.
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3
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Abstract
Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins in vivo. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both in vivo and in vitro, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
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4
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso J, Sheen CR, Koch B. Linocin M18 protein from the insect pathogenic bacterium Brevibacillus laterosporus isolates. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12563-8. [PMID: 37204448 DOI: 10.1007/s00253-023-12563-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/20/2023]
Abstract
Brevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium. Insect pathogenic strains have been characterised in New Zealand, and two isolates, Bl 1821L and Bl 1951, are under development for use in biopesticides. However, growth in culture is sometimes disrupted, affecting mass production. Based on previous work, it was hypothesised that Tectiviridae phages might be implicated. While investigating the cause of the disrupted growth, electron micrographs of crude lysates showed structural components of putative phages including capsid and tail-like structures. Sucrose density gradient purification yielded a putative self-killing protein of ~30 kDa. N-terminal sequencing of the ~30 kDa protein identified matches to a predicted 25 kDa hypothetical and a 31.4 kDa putative encapsulating protein homologs, with the genes encoding each protein adjacent in the genomes. BLASTp analysis of the homologs of 31.4 kDa amino acid sequences shared 98.6% amino acid identity to the Linocin M18 bacteriocin family protein of Brevibacterium sp. JNUCC-42. Bioinformatic tools including AMPA and CellPPD defined that the bactericidal potential originated from a putative encapsulating protein. Antagonistic activity of the ~30 kDa encapsulating protein of Bl 1821L and Bl 1951during growth in broth exhibited bacterial autolytic activity. LIVE/DEAD staining of Bl 1821L cells after treatment with the ~30 kDa encapsulating protein of Bl 1821L substantiated the findings by showing 58.8% cells with the compromised cell membranes as compared to 37.5% cells in the control. Furthermore, antibacterial activity of the identified proteins of Bl 1821L was validated through gene expression in a Gram-positive bacterium Bacillus subtilis WB800N. KEY POINTS: • Gene encoding the 31.4 kDa antibacterial Linocin M18 protein was identified • It defined the autocidal activity of Linocin M18 (encapsulating) protein • Identified the possible killing mechanism of the encapsulins.
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Affiliation(s)
- Tauseef K Babar
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand.
- Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Travis R Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - John G Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - Mark R H Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch, New Zealand
| | - Josefina Narciso
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - Campbell R Sheen
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
| | - Barbara Koch
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
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5
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Abrahamson CH, Palmero BJ, Kennedy NW, Tullman-Ercek D. Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation. Annu Rev Biophys 2023; 52:553-572. [PMID: 36854212 DOI: 10.1146/annurev-biophys-092222-020832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The advent of biotechnology has enabled metabolic engineers to assemble heterologous pathways in cells to produce a variety of products of industrial relevance, often in a sustainable way. However, many pathways face challenges of low product yield. These pathways often suffer from issues that are difficult to optimize, such as low pathway flux and off-target pathway consumption of intermediates. These issues are exacerbated by the need to balance pathway flux with the health of the cell, particularly when a toxic intermediate builds up. Nature faces similar challenges and has evolved spatial organization strategies to increase metabolic pathway flux and efficiency. Inspired by these strategies, bioengineers have developed clever strategies to mimic spatial organization in nature. This review explores the use of spatial organization strategies, including protein scaffolding and protein encapsulation inside of proteinaceous shells, toward overcoming bottlenecks in metabolic engineering efforts.
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Affiliation(s)
- Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA;
| | - Brett J Palmero
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, USA
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA;
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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6
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Nucleic acid-based scaffold systems and application in enzyme cascade catalysis. Appl Microbiol Biotechnol 2022; 107:9-23. [DOI: 10.1007/s00253-022-12315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022]
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Kwon S, Giessen TW. Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo. ACS Synth Biol 2022; 11:3504-3515. [PMID: 36170610 PMCID: PMC9944510 DOI: 10.1021/acssynbio.2c00391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tobias W. Giessen
- Department of Biological Chemistry and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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8
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Adamson LSR, Tasneem N, Andreas MP, Close W, Jenner EN, Szyszka TN, Young R, Cheah LC, Norman A, MacDermott-Opeskin HI, O'Mara ML, Sainsbury F, Giessen TW, Lau YH. Pore structure controls stability and molecular flux in engineered protein cages. SCIENCE ADVANCES 2022. [PMID: 35119930 DOI: 10.1101/2021.01.27.428512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the Thermotoga maritima encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux.
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Affiliation(s)
- Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Nuren Tasneem
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William Close
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Li Chen Cheah
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander Norman
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Frank Sainsbury
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Campderdown, NSW 2006, Australia
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9
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Adamson LSR, Tasneem N, Andreas MP, Close W, Jenner EN, Szyszka TN, Young R, Cheah LC, Norman A, MacDermott-Opeskin HI, O’Mara ML, Sainsbury F, Giessen TW, Lau YH. Pore structure controls stability and molecular flux in engineered protein cages. SCIENCE ADVANCES 2022; 8:eabl7346. [PMID: 35119930 PMCID: PMC8816334 DOI: 10.1126/sciadv.abl7346] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the Thermotoga maritima encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux.
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Affiliation(s)
- Lachlan S. R. Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Nuren Tasneem
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P. Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William Close
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Eric N. Jenner
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Li Chen Cheah
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander Norman
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Frank Sainsbury
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Tobias W. Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
- Corresponding author. (T.W.G.); (Y.H.L.)
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Campderdown, NSW 2006, Australia
- Corresponding author. (T.W.G.); (Y.H.L.)
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Hou Q, Zhang H, Bao L, Song Z, Liu C, Jiang Z, Zheng Y. NCs-Delivered Pesticides: A Promising Candidate in Smart Agriculture. Int J Mol Sci 2021; 22:ijms222313043. [PMID: 34884846 PMCID: PMC8657871 DOI: 10.3390/ijms222313043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 02/01/2023] Open
Abstract
Pesticides have been used extensively in the field of plant protection to maximize crop yields. However, the long-term, unmanaged application of pesticides has posed severe challenges such as pesticide resistance, environmental contamination, risk in human health, soil degradation, and other important global issues. Recently, the combination of nanotechnology with plant protection strategies has offered new perspectives to mitigate these global issues, which has promoted a rapid development of NCs-based pesticides. Unlike certain conventional pesticides that have been applied inefficiently and lacked targeted control, pesticides delivered by nanocarriers (NCs) have optimized formulations, controlled release rate, and minimized or site-specific application. They are receiving increasing attention and are considered as an important part in sustainable and smart agriculture. This review discussed the limitation of traditional pesticides or conventional application mode, focused on the sustainable features of NCs-based pesticides such as improved formulation, enhanced stability under harsh condition, and controlled release/degradation. The perspectives of NCs-based pesticides and their risk assessment were also suggested in this view for a better use of NCs-based pesticides to facilitate sustainable, smart agriculture in the future.
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Affiliation(s)
- Qiuli Hou
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
| | - Hanqiao Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
| | - Lixia Bao
- Analysis & Testing Center, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; (L.B.); (Z.S.)
| | - Zeyu Song
- Analysis & Testing Center, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; (L.B.); (Z.S.)
| | - Changpeng Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
| | - Zhenqi Jiang
- Analysis & Testing Center, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; (L.B.); (Z.S.)
- Correspondence: (Z.J.); (Y.Z.)
| | - Yang Zheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
- Correspondence: (Z.J.); (Y.Z.)
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11
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Artunduaga Bonilla JJ, Honorato L, Cordeiro de Oliveira DF, Araújo Gonçalves R, Guimarães A, Miranda K, Nimrichter L. Silver chitosan nanocomposites as a potential treatment for superficial candidiasis. Med Mycol 2021; 59:993-1005. [PMID: 34036352 DOI: 10.1093/mmy/myab028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/14/2021] [Accepted: 04/29/2021] [Indexed: 11/14/2022] Open
Abstract
Silver compounds are widely known for their antimicrobial activity, but can exert toxic effects to the host. Among the strategies to reduce its toxicity, incorporation into biopolymers has shown promising results. We investigated the green syntheses of silver nanoparticles (AgNPs) and their functionalization in a chitosan matrix (AgNPs@Chi) as a potential treatment against Candida spp. Inhibitory concentrations ranging between 0.06 and 1 μg/ml were observed against distinct Candida species. Nanocomposite-treated cells displayed cytoplasmic degeneration and a cell membrane and wall disruption. Silver nanocomposites in combination with fluconazole and amphotericin B showed an additive effect when analyzed by the Bliss method. The low cytotoxicity displayed in mammalian cells and in the Galleria mellonella larvae suggested their potential use in vivo. When tested as a topical treatment against murine cutaneous candidiasis, silver nanocomposites reduced the skin fungal burden in a dose-response behavior and favored tissue repair. In addition, the anti-biofilm effect of AgNPs@Chi in human nail model was demonstrated, suggesting that the polymeric formulation of AgNPs does not affect antifungal activity even against sessile cells. Our results suggest that AgNPs@Chi seems to be a less toxic and effective topical treatment for superficial candidiasis. LAY SUMMARY This study demonstrated the efficacy of silver nanoparticles (AgNPs) in inhibiting the growth of Candida. AgNPs incorporated in chitosan displayed a reduced toxicity. Tests in infected mice showed the effectiveness of the treatment. AgNPs-chitosan could be an alternative to combat candidiasis.
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Affiliation(s)
- Jhon Jhamilton Artunduaga Bonilla
- Laboratório de Glicobiología de Eucariotos (LaGE), Depto. Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, Brazil
| | - Leandro Honorato
- Laboratório de Glicobiología de Eucariotos (LaGE), Depto. Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, Brazil
| | | | - Rodrigo Araújo Gonçalves
- Depto de Química, Pontifícia Universidade Católica do Rio de Janeiro, 22451-900, Rio de Janeiro, Brazil
| | - Allan Guimarães
- Laboratório de Bioquímica e Imunologia das Micoses, Depto de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói, 24220-900, Brazil
| | - Kildare Miranda
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho and Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-590, Brazil
| | - Leonardo Nimrichter
- Laboratório de Glicobiología de Eucariotos (LaGE), Depto. Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, Brazil
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12
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Maffeis V, Belluati A, Craciun I, Wu D, Novak S, Schoenenberger CA, Palivan CG. Clustering of catalytic nanocompartments for enhancing an extracellular non-native cascade reaction. Chem Sci 2021; 12:12274-12285. [PMID: 34603657 PMCID: PMC8480338 DOI: 10.1039/d1sc04267j] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/14/2021] [Indexed: 01/10/2023] Open
Abstract
Compartmentalization is fundamental in nature, where the spatial segregation of biochemical reactions within and between cells ensures optimal conditions for the regulation of cascade reactions. While the distance between compartments or their interaction are essential parameters supporting the efficiency of bio-reactions, so far they have not been exploited to regulate cascade reactions between bioinspired catalytic nanocompartments. Here, we generate individual catalytic nanocompartments (CNCs) by encapsulating within polymersomes or attaching to their surface enzymes involved in a cascade reaction and then, tether the polymersomes together into clusters. By conjugating complementary DNA strands to the polymersomes' surface, DNA hybridization drove the clusterization process of enzyme-loaded polymersomes and controlled the distance between the respective catalytic nanocompartments. Owing to the close proximity of CNCs within clusters and the overall stability of the cluster architecture, the cascade reaction between spatially segregated enzymes was significantly more efficient than when the catalytic nanocompartments were not linked together by DNA duplexes. Additionally, residual DNA single strands that were not engaged in clustering, allowed for an interaction of the clusters with the cell surface as evidenced by A549 cells, where clusters decorating the surface endowed the cells with a non-native enzymatic cascade. The self-organization into clusters of catalytic nanocompartments confining different enzymes of a cascade reaction allows for a distance control of the reaction spaces which opens new avenues for highly efficient applications in domains such as catalysis or nanomedicine.
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Affiliation(s)
- Viviana Maffeis
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
| | - Andrea Belluati
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Ioana Craciun
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Dalin Wu
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Samantha Novak
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
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13
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Berckman EA, Chen W. Self-assembling protein nanocages for modular enzyme assembly by orthogonal bioconjugation. Biotechnol Prog 2021; 37:e3190. [PMID: 34173352 DOI: 10.1002/btpr.3190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/24/2021] [Indexed: 11/06/2022]
Abstract
The wide variety of enzymatic pathways that can benefit from enzyme scaffolding is astronomical. While enzyme co-localization based on protein, DNA, and RNA scaffolds has been reported, we still lack scaffolds that offer well-defined and uniform three-dimensional structures for enzyme organization. Here we reported a new approach for protein co-localization using naturally occurring protein nanocages as a scaffold. Two different nanocages, the 25 nm E2 and the 34 nm heptatitis B virus, were used to demonstrate the successfully co-localization of the endoglucanase CelA and cellulose binding domain using the robust SpyTag/SpyCatcher bioconjugation chemistry. Because of the simplicity of the assembly, this strategy is useful not only for in vivo enzyme cascading but also the potential for in vivo applications as well.
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Affiliation(s)
- Emily A Berckman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
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14
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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15
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Karkaria BD, Treloar NJ, Barnes CP, Fedorec AJH. From Microbial Communities to Distributed Computing Systems. Front Bioeng Biotechnol 2020; 8:834. [PMID: 32793576 PMCID: PMC7387671 DOI: 10.3389/fbioe.2020.00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
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Affiliation(s)
- Behzad D. Karkaria
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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16
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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17
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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18
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Chowdhury C, Bobik TA. Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella. MICROBIOLOGY-SGM 2020; 165:1355-1364. [PMID: 31674899 DOI: 10.1099/mic.0.000872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that consist of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by increasing reaction rates and sequestering toxic pathway intermediates. A substantial amount of effort has been directed toward engineering synthetic MCPs as intracellular nanoreactors for the improved production of renewable chemicals. A key challenge in this area is engineering protein shells that allow the entry of desired substrates. In this study, we used site-directed mutagenesis of the PduT shell protein to remove its central iron-sulfur cluster and create openings (pores) in the shell of the Pdu MCP that have varied chemical properties. Subsequently, in vivo and in vitro studies were used to show that PduT-C38S and PduT-C38A variants increased the diffusion of 1,2-propanediol, propionaldehyde, NAD+ and NADH across the shell of the MCP. In contrast, PduT-C38I and PduT-C38W eliminated the iron-sulfur cluster without altering the permeability of the Pdu MCP, suggesting that the side-chains of C38I and C38W occluded the opening formed by removal of the iron-sulfur cluster. Thus, genetic modification offers an approach to engineering the movement of larger molecules (such as NAD/H) across MCP shells, as well as a method for blocking transport through trimeric bacterial microcompartment (BMC) domain shell proteins.
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Affiliation(s)
- Chiranjit Chowdhury
- Present address: Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Campus, Sector-125, Noida, UP-201313, India.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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19
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Sharma J, Douglas T. Tuning the catalytic properties of P22 nanoreactors through compositional control. NANOSCALE 2020; 12:336-346. [PMID: 31825057 PMCID: PMC8859858 DOI: 10.1039/c9nr08348k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Enzymes are biomacromolecular protein catalysts that are widely used in a plethora of industrial-scale applications due to their high selectivity, efficiency and ability to work under mild conditions. Many industrial processes require the immobilization of enzymes to enhance their performance and stability. Encapsulation of enzymes in protein cages provides an excellent immobilization platform to create nanoreactors with enhanced enzymatic stability and desired catalytic activities. Here we show that the catalytic activity of nanoreactors, derived from the bacteriophage P22 viral capsids, can be finely-tuned by controlling the packaging stoichiometry and packing density of encapsulated enzymes. The packaging stoichiometry of the enzyme alcohol dehydrogenase (AdhD) was controlled by co-encapsulating it with wild-type scaffold protein (wtSP) at different stoichiometric ratios using an in vitro assembly approach and the packing density was controlled by selectively removing wtSP from the assembled nanoreactors. An inverse relationship was observed between the catalytic activity (kcat) of AdhD enzyme and the concentration of co-encapsulated wtSP. Selective removal of the wtSP resulted in the similar activity of AdhD in all nanoreactors despite the difference in the volume occupied by enzymes inside nanoreactors, indicating that the AdhD enzymes do not experience self-crowding even under high molarity of confinement (Mconf) conditions. The approach demonstrated here not only allowed us to tailor the activity of encapsulated AdhD catalysts but also the overall functional output of nanoreactors (enzyme-VLP complex). The approach also allowed us to differentiate the effects of crowding and confinement on the functional properties of enzymes encapsulated in an enclosed system, which could pave the way for designing more efficient nanoreactors.
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Affiliation(s)
- Jhanvi Sharma
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA.
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA.
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20
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Affiliation(s)
- Aleksei Solomonov
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
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21
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Knudsen C, Gallage NJ, Hansen CC, Møller BL, Laursen T. Dynamic metabolic solutions to the sessile life style of plants. Nat Prod Rep 2019; 35:1140-1155. [PMID: 30324199 PMCID: PMC6254060 DOI: 10.1039/c8np00037a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand dynamic biosynthesis and storage of a plethora of phytochemicals.
Covering: up to 2018 Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand synthesis of a plethora of phytochemicals to specifically respond to the challenges arising during plant ontogeny. Key steps in the biosynthesis of phytochemicals are catalyzed by membrane-bound cytochrome P450 enzymes which in plants constitute a superfamily. In planta, the P450s may be organized in dynamic enzyme clusters (metabolons) and the genes encoding the P450s and other enzymes in a specific pathway may be clustered. Metabolon formation facilitates transfer of substrates between sequential enzymes and therefore enables the plant to channel the flux of general metabolites towards biosynthesis of specific phytochemicals. In the plant cell, compartmentalization of the operation of specific biosynthetic pathways in specialized plastids serves to avoid undesired metabolic cross-talk and offers distinct storage sites for molar concentrations of specific phytochemicals. Liquid–liquid phase separation may lead to formation of dense biomolecular condensates within the cytoplasm or vacuole allowing swift activation of the stored phytochemicals as required upon pest or herbivore attack. The molecular grid behind plant plasticity offers an endless reservoir of functional modules, which may be utilized as a synthetic biology tool-box for engineering of novel biological systems based on rational design principles. In this review, we highlight some of the concepts used by plants to coordinate biosynthesis and storage of phytochemicals.
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Affiliation(s)
- Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.
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22
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Torres AF, Xu X, Nikiforidis CV, Bitter JH, Trindade LM. Exploring the Treasure of Plant Molecules With Integrated Biorefineries. FRONTIERS IN PLANT SCIENCE 2019; 10:478. [PMID: 31040858 PMCID: PMC6476976 DOI: 10.3389/fpls.2019.00478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Despite significant progress toward the commercialization of biobased products, today's biorefineries are far from achieving their intended goal of total biomass valorization and effective product diversification. The problem is conceptual. Modern biorefineries were built around well-optimized, cost-effective chemical synthesis routes, like those used in petroleum refineries for the synthesis of fuels, plastics, and solvents. However, these were designed for the conversion of fossil resources and are far from optimal for the processing of biomass, which has unique chemical characteristics. Accordingly, existing biomass commodities were never intended for modern biorefineries as they were bred to meet the needs of conventional agriculture. In this perspective paper, we propose a new path toward the design of efficient biorefineries, which capitalizes on a cross-disciplinary synergy between plant, physical, and catalysis science. In our view, the best opportunity to advance profitable and sustainable biorefineries requires the parallel development of novel feedstocks, conversion protocols and synthesis routes specifically tailored for total biomass valorization. Above all, we believe that plant biologists and process technologists can jointly explore the natural diversity of plants to synchronously develop both, biobased crops with designer chemistries and compatible conversion protocols that enable maximal biomass valorization with minimum input utilization. By building biorefineries from the bottom-up (i.e., starting with the crop), the envisioned partnership promises to develop cost-effective, biomass-dedicated routes which can be effectively scaled-up to deliver profitable and resource-use efficient biorefineries.
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Affiliation(s)
- Andres F. Torres
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
- Biobased Chemistry and Technology, Wageningen University, Wageningen, Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, Netherlands
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Xuan Xu
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | | | - Johannes H. Bitter
- Biobased Chemistry and Technology, Wageningen University, Wageningen, Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, Netherlands
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23
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Biological synthesis of metallic nanoparticles (MNPs) by plants and microbes: their cellular uptake, biocompatibility, and biomedical applications. Appl Microbiol Biotechnol 2019; 103:2913-2935. [PMID: 30778643 DOI: 10.1007/s00253-019-09675-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 12/13/2022]
Abstract
Metallic nanoparticles (MNPs) with their diverse physical and chemical properties have been applied in various biomedical domains. The increasing demand for MNPs has attracted researchers to develop straightforward, inexpensive, simple, and eco-friendly processes for the enhanced production of MNPs. To discover new biomedical applications first requires knowledge of the interactions of MNPs with target cells. This review focuses on plant and microbial synthesis of biological MNPs, their cellular uptake, biocompatibility, any biological consequences such as cytotoxicity, and biomedical applications. We highlighted the involvement of biomolecules in capping and stabilization of MNPs and the effect of physicochemical parameters particularly the pH on the synthesis of MNPs. Recently achieved milestones to understand the role of synthetic biology (SynBiol) in the synthesis of tailored MNPs are also discussed.
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24
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Nanoreactor Design Based on Self-Assembling Protein Nanocages. Int J Mol Sci 2019; 20:ijms20030592. [PMID: 30704048 PMCID: PMC6387247 DOI: 10.3390/ijms20030592] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/18/2022] Open
Abstract
Self-assembling proteins that form diverse architectures are widely used in material science and nanobiotechnology. One class belongs to protein nanocages, which are compartments with nanosized internal spaces. Because of the precise nanoscale structures, proteinaceous compartments are ideal materials for use as general platforms to create distinct microenvironments within confined cellular environments. This spatial organization strategy brings several advantages including the protection of catalyst cargo, faster turnover rates, and avoiding side reactions. Inspired by diverse molecular machines in nature, bioengineers have developed a variety of self-assembling supramolecular protein cages for use as biosynthetic nanoreactors that mimic natural systems. In this mini-review, we summarize current progress and ongoing efforts creating self-assembling protein based nanoreactors and their use in biocatalysis and synthetic biology. We also highlight the prospects for future research on these versatile nanomaterials.
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25
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Kumar S, Nehra M, Dilbaghi N, Marrazza G, Hassan AA, Kim KH. Nano-based smart pesticide formulations: Emerging opportunities for agriculture. J Control Release 2019; 294:131-153. [PMID: 30552953 DOI: 10.1016/j.jconrel.2018.12.012] [Citation(s) in RCA: 227] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/08/2018] [Accepted: 12/10/2018] [Indexed: 12/11/2022]
Abstract
The incorporation of nanotechnology as a means for nanopesticides is in the early stage of development. The main idea behind this incorporation is to lower the indiscriminate use of conventional pesticides to be in line with safe environmental applications. Nanoencapsulated pesticides can provide controlled release kinetics, while efficiently enhancing permeability, stability, and solubility. Nanoencapsulation can enhance the pest-control efficiency over extended durations by preventing the premature degradation of active ingredients (AIs) under harsh environmental conditions. This review is thus organized to critically assess the significant role of nanotechnology for encapsulation of AIs for pesticides. The smart delivery of pesticides is essential to reduce the dosage of AIs with enhanced efficacy and to overcome pesticide loss (e.g., due to leaching and evaporation). The future trends of pesticide nanoformulations including nanomaterials as AIs and nanoemulsions of biopesticides are also explored. This review should thus offer a valuable guide for establishing regulatory frameworks related to field applications of these nano-based pesticides in the near future.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska Lincoln, P.O. Box 886105, Lincoln, NE 68588-6105, United States.
| | - Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India; Department of Electronics and Communication Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Giovanna Marrazza
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; Istituto Nazionale Biostrutture e Biosistemi (INBB), Unit of Florence, Viale delle Medaglie d'Oro 305, 00136, Roma, Italy
| | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska Lincoln, P.O. Box 886105, Lincoln, NE 68588-6105, United States
| | - Ki-Hyun Kim
- Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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26
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Abstract
Spatial organization is a hallmark of all living systems. Even bacteria, the smallest forms of cellular life, display defined shapes and complex internal organization, showcasing a highly structured genome, cytoskeletal filaments, localized scaffolding structures, dynamic spatial patterns, active transport, and occasionally, intracellular organelles. Spatial order is required for faithful and efficient cellular replication and offers a powerful means for the development of unique biological properties. Here, we discuss organizational features of bacterial cells and highlight how bacteria have evolved diverse spatial mechanisms to overcome challenges cells face as self-replicating entities.
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27
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28
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Williams EM, Jung SM, Coffman JL, Lutz S. Pore Engineering for Enhanced Mass Transport in Encapsulin Nanocompartments. ACS Synth Biol 2018; 7:2514-2517. [PMID: 30376298 DOI: 10.1021/acssynbio.8b00295] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Encapsulins are robust and engineerable proteins that form hollow, nanosized, icosahedral capsids, making them attractive vehicles for drug delivery, scaffolds for synthetic bionanoreactors, and artificial organelles. A major limitation of native encapsulins is the small size of pores in the protein shell. At 3 Å diameter, these pores impose significant restrictions on the molecular weight and diffusion rate of potential substrates. By redesigning the pore-forming loop region in encapsulin from Thermotoga maritima, we successfully enlarged pore diameter up to an estimated 11 Å and increased mass transport rates by 7-fold as measured by lanthanide ion diffusion assay. Our study demonstrates the high tolerance of encapsulin for protein engineering and has created a set of novel, functionally improved scaffolds for applications as bionanoreactors.
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Affiliation(s)
- Elsie M. Williams
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30084, United States
| | - Se Min Jung
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30084, United States
| | - Jennifer L. Coffman
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30084, United States
| | - Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30084, United States
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29
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Timmermans SBPE, Vervoort DFM, Schoonen L, Nolte RJM, van Hest JCM. Self-Assembly and Stabilization of Hybrid Cowpea Chlorotic Mottle Virus Particles under Nearly Physiological Conditions. Chem Asian J 2018; 13:3518-3525. [PMID: 29975459 DOI: 10.1002/asia.201800842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Capsids of the cowpea chlorotic mottle virus (CCMV) hold great promise for use as nanocarriers in vivo. A major drawback, however, is the lack of stability of the empty wild-type virus particles under physiological conditions. Herein, the assembly behavior and stability under nearly physiological conditions of protein-based block copolymers composed of the CCMV capsid protein and two hydrophobic elastin-like polypeptides are reported. UV/Vis spectroscopy studies, dynamic light-scattering analysis, and TEM measurements demonstrate that both hybrid variants form stable capsids at pH 7.5, physiological NaCl concentration, and 37 °C. The more hydrophobic variant also remains stable in a cell culture medium. These engineered, hybrid CCMV capsid particles can therefore be regarded as suitable candidates for in vivo applications.
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Affiliation(s)
- Suzanne B P E Timmermans
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
| | - Daan F M Vervoort
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
| | - Lise Schoonen
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jan C M van Hest
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
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30
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Zhang G, Quin MB, Schmidt-Dannert C. Self-Assembling Protein Scaffold System for Easy in Vitro Coimmobilization of Biocatalytic Cascade Enzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00986] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Guoqiang Zhang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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31
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Li H, Zheng G, Zhu S. Construction of an organelle-like nanodevice via supramolecular self-assembly for robust biocatalysts. Microb Cell Fact 2018; 17:26. [PMID: 29458431 PMCID: PMC5819227 DOI: 10.1186/s12934-018-0873-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/09/2018] [Indexed: 11/13/2022] Open
Abstract
Background When using the microbial cell factories for green manufacturing, several important issues need to be addressed such as how to maintain the stability of biocatalysts used in the bioprocess and how to improve the synthetic efficiency of the biological system. One strategy widely used during natural evolution is the creation of organelles which can be used for regional control. This kind of compartmentalization strategy has inspired the design of artificial organelle-like nanodevice for synthetic biology and “green chemistry”. Results Mimicking the natural concept of functional compartments, here we show that the engineered thermostable ketohydroxyglutarate aldolase from Thermotoga maritima could be developed as a general platform for nanoreactor design via supramolecular self-assembly. An industrial biocatalyst-(+)-γ-lactamase was selected as a model catalyst and successful encapsulated in the nanoreactor with high copies. These nanomaterials could easily be synthesized by Escherichia coli by heterologous expression and subsequently self-assembles into the target organelle-like nanoreactors both in vivo and in vitro. By probing their structural characteristics via transmission electronic microscopy and their catalytic activity under diverse conditions, we proved that these nanoreactors could confer a significant benefit to the cargo proteins. The encapsulated protein exhibits significantly improved stability under conditions such as in the presence of organic solvent or proteases, and shows better substrate tolerance than free enzyme. Conclusions Our biodesign strategy provides new methods to develop new catalytically active protein-nanoreactors and could easily be applied into other biocatalysts. These artificial organelles could have widely application in sustainable catalysis, synthetic biology and could significantly improve the performance of microbial cell factories. Graphical Abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12934-018-0873-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongxia Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China.
| | - Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China.
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32
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Fuentes P, Armarego-Marriott T, Bock R. Plastid transformation and its application in metabolic engineering. Curr Opin Biotechnol 2018; 49:10-15. [DOI: 10.1016/j.copbio.2017.07.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/14/2017] [Accepted: 07/03/2017] [Indexed: 12/31/2022]
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33
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Fang Y, Huang F, Faulkner M, Jiang Q, Dykes GF, Yang M, Liu LN. Engineering and Modulating Functional Cyanobacterial CO 2-Fixing Organelles. FRONTIERS IN PLANT SCIENCE 2018; 9:739. [PMID: 29922315 PMCID: PMC5996877 DOI: 10.3389/fpls.2018.00739] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 05/12/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla and provide a means for compartmentalizing specific metabolic pathways. They sequester catalytic enzymes from the cytoplasm, using an icosahedral proteinaceous shell with selective permeability to metabolic molecules and substrates, to enhance metabolic efficiency. Carboxysomes were the first BMCs discovered and their unprecedented capacity of CO2 fixation allows cyanobacteria to make a significant contribution to global carbon fixation. There is an increasing interest in utilizing synthetic biology to construct synthetic carboxysomes in new hosts, i.e., higher plants, to enhance carbon fixation and productivity. Here, we report the construction of a synthetic operon of the β-carboxysome from the cyanobacterium Synechococcus elongatus PCC7942 to generate functional β-carboxysome-like structures in Escherichia coli. The protein expression, structure, assembly, and activity of synthetic β-carboxysomes were characterized in depth using confocal, electron and atomic force microscopy, proteomics, immunoblot analysis, and enzymatic assays. Furthermore, we examined the in vivo interchangeability of β-carboxysome building blocks with other BMC components. To our knowledge, this is the first production of functional β-carboxysome-like structures in heterologous organisms. It provides important information for the engineering of fully functional carboxysomes and CO2-fixing modules in higher plants. The study strengthens our synthetic biology toolbox for generating BMC-based organelles with tunable activities and new scaffolding biomaterials for metabolic improvement and molecule delivery.
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34
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Nangle SN, Sakimoto KK, Silver PA, Nocera DG. Biological-inorganic hybrid systems as a generalized platform for chemical production. Curr Opin Chem Biol 2017; 41:107-113. [DOI: 10.1016/j.cbpa.2017.10.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 12/16/2022]
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35
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Han X, Woycechowsky KJ. Encapsulation and Controlled Release of Protein Guests by the Bacillus subtilis Lumazine Synthase Capsid. Biochemistry 2017; 56:6211-6220. [PMID: 29087189 DOI: 10.1021/acs.biochem.7b00669] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Bacillus subtilis, the 60-subunit dodecahedral capsid formed by lumazine synthase (BsLS) acts as a container for trimeric riboflavin synthase (BsRS). To test whether the C-terminal sequence of BsRS is responsible for its encapsulation by BsLS, the green fluorescent protein (GFP) was fused to either the last 11 or the last 32 amino acids of BsRS, yielding variant GFP11 or GFP32, respectively. After purification, BsLS capsids that had been co-produced in bacteria with GFP11 and GFP32 are 15- and 6-fold more fluorescent, respectively, than BsLS co-produced with GFP lacking any BsRS fragment, indicating complex formation. Enzyme-linked immunosorbent assay experiments confirm that GFP11 is localized within the BsLS capsid. In addition, fusing the last 11 amino acids of BsRS to the C-terminus of the Abrin A chain also led to its encapsulation by BsLS at a level similar to that of GFP11. Together, these results demonstrate that the C-terminal tail of BsRS can act as an encapsulation tag capable of targeting other proteins to the BsLS capsid interior. As with the natural BsLS-BsRS complex, mild changes in pH and buffer identity trigger dissociation of the GFP11 guest, accompanied by a substantial expansion of the BsLS capsid. This system for protein encapsulation and release provides a novel tool for bionanotechnology.
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Affiliation(s)
- Xue Han
- School of Pharmaceutical Science and Technology, Tianjin University , Tianjin 300072, China
| | - Kenneth J Woycechowsky
- School of Pharmaceutical Science and Technology, Tianjin University , Tianjin 300072, China
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36
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Giessen TW, Silver PA. Engineering carbon fixation with artificial protein organelles. Curr Opin Biotechnol 2017; 46:42-50. [DOI: 10.1016/j.copbio.2017.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
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37
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Young EJ, Burton R, Mahalik JP, Sumpter BG, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications. Front Microbiol 2017; 8:1441. [PMID: 28824573 PMCID: PMC5534457 DOI: 10.3389/fmicb.2017.01441] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/17/2017] [Indexed: 01/03/2023] Open
Abstract
As synthetic biology advances the intricacy of engineered biological systems, the importance of spatial organization within the cellular environment must not be marginalized. Increasingly, biological engineers are investigating means to control spatial organization within the cell, mimicking strategies used by natural pathways to increase flux and reduce cross-talk. A modular platform for constructing a diverse set of defined, programmable architectures would greatly assist in improving yields from introduced metabolic pathways and increasing insulation of other heterologous systems. Here, we review recent research on the shell proteins of bacterial microcompartments and discuss their potential application as "building blocks" for a range of customized intracellular scaffolds. We summarize the state of knowledge on the self-assembly of BMC shell proteins and discuss future avenues of research that will be important to realize the potential of BMC shell proteins as predictively assembling and programmable biological materials for bioengineering.
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Affiliation(s)
- Eric J. Young
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
| | - Rodney Burton
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
| | - Jyoti P. Mahalik
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Bobby G. Sumpter
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Miguel Fuentes-Cabrera
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Cheryl A. Kerfeld
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
- Molecular Biophysics and Integrated Bioimaging Division, Berkeley National Laboratory, BerkeleyCA, United States
| | - Daniel C. Ducat
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
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38
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Jakobson CM, Slininger Lee MF, Tullman‐Ercek D. De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment. Protein Sci 2017; 26:1086-1092. [PMID: 28241402 PMCID: PMC5405430 DOI: 10.1002/pro.3144] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 12/24/2022]
Abstract
Organizing heterologous biosyntheses inside bacterial cells can alleviate common problems owing to toxicity, poor kinetic performance, and cofactor imbalances. A subcellular organelle known as a bacterial microcompartment, such as the 1,2-propanediol utilization microcompartment of Salmonella, is a promising chassis for this strategy. Here we demonstrate de novo design of the N-terminal signal sequences used to direct cargo to these microcompartment organelles. We expand the native repertoire of signal sequences using rational and library-based approaches and show that a canonical leucine-zipper motif can function as a signal sequence for microcompartment localization. Our strategy can be applied to generate new signal sequences localizing arbitrary cargo proteins to the 1,2-propanediol utilization microcompartments.
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Affiliation(s)
- Christopher M. Jakobson
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIllinois60208
- Present address: Department of Chemical and Systems BiologyStanford UniversityStanfordCA94305
| | - Marilyn F. Slininger Lee
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIllinois60208
- Department of Chemical and Biomolecular EngineeringUniversity of California BerkeleyBerkeleyCalifornia94720
| | - Danielle Tullman‐Ercek
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIllinois60208
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39
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Sakimoto KK, Kornienko N, Yang P. Cyborgian Material Design for Solar Fuel Production: The Emerging Photosynthetic Biohybrid Systems. Acc Chem Res 2017; 50:476-481. [PMID: 28945394 DOI: 10.1021/acs.accounts.6b00483] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photosynthetic biohybrid systems (PBSs) combine the strengths of inorganic materials and biological catalysts by exploiting semiconductor broadband light absorption to capture solar energy and subsequently transform it into valuable CO2-derived chemicals by taking advantage of the metabolic pathways in living organisms. In this work, we first traverse through a brief history of recent PBSs, demonstrating the modularity and diversity of possible architectures to rival and, in many cases, surpass the performance of chemistry or biology alone before envisioning the future of these hybrid systems, opportunities for improvement, and its role in sustainable living here on earth and beyond.
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Affiliation(s)
- Kelsey K. Sakimoto
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Nikolay Kornienko
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Peidong Yang
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
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40
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Widespread distribution of encapsulin nanocompartments reveals functional diversity. Nat Microbiol 2017; 2:17029. [DOI: 10.1038/nmicrobiol.2017.29] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/03/2017] [Indexed: 11/09/2022]
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41
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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42
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Guo Q, Thomas GC, Woycechowsky KJ. Reversible loading of thiol-modified curcumin in an engineered protein capsid. RSC Adv 2017. [DOI: 10.1039/c7ra05890j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The dodecahedral capsid formed by Aquifex aeolicus lumazine synthase (AaLS) is a promising protein scaffold for bionanotechnological applications.
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Affiliation(s)
- Q. Guo
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin
- China
| | - G. C. Thomas
- Department of Chemistry
- University of Utah
- Salt Lake City
- USA
| | - K. J. Woycechowsky
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin
- China
- Department of Chemistry
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43
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Torres L, Krüger A, Csibra E, Gianni E, Pinheiro VB. Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem 2016; 60:393-410. [PMID: 27903826 PMCID: PMC5264511 DOI: 10.1042/ebc20160013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022]
Abstract
Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs.
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Affiliation(s)
- Leticia Torres
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - Antje Krüger
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Eszter Csibra
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Edoardo Gianni
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Vitor B Pinheiro
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
- Birkbeck, Department of Biological Sciences, University of London, Malet Street, WC1E 7HX, U.K
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44
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MacDonald IC, Deans TL. Tools and applications in synthetic biology. Adv Drug Deliv Rev 2016; 105:20-34. [PMID: 27568463 DOI: 10.1016/j.addr.2016.08.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 12/25/2022]
Abstract
Advances in synthetic biology have enabled the engineering of cells with genetic circuits in order to program cells with new biological behavior, dynamic gene expression, and logic control. This cellular engineering progression offers an array of living sensors that can discriminate between cell states, produce a regulated dose of therapeutic biomolecules, and function in various delivery platforms. In this review, we highlight and summarize the tools and applications in bacterial and mammalian synthetic biology. The examples detailed in this review provide insight to further understand genetic circuits, how they are used to program cells with novel functions, and current methods to reliably interface this technology in vivo; thus paving the way for the design of promising novel therapeutic applications.
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Affiliation(s)
- I Cody MacDonald
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, United States
| | - Tara L Deans
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, United States.
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45
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Giessen TW, Silver PA. A Catalytic Nanoreactor Based on in Vivo Encapsulation of Multiple Enzymes in an Engineered Protein Nanocompartment. Chembiochem 2016; 17:1931-1935. [DOI: 10.1002/cbic.201600431] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias W. Giessen
- Department of Systems Biology; Harvard Medical School; 200 Longwood Avenue WAB 536 Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; 3 Blackfan Circle Boston MA 02115 USA
| | - Pamela A. Silver
- Department of Systems Biology; Harvard Medical School; 200 Longwood Avenue WAB 536 Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; 3 Blackfan Circle Boston MA 02115 USA
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46
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Encapsulation of multiple cargo proteins within recombinant Eut nanocompartments. Appl Microbiol Biotechnol 2016; 100:9187-9200. [PMID: 27450681 DOI: 10.1007/s00253-016-7737-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/07/2016] [Accepted: 07/10/2016] [Indexed: 01/08/2023]
Abstract
Spatial organization via encapsulation of enzymes within recombinant nanocompartments may increase efficiency in multienzyme cascades. Previously, we reported the encapsulation of single cargo proteins within nanocompartments in the heterologous host Escherichia coli. This was achieved by coexpression of the Salmonella enterica LT2 ethanolamine utilization bacterial microcompartment shell proteins EutS or EutSMNLK, with a signal sequence EutC1-19 cargo protein fusion. Optimization of this system, leading to the targeting of more than one cargo protein, requires an understanding of the encapsulation mechanism. In this work, we report that the signal sequence EutC1-19 targets cargo to the interior of nanocompartments via a hydrophobic interaction with a helix on shell protein EutS. We confirm that EutC1-19 does not interact with other Eut BMC shell proteins, EutMNLK. Furthermore, we show that a second signal sequence EutE1-21 interacts specifically with the same helix on EutS. Both signal sequences appear to compete for the same EutS helix to simultaneously colocalize two cargo proteins to the interior of recombinant nanocompartments. This work offers the first insights into signal sequence-shell protein interactions required for cargo sequestration within Eut BMCs. It also provides a basis for the future engineering of Eut nanocompartments as a platform for the potential colocalization of multienzyme cascades for synthetic biology applications.
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47
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Schmidt-Dannert C, Lopez-Gallego F. A roadmap for biocatalysis - functional and spatial orchestration of enzyme cascades. Microb Biotechnol 2016; 9:601-9. [PMID: 27418373 PMCID: PMC4993178 DOI: 10.1111/1751-7915.12386] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/25/2016] [Indexed: 12/23/2022] Open
Abstract
Advances in biological engineering and systems biology have provided new approaches and tools for the industrialization of biology. In the next decade, advanced biocatalytic systems will increasingly be used for the production of chemicals that cannot be made by current processes and/or where the use of enzyme catalysts is more resource efficient with a much reduced environmental impact. We expect that in the future, manufacture of chemicals and materials will utilize both biocatalytic and chemical synthesis synergistically. The realization of such advanced biomanufacturing processes currently faces a number of major challenges. Ready‐to‐deploy portfolios of biocatalysts for design to production must be created from biological diverse sources and through protein engineering. Robust and efficient multi‐step enzymatic reaction cascades must be developed that can operate simultaneously in one‐pot. For this to happen, bio‐orthogonal strategies for spatial and temporal control of biocatalyst activities must be developed. Promising approaches and technologies are emerging that will eventually lead to the design of in vitro biocatalytic systems that mimic the metabolic pathways and networks of cellular systems which will be discussed in this roadmap.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Fernando Lopez-Gallego
- Heterogeneous Biocatalysis Group, CIC BiomaGUNE, Pase Miramon 182, San Sebastian-Donostia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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48
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Lu TK, Chandrasegaran S, Hodak H. The Era of Synthetic Biology and Genome Engineering: Where No Man Has Gone Before. J Mol Biol 2016; 428:835-6. [PMID: 26827726 DOI: 10.1016/j.jmb.2016.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Timothy K Lu
- MIT Microbiology Program, Massachusetts Institute of Technology, Cambridge, MA, United States; MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Harvard Biophysics Program, Harvard University, Boston, MA, United States; Broad Institute of MIT and Harvard, Cambridge, MA, United States.
| | - Srinivasan Chandrasegaran
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.
| | - Hélène Hodak
- Journal of Molecular Biology, Cambridge, MA, United States.
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