51
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Ouyang X, Zhou X, Lai SN, Liu Q, Zheng B. Immobilization of Proteins of Cell Extract to Hydrogel Networks Enhances the Longevity of Cell-Free Protein Synthesis and Supports Gene Networks. ACS Synth Biol 2021; 10:749-755. [PMID: 33784075 DOI: 10.1021/acssynbio.0c00541] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we constructed a new type of hydrogel based artificial cells supporting long-lived protein synthesis, post-translational modification, and gene networks. We constructed the artificial cells by immobilizing the transcription and translation system from E. coli cytoplasmic extract onto the polyacrylamide hydrogel. With the continuous supply of energy and nutrition, the artificial cells were capable of stable protein expression for at least 30 days. Functional proteins which were difficult to produce in vivo, including colicin E1 and urokinase, were synthesized in the artificial cells with high bioactivity. Furthermore, we constructed a sigma factor based genetic oscillator in the artificial cells. The artificial cells not only provide a powerful platform for continuous protein synthesis and convenient design and testing of genetic networks, but also hold great promise for the development of metabolic engineering, drug delivery, and biosensors.
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Affiliation(s)
- Xiaofei Ouyang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiaoyu Zhou
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sze Nga Lai
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Qi Liu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
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52
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Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
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Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
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53
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Nicolaus F, Metola A, Mermans D, Liljenström A, Krč A, Abdullahi SM, Zimmer M, Miller Iii TF, von Heijne G. Residue-by-residue analysis of cotranslational membrane protein integration in vivo. eLife 2021; 10:64302. [PMID: 33554862 PMCID: PMC7886326 DOI: 10.7554/elife.64302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
We follow the cotranslational biosynthesis of three multispanning Escherichia coli inner membrane proteins in vivo using high-resolution force profile analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domain can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process. Our results support the 'sliding' model of translocon-mediated membrane protein integration, in which hydrophobic segments are continually exposed to the lipid bilayer during their passage through the SecYEG translocon.
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Affiliation(s)
- Felix Nicolaus
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Metola
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daphne Mermans
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Amanda Liljenström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ajda Krč
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Matthew Zimmer
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Thomas F Miller Iii
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory Stockholm University, Solna, Sweden
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54
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Chen J, Zheng S, Zhao H, Yang Y. Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J Cheminform 2021; 13:7. [PMID: 33557952 PMCID: PMC7869490 DOI: 10.1186/s13321-021-00488-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/20/2021] [Indexed: 11/26/2022] Open
Abstract
Protein solubility is significant in producing new soluble proteins that can reduce the cost of biocatalysts or therapeutic agents. Therefore, a computational model is highly desired to accurately predict protein solubility from the amino acid sequence. Many methods have been developed, but they are mostly based on the one-dimensional embedding of amino acids that is limited to catch spatially structural information. In this study, we have developed a new structure-aware method GraphSol to predict protein solubility by attentive graph convolutional network (GCN), where the protein topology attribute graph was constructed through predicted contact maps only from the sequence. GraphSol was shown to substantially outperform other sequence-based methods. The model was proven to be stable by consistent [Formula: see text] of 0.48 in both the cross-validation and independent test of the eSOL dataset. To our best knowledge, this is the first study to utilize the GCN for sequence-based protein solubility predictions. More importantly, this architecture could be easily extended to other protein prediction tasks requiring a raw protein sequence.
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Affiliation(s)
- Jianwen Chen
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China
| | - Shuangjia Zheng
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China
| | - Huiying Zhao
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-Sen University), Guangzhou, 510000, China.
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55
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Reyes SG, Kuruma Y, Fujimi M, Yamazaki M, Eto S, Nishikawa S, Tamaki S, Kobayashi A, Mizuuchi R, Rothschild L, Ditzler M, Fujishima K. PURE mRNA display and cDNA display provide rapid detection of core epitope motif via high-throughput sequencing. Biotechnol Bioeng 2021; 118:1736-1749. [PMID: 33501662 DOI: 10.1002/bit.27696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/02/2021] [Accepted: 01/17/2021] [Indexed: 12/17/2022]
Abstract
The reconstructed in vitro translation system known as the PURE system has been used in a variety of cell-free experiments such as the expression of native and de novo proteins as well as various display methods to select for functional polypeptides. We developed a refined PURE-based display method for the preparation of stable messenger RNA (mRNA) and complementary DNA (cDNA)-peptide conjugates and validated its utility for in vitro selection. Our conjugate formation efficiency exceeded 40%, followed by gel purification to allow minimum carry-over of components from the translation system to the downstream assay enabling clean and efficient random peptide sequence screening. We chose the commercially available anti-FLAG M2 antibody as a target molecule for validation. Starting from approximately 1.7 × 1012 random sequences, a round-by-round high-throughput sequencing showed clear enrichment of the FLAG epitope DYKDDD as well as revealing consensus FLAG epitope motif DYK(D/L/N)(L/Y/D/N/F)D. Enrichment of core FLAG motifs lacking one of the four key residues (DYKxxD) indicates that Tyr (Y) and Lys (K) appear as the two key residues essential for binding. Furthermore, the comparison between mRNA display and cDNA display method resulted in overall similar performance with slightly higher enrichment for mRNA display. We also show that gel purification steps in the refined PURE-based display method improve conjugate formation efficiency and enhance the enrichment rate of FLAG epitope motifs in later rounds of selection especially for mRNA display. Overall, the generalized procedure and consistent performance of two different display methods achieved by the commercially available PURE system will be useful for future studies to explore the sequence and functional space of diverse polypeptides.
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Affiliation(s)
- Sabrina Galiñanes Reyes
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan.,James Watt School of Engineering, The University of Glasgow, Glasgow, UK
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan.,JST, PRESTO, Saitama, Japan
| | - Mai Fujimi
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | | | - Sumie Eto
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,MOLCURE Inc., Shinagawa, Tokyo, Japan
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Asaki Kobayashi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Ryo Mizuuchi
- JST, PRESTO, Saitama, Japan.,Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Lynn Rothschild
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, California, USA
| | - Mark Ditzler
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, California, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
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56
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Wang X, Du H, Wang Z, Mu W, Han X. Versatile Phospholipid Assemblies for Functional Synthetic Cells and Artificial Tissues. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2002635. [PMID: 32830387 DOI: 10.1002/adma.202002635] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/09/2020] [Indexed: 06/11/2023]
Abstract
The bottom-up construction of a synthetic cell from nonliving building blocks capable of mimicking cellular properties and behaviors helps to understand the particular biophysical properties and working mechanisms of a cell. A synthetic cell built in this way possesses defined chemical composition and structure. Since phospholipids are native biomembrane components, their assemblies are widely used to mimic cellular structures. Here, recent developments in the formation of versatile phospholipid assemblies are described, together with the applications of these assemblies for functional membranes (protein reconstituted giant unilamellar vesicles), spherical and nonspherical protoorganelles, and functional synthetic cells, as well as the high-order hierarchical structures of artificial tissues. Their biomedical applications are also briefly summarized. Finally, the challenges and future directions in the field of synthetic cells and artificial tissues based on phospholipid assemblies are proposed.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Hang Du
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Marine Antifouling Engineering Technology Center of Shangdong Province, Harbin Institute of Technology, Weihai, 264209, China
| | - Zhao Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Wei Mu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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57
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Lavickova B, Laohakunakorn N, Maerkl SJ. A partially self-regenerating synthetic cell. Nat Commun 2020; 11:6340. [PMID: 33311509 PMCID: PMC7733450 DOI: 10.1038/s41467-020-20180-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/16/2020] [Indexed: 01/16/2023] Open
Abstract
Self-regeneration is a fundamental function of all living systems. Here we demonstrate partial molecular self-regeneration in a synthetic cell. By implementing a minimal transcription-translation system within microfluidic reactors, the system is able to regenerate essential protein components from DNA templates and sustain synthesis activity for over a day. By quantitating genotype-phenotype relationships combined with computational modeling we find that minimizing resource competition and optimizing resource allocation are both critically important for achieving robust system function. With this understanding, we achieve simultaneous regeneration of multiple proteins by determining the required DNA ratios necessary for sustained self-regeneration. This work introduces a conceptual and experimental framework for the development of a self-replicating synthetic cell.
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Affiliation(s)
- Barbora Lavickova
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nadanai Laohakunakorn
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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58
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Müller J, Siemann-Herzberg M, Takors R. Modeling Cell-Free Protein Synthesis Systems-Approaches and Applications. Front Bioeng Biotechnol 2020; 8:584178. [PMID: 33195146 PMCID: PMC7655533 DOI: 10.3389/fbioe.2020.584178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/29/2020] [Indexed: 01/03/2023] Open
Abstract
In vitro systems are ideal setups to investigate the basic principles of biochemical reactions and subsequently the bricks of life. Cell-free protein synthesis (CFPS) systems mimic the transcription and translation processes of whole cells in a controlled environment and allow the detailed study of single components and reaction networks. In silico studies of CFPS systems help us to understand interactions and to identify limitations and bottlenecks in those systems. Black-box models laid the foundation for understanding the production and degradation dynamics of macromolecule components such as mRNA, ribosomes, and proteins. Subsequently, more sophisticated models revealed shortages in steps such as translation initiation and tRNA supply and helped to partially overcome these limitations. Currently, the scope of CFPS modeling has broadened to various applications, ranging from the screening of kinetic parameters to the stochastic analysis of liposome-encapsulated CFPS systems and the assessment of energy supply properties in combination with flux balance analysis (FBA).
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Affiliation(s)
| | | | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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59
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Morató A, Elena-Real CA, Popovic M, Fournet A, Zhang K, Allemand F, Sibille N, Urbanek A, Bernadó P. Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins. Biomolecules 2020; 10:E1458. [PMID: 33086646 PMCID: PMC7603387 DOI: 10.3390/biom10101458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022] Open
Abstract
The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.
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Affiliation(s)
| | | | | | | | | | | | | | - Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
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60
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Challenges & opportunities for phage-based in situ microbiome engineering in the gut. J Control Release 2020; 326:106-119. [DOI: 10.1016/j.jconrel.2020.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
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61
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Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
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Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
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62
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Hou Q, Kwasigroch JM, Rooman M, Pucci F. SOLart: a structure-based method to predict protein solubility and aggregation. Bioinformatics 2020; 36:1445-1452. [PMID: 31603466 DOI: 10.1093/bioinformatics/btz773] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/31/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION The solubility of a protein is often decisive for its proper functioning. Lack of solubility is a major bottleneck in high-throughput structural genomic studies and in high-concentration protein production, and the formation of protein aggregates causes a wide variety of diseases. Since solubility measurements are time-consuming and expensive, there is a strong need for solubility prediction tools. RESULTS We have recently introduced solubility-dependent distance potentials that are able to unravel the role of residue-residue interactions in promoting or decreasing protein solubility. Here, we extended their construction by defining solubility-dependent potentials based on backbone torsion angles and solvent accessibility, and integrated them, together with other structure- and sequence-based features, into a random forest model trained on a set of Escherichia coli proteins with experimental structures and solubility values. We thus obtained the SOLart protein solubility predictor, whose most informative features turned out to be folding free energy differences computed from our solubility-dependent statistical potentials. SOLart performances are very good, with a Pearson correlation coefficient between experimental and predicted solubility values of almost 0.7 both in cross-validation on the training dataset and in an independent set of Saccharomyces cerevisiae proteins. On test sets of modeled structures, only a limited drop in performance is observed. SOLart can thus be used with both high-resolution and low-resolution structures, and clearly outperforms state-of-art solubility predictors. It is available through a user-friendly webserver, which is easy to use by non-expert scientists. AVAILABILITY AND IMPLEMENTATION The SOLart webserver is freely available at http://babylone.ulb.ac.be/SOLART/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qingzhen Hou
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Avenue Roosevelt 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Jean Marc Kwasigroch
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Avenue Roosevelt 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Avenue Roosevelt 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Avenue Roosevelt 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, 52428 Jülich, Germany
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63
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Burgenson D, Linton J, Ge X, Kostov Y, Tolosa L, Szeto GL, Rao G. A Cell-Free Protein Expression System Derived from Human Primary Peripheral Blood Mononuclear Cells. ACS Synth Biol 2020; 9:2188-2196. [PMID: 32698572 DOI: 10.1021/acssynbio.0c00256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Historically, some of the first cell-free protein expression systems studied in vitro translation in various human blood cells. However, because of limited knowledge of eukaryotic translation and the advancement of cell line development, interest in these systems decreased. Eukaryotic translation is a complex system of factors that contribute to the overall translation of mRNA to produce proteins. The intracellular translateome of a cell can be modified by various factors and disease states, but it is impossible to individually measure all factors involved when there is no comprehensive understanding of eukaryotic translation. The present work outlines the use of a coupled transcription and translation cell-free protein expression system to produce recombinant proteins derived from human donor peripheral blood mononuclear cells (PBMCs) activated with phytohemagglutinin-M (PHA-M). The methods outlined here could result in tools to aid immunology, gene therapy, cell therapy, and synthetic biology research and provide a convenient and holistic method to study and assess the intracellular translation environment of primary immune cells.
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Affiliation(s)
- David Burgenson
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Jonathan Linton
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Xudong Ge
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Yordan Kostov
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Leah Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Gregory L. Szeto
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland 21201, United States
| | - Govind Rao
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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64
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Ueta M, Wada C, Wada A. YkgM and YkgO maintain translation by replacing their paralogs, zinc‐binding ribosomal proteins L31 and L36, with identical activities. Genes Cells 2020; 25:562-581. [DOI: 10.1111/gtc.12796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022]
Affiliation(s)
| | | | - Akira Wada
- Yoshida Biological Laboratory Kyoto Japan
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65
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Jaroentomeechai T, Taw MN, Li M, Aquino A, Agashe N, Chung S, Jewett MC, DeLisa MP. Cell-Free Synthetic Glycobiology: Designing and Engineering Glycomolecules Outside of Living Cells. Front Chem 2020; 8:645. [PMID: 32850660 PMCID: PMC7403607 DOI: 10.3389/fchem.2020.00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Glycans and glycosylated biomolecules are directly involved in almost every biological process as well as the etiology of most major diseases. Hence, glycoscience knowledge is essential to efforts aimed at addressing fundamental challenges in understanding and improving human health, protecting the environment and enhancing energy security, and developing renewable and sustainable resources that can serve as the source of next-generation materials. While much progress has been made, there remains an urgent need for new tools that can overexpress structurally uniform glycans and glycoconjugates in the quantities needed for characterization and that can be used to mechanistically dissect the enzymatic reactions and multi-enzyme assembly lines that promote their construction. To address this technology gap, cell-free synthetic glycobiology has emerged as a simplified and highly modular framework to investigate, prototype, and engineer pathways for glycan biosynthesis and biomolecule glycosylation outside the confines of living cells. From nucleotide sugars to complex glycoproteins, we summarize here recent efforts that harness the power of cell-free approaches to design, build, test, and utilize glyco-enzyme reaction networks that produce desired glycomolecules in a predictable and controllable manner. We also highlight novel cell-free methods for shedding light on poorly understood aspects of diverse glycosylation processes and engineering these processes toward desired outcomes. Taken together, cell-free synthetic glycobiology represents a promising set of tools and techniques for accelerating basic glycoscience research (e.g., deciphering the "glycan code") and its application (e.g., biomanufacturing high-value glycomolecules on demand).
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - May N. Taw
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Mingji Li
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Alicia Aquino
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Ninad Agashe
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Sean Chung
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
| | - Matthew P. DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
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66
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Dalphin MD, Stangl AJ, Liu Y, Cavagnero S. KLR-70: A Novel Cationic Inhibitor of the Bacterial Hsp70 Chaperone. Biochemistry 2020; 59:1946-1960. [PMID: 32326704 DOI: 10.1021/acs.biochem.0c00320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The heat-shock factor Hsp70 and other molecular chaperones play a central role in nascent protein folding. Elucidating the task performed by individual chaperones within the complex cellular milieu, however, has been challenging. One strategy for addressing this goal has been to monitor protein biogenesis in the absence and presence of inhibitors of a specific chaperone, followed by analysis of folding outcomes under both conditions. In this way, the role of the chaperone of interest can be discerned. However, development of chaperone inhibitors, including well-known proline-rich antimicrobial peptides, has been fraught with undesirable side effects, including decreased protein expression yields. Here, we introduce KLR-70, a rationally designed cationic inhibitor of the Escherichia coli Hsp70 chaperone (also known as DnaK). KLR-70 is a 14-amino acid peptide bearing naturally occurring residues and engineered to interact with the DnaK substrate-binding domain. The interaction of KLR-70 with DnaK is enantioselective and is characterized by high affinity in a buffered solution. Importantly, KLR-70 does not significantly interact with the DnaJ and GroEL/ES chaperones, and it does not alter nascent protein biosynthesis yields across a wide concentration range. Some attenuation of the anti-DnaK activity of KLR-70, however, has been observed in the complex E. coli cell-free environment. Interestingly, the d enantiomer D-KLR-70, unlike its all-L KLR-70 counterpart, does not bind the DnaK and DnaJ chaperones, yet it strongly inhibits translation. This outcome suggests that the two enantiomers (KLR-70 and D-KLR-70) may serve as orthogonal inhibitors of chaperone binding and translation. In summary, KLR-70 is a novel chaperone inhibitor with high affinity and selectivity for bacterial Hsp70 and with considerable potential to help in parsing out the role of Hsp70 in nascent protein folding.
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Affiliation(s)
- Matthew D Dalphin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew J Stangl
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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67
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Kelwick RJR, Webb AJ, Freemont PS. Biological Materials: The Next Frontier for Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:399. [PMID: 32478045 PMCID: PMC7235315 DOI: 10.3389/fbioe.2020.00399] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Alexander J. Webb
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- The London Biofoundry, Imperial College Translation & Innovation Hub, London, United Kingdom
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, United Kingdom
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68
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Affiliation(s)
- Nathaniel J Gaut
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
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69
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Ribosome Dimerization Protects the Small Subunit. J Bacteriol 2020; 202:JB.00009-20. [PMID: 32123037 PMCID: PMC7186458 DOI: 10.1128/jb.00009-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/25/2020] [Indexed: 01/21/2023] Open
Abstract
When nutrients become scarce, bacteria can enter an extended state of quiescence. A major challenge of this state is how to preserve ribosomes for the return to favorable conditions. Here, we show that the ribosome dimerization protein hibernation-promoting factor (HPF) functions to protect essential ribosomal proteins. Ribosomes isolated from strains lacking HPF (Δhpf) or encoding a mutant allele of HPF that binds the ribosome but does not mediate dimerization were substantially depleted of the small subunit proteins S2 and S3. Strikingly, these proteins are located directly at the ribosome dimer interface. We used single-particle cryo-electron microscopy (cryo-EM) to further characterize these ribosomes and observed that a high percentage of ribosomes were missing S2, S3, or both. These data support a model in which the ribosome dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome function. HPF is almost universally conserved in bacteria, and HPF deletions in diverse species exhibit decreased viability during starvation. Our data provide mechanistic insight into this phenotype and establish a mechanism for how HPF protects ribosomes during quiescence.IMPORTANCE The formation of ribosome dimers during periods of dormancy is widespread among bacteria. Dimerization is typically mediated by a single protein, hibernation-promoting factor (HPF). Bacteria lacking HPF exhibit strong defects in viability and pathogenesis and, in some species, extreme loss of rRNA. The mechanistic basis of these phenotypes has not been determined. Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves ribosomes by preventing the loss of essential ribosomal proteins at the dimer interface. This protection may explain phenotypes associated with the loss of HPF, since ribosome protection would aid survival during nutrient limitation and impart a strong selective advantage when the bacterial cell rapidly reinitiates growth in the presence of sufficient nutrients.
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70
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Abstract
Synthetic biology is a field of scientific research that applies engineering principles to living organisms and living systems. It is a field that is increasing in scope with respect to organisms engineered, practical outcomes, and systems integration. There is a commercial dimension as well, where living organisms are engineered as green technologies that could offer alternatives to industrial standards in the pharmaceutical and petroleum-based chemical industries. This review attempts to provide an introduction to this field as well as a consideration of important contributions that exemplify how synthetic biology may be commensurate or even disproportionate with the complexity of living systems. The engineerability of living systems remains a difficult task, yet advancements are reported at an ever-increasing pace.
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Affiliation(s)
- Martin M Hanczyc
- University of Trento, Department of Cellular, Computational, and Integrative Biology (CIBIO)
- University of New Mexico, Chemical and Biological Engineering.
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71
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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72
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Abstract
A functional characterization of channel proteins has been performed using planar lipid bilayers as the following procedure. For bacterial channels, such as the KcsA potassium channel, channel proteins were synthesized in Escherichia coli, followed by solubilization, purification, and incorporation into liposomes. Similarly, channel proteins were synthesized using an in vitro transcription/translation kit in the presence of liposomes. Then, these liposome-incorporated channels were served for electrophysiological recordings after liposome fusion into a preformed planar lipid bilayer. Here, we established a straightforward method for concurrent channel synthesis and functional measurement using a water-in-oil bubble bilayer system. Channel proteins were synthesized in vitro within a water-in-oil bubble, having a lipid bilayer at the contact with another bubble (in bulla synthesis). The channels were spontaneously incorporated into the lipid bilayer under application of the membrane potential, and we successfully detected nascent channel activities. This way our experiment has mimicked bacterial synthetic membrane in the presence of a resting membrane potential. Technical details for establishing the in bulla expression system are described.
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73
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Ling J, Fan C, Qin H, Wang M, Chen J, Wittung‐Stafshede P, Zhu TF. Mirror‐Image 5S Ribonucleoprotein Complexes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jun‐Jie Ling
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Chuyao Fan
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Hong Qin
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Min Wang
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Ji Chen
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Pernilla Wittung‐Stafshede
- Chemical Biology DivisionDepartment of Biology and Biological EngineeringChalmers University of Technology 41296 Gothenburg Sweden
| | - Ting F. Zhu
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
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74
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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75
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Escherichia coli Extract-Based Cell-Free Expression System as an Alternative for Difficult-to-Obtain Protein Biosynthesis. Int J Mol Sci 2020; 21:ijms21030928. [PMID: 32023820 PMCID: PMC7037961 DOI: 10.3390/ijms21030928] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Before utilization in biomedical diagnosis, therapeutic treatment, and biotechnology, the diverse variety of peptides and proteins must be preliminarily purified and thoroughly characterized. The recombinant DNA technology and heterologous protein expression have helped simplify the isolation of targeted polypeptides at high purity and their structure-function examinations. Recombinant protein expression in Escherichia coli, the most-established heterologous host organism, has been widely used to produce proteins of commercial and fundamental research interests. Nonetheless, many peptides/proteins are still difficult to express due to their ability to slow down cell growth or disrupt cellular metabolism. Besides, special modifications are often required for proper folding and activity of targeted proteins. The cell-free (CF) or in vitro recombinant protein synthesis system enables the production of such difficult-to-obtain molecules since it is possible to adjust reaction medium and there is no need to support cellular metabolism and viability. Here, we describe E. coli-based CF systems, the optimization steps done toward the development of highly productive and cost-effective CF methodology, and the modification of an in vitro approach required for difficult-to-obtain protein production.
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76
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Yamasaki A, Alam JM, Noshiro D, Hirata E, Fujioka Y, Suzuki K, Ohsumi Y, Noda NN. Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates. Mol Cell 2020; 77:1163-1175.e9. [PMID: 31995729 DOI: 10.1016/j.molcel.2019.12.026] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/22/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022]
Abstract
Clearance of biomolecular condensates by selective autophagy is thought to play a crucial role in cellular homeostasis. However, the mechanism underlying selective autophagy of condensates and whether liquidity determines a condensate's susceptibility to degradation by autophagy remain unknown. Here, we show that the selective autophagic cargo aminopeptidase I (Ape1) undergoes phase separation to form semi-liquid droplets. The Ape1-specific receptor protein Atg19 localizes to the surface of Ape1 droplets both in vitro and in vivo, with the "floatability" of Atg19 preventing its penetration into droplets. In vitro reconstitution experiments reveal that Atg19 and lipidated Atg8 are necessary and sufficient for selective sequestration of Ape1 droplets by membranes. This sequestration is impaired by mutational solidification of Ape1 droplets or diminished ability of Atg19 to float. Taken together, we propose that cargo liquidity and the presence of sufficient amounts of autophagic receptor on cargo are crucial for selective autophagy of biomolecular condensates.
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Affiliation(s)
- Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Jahangir Md Alam
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Life Science Data Research Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Collaborative Research Institute for Innovative Microbiology, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
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77
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Lukasiewicz AJ, Contreras LM. Antisense probing of dynamic RNA structures. Methods 2020; 183:76-83. [PMID: 31991194 DOI: 10.1016/j.ymeth.2020.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 01/20/2023] Open
Abstract
RNA regulation is influenced by the dynamic changes in conformational accessibility on the transcript. Here we discuss the initial validation of a cell-free antisense probing method for structured RNAs, using the Tetrahymena group I intron as a control target. We observe changes in signal that qualitatively match prior traditional DMS footprinting experiments. Importantly, we have shown that application of this technique can elucidate new RNA information given its sensitivity for detecting rare intermediates that are not as readily observed by single-hit kinetics chemical probing techniques. Observing changes in RNA accessibility has broad applications in determining the effect that regulatory elements have on regional structures. We speculate that this method could be useful in quickly observing those interactions, along with other phenomena that influence RNA accessibility including RNA-RNA interactions and small molecules.
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Affiliation(s)
- Alexandra J Lukasiewicz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States.
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78
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Ling JJ, Fan C, Qin H, Wang M, Chen J, Wittung-Stafshede P, Zhu TF. Mirror-Image 5S Ribonucleoprotein Complexes. Angew Chem Int Ed Engl 2020; 59:3724-3731. [PMID: 31841243 PMCID: PMC7217020 DOI: 10.1002/anie.201914799] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Indexed: 12/01/2022]
Abstract
After realizing mirror‐image genetic replication, transcription, and reverse transcription, the biggest challenge in establishing a mirror‐image version of the central dogma is to build a mirror‐image ribosome‐based translation machine. Here, we chemically synthesized the natural and mirror‐image versions of three ribosomal proteins (L5, L18, and L25) in the large subunit of the Escherichia coli ribosome with post‐translational modifications. We show that the synthetic mirror‐image proteins can fold in vitro despite limited efficiency and assemble with enzymatically transcribed mirror‐image 5S ribosomal RNA into ribonucleoprotein complexes. In addition, the RNA–protein interactions are chiral‐specific in that the mirror‐image ribosomal proteins do not bind with natural 5S ribosomal RNA and vice versa. The synthesis and assembly of mirror‐image 5S ribonucleoprotein complexes are important steps towards building a functional mirror‐image ribosome.
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Affiliation(s)
- Jun-Jie Ling
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Hong Qin
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Min Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Ji Chen
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Pernilla Wittung-Stafshede
- Chemical Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
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79
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Nakamoto K, Abe N, Tsuji G, Kimura Y, Tomoike F, Shimizu Y, Abe H. Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation. Chem Commun (Camb) 2020; 56:6217-6220. [DOI: 10.1039/d0cc02140g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circular RNA without a stop codon enables rolling circle translation. we carried out one-pot chemical synthesis of circular RNA from RNA fragments. The synthesized circular RNAs acted as translation templates, despite the presence of unnatural phosphoramidate linkages.
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Affiliation(s)
| | - Naoko Abe
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
| | - Genichiro Tsuji
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
- National Institute of Health Sciences
| | | | - Fumiaki Tomoike
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
- Faculty of Science
| | | | - Hiroshi Abe
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
- JST CREST, Science and Technology Agency
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80
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Lyu Y, Peng R, Liu H, Kuai H, Mo L, Han D, Li J, Tan W. Protocells programmed through artificial reaction networks. Chem Sci 2019; 11:631-642. [PMID: 34123035 PMCID: PMC8145531 DOI: 10.1039/c9sc05043d] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
As the smallest unit of life, cells attract interest due to their structural complexity and functional reliability. Protocells assembled by inanimate components are created as an artificial entity to mimic the structure and some essential properties of a natural cell, and artificial reaction networks are used to program the functions of protocells. Although the bottom-up construction of a protocell that can be considered truly ‘alive’ is still an ambitious goal, these man-made constructs with a certain degree of ‘liveness’ can offer effective tools to understand fundamental processes of cellular life, and have paved the new way for bionic applications. In this review, we highlight both the milestones and recent progress of protocells programmed by artificial reaction networks, including genetic circuits, enzyme-assisted non-genetic circuits, prebiotic mimicking reaction networks, and DNA dynamic circuits. Challenges and opportunities have also been discussed. In this review, the milestones and recent progress of protocells programmed by various types of artificial reaction networks are highlighted.![]()
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Affiliation(s)
- Yifan Lyu
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Liuting Mo
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Da Han
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China
| | - Juan Li
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China.,MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
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81
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Controlled deprotection and release of a small molecule from a compartmented synthetic tissue module. Commun Chem 2019. [DOI: 10.1038/s42004-019-0244-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
AbstractSynthetic tissues built from communicating aqueous droplets offer potential applications in biotechnology, however, controlled release of their contents has not been achieved. Here we construct two-droplet synthetic tissue modules that function in an aqueous environment. One droplet contains a cell-free protein synthesis system and a prodrug-activating enzyme and the other a small-molecule prodrug analog. When a Zn2+-sensitive protein pore is made in the first droplet, it allows the prodrug to migrate from the second droplet and become activated by the enzyme. With Zn2+ in the external medium, the activated molecule is retained in the module until it is released on-demand by a divalent cation chelator. The module is constructed in such a manner that one or more, potentially with different properties, might be incorporated into extended synthetic tissues, including patterned materials generated by 3D-printing. Such modules will thereby increase the sophistication of synthetic tissues for applications including controlled multidrug delivery.
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82
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Chiuchiú D, Tu Y, Pigolotti S. Error-Speed Correlations in Biopolymer Synthesis. PHYSICAL REVIEW LETTERS 2019; 123:038101. [PMID: 31386470 PMCID: PMC7402413 DOI: 10.1103/physrevlett.123.038101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Indexed: 06/10/2023]
Abstract
Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. The performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these single-molecule processes, both error and speed are inherently stochastic quantities. In this Letter, we study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. This means that, under equal conditions, polymers that are synthesized faster due to a fluctuation tend to have either better or worse errors than the average. The error-correction mechanism implemented by the enzyme determines which of the two cases holds. For example, discrimination in the forward reaction rates tends to grant smaller errors to polymers with faster synthesis. The opposite occurs for discrimination in monomer rejection rates. Our results provide an experimentally feasible way to identify error-correction mechanisms by measuring the error-speed correlations.
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Affiliation(s)
- Davide Chiuchiú
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yuhai Tu
- IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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83
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Dwidar M, Seike Y, Kobori S, Whitaker C, Matsuura T, Yokobayashi Y. Programmable Artificial Cells Using Histamine-Responsive Synthetic Riboswitch. J Am Chem Soc 2019; 141:11103-11114. [PMID: 31241330 DOI: 10.1021/jacs.9b03300] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Artificial cells that encapsulate DNA-programmable protein expression machinery are emerging as an attractive platform for studying fundamental cellular properties and applications in synthetic biology. However, interfacing these artificial cells with the complex and dynamic chemical environment remains a major and urgent challenge. We demonstrate that the repertoire of molecules that artificial cells respond to can be expanded by synthetic RNA-based gene switches, or riboswitches. We isolated an RNA aptamer that binds histamine with high affinity and specificity and used it to design robust riboswitches that activate protein expression in the presence of histamine. Finally, the riboswitches were incorporated in artificial cells to achieve controlled release of an encapsulated small molecule and to implement a self-destructive kill-switch. Synthetic riboswitches should serve as modular and versatile interfaces to link artificial cell phenotypes with the complex chemical environment.
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Affiliation(s)
- Mohammed Dwidar
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
| | - Yusuke Seike
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
| | - Charles Whitaker
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
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84
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Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding. Nat Commun 2019; 10:2709. [PMID: 31221966 PMCID: PMC6586675 DOI: 10.1038/s41467-019-10647-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
Protein folding can begin co-translationally. Due to the difference in timescale between folding and synthesis, co-translational folding is thought to occur at equilibrium for fast-folding domains. In this scenario, the folding kinetics of stalled ribosome-bound nascent chains should match the folding of nascent chains in real time. To test if this assumption is true, we compare the folding of a ribosome-bound, multi-domain calcium-binding protein stalled at different points in translation with the nascent chain as is it being synthesized in real-time, via optical tweezers. On stalled ribosomes, a misfolded state forms rapidly (1.5 s). However, during translation, this state is only attained after a long delay (63 s), indicating that, unexpectedly, the growing polypeptide is not equilibrated with its ensemble of accessible conformations. Slow equilibration on the ribosome can delay premature folding until adequate sequence is available and/or allow time for chaperone binding, thus promoting productive folding. Co-translational protein folding is thought to occur at equilibrium for fast-folding domains. Here authors use optical tweezers to show that the folding kinetics of stalled ribosome-bound nascent chains do not match the folding of nascent chains in real time.
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85
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Kamiura R, Matsuda F, Ichihashi N. Survival of membrane-damaged Escherichia coli in a cytosol-mimicking solution. J Biosci Bioeng 2019; 128:558-563. [PMID: 31182278 DOI: 10.1016/j.jbiosc.2019.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 11/19/2022]
Abstract
Selective permeability of cell membrane is critically important for cell survival. The damage caused to cell membrane by pore-forming antimicrobial peptides may result in the loss of selective permeability and leakage of intracellular molecules, eventually leading to cell death. Here, we examined whether the membrane-damaged Escherichia coli cells survive in a cytosol-mimicking solution (CMS), which compensates for the lethal leakage of intracellular molecules. We prepared a CMS comprising 34 low molecular weight compounds from the cytosol and found that the cells were able to grow in CMS even in the presence of a pore-forming peptide, melittin. We confirmed that the melittin-treated cells lost selective membrane permeability by staining with membrane-impermeable dyes, propidium iodide and SYTOX green. Some stained cells maintained the colony formation ability in CMS. These results provide an evidence that E. coli cells can at least partially survive in the CMS even after the temporary impairment of membrane selective permeability. This study demonstrates a technique that allows temporal loss of the selective permeability of the cell membrane while maintaining the viability of cells that may be useful for the introduction of membrane-impermeable molecules into E. coli cells.
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Affiliation(s)
- Rikuto Kamiura
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Bioscience, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Arts and Science, Komaba Institute for Science, Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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86
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Gao W, Cho E, Liu Y, Lu Y. Advances and Challenges in Cell-Free Incorporation of Unnatural Amino Acids Into Proteins. Front Pharmacol 2019; 10:611. [PMID: 31191324 PMCID: PMC6549004 DOI: 10.3389/fphar.2019.00611] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022] Open
Abstract
Incorporation of unnatural amino acids (UNAAs) into proteins currently is an active biological research area for various fundamental and applied science. In this context, cell-free synthetic biology (CFSB) has been developed and recognized as a robust testing and biomanufacturing platform for highly efficient UNAA incorporation. It enables the orchestration of unnatural biological machinery toward an exclusive user-defined objective of unnatural protein synthesis. This review aims to overview the principles of cell-free unnatural protein synthesis (CFUPS) systems, their advantages, different UNAA incorporation approaches, and recent achievements. These have catalyzed cutting-edge research and diverse emerging applications. Especially, present challenges and future trends are focused and discussed. With the development of CFSB and the fusion with other advanced next-generation technologies, CFUPS systems would explicitly deliver their values for biopharmaceutical applications.
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Affiliation(s)
- Wei Gao
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Eunhee Cho
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yingying Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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87
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Evolving methods for rational de novo design of functional RNA molecules. Methods 2019; 161:54-63. [PMID: 31059832 DOI: 10.1016/j.ymeth.2019.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022] Open
Abstract
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to experimental screening and selection pipelines. In this review, we describe methods common to many such computational approaches, thoroughly dissect these methods and highlight open questions for the individual steps. Initially, it is essential to investigate the biological target system, the regulatory mechanism that will be exploited, as well as the desired components in order to define design objectives. Subsequent computational design is needed to combine the selected components and to obtain novel functionality. This process can usually be split into constrained sequence sampling, the formulation of an optimization problem and an in silico analysis to narrow down the number of candidates with respect to secondary goals. Finally, experimental analysis is important to check whether the defined design objectives are indeed met in the target environment and detailed characterization experiments should be performed to improve the mechanistic models and detect missing design requirements.
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88
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Endoh T, Sugimoto N. Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency. Molecules 2019; 24:molecules24081613. [PMID: 31022854 PMCID: PMC6514569 DOI: 10.3390/molecules24081613] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 11/16/2022] Open
Abstract
During translation, intracellular mRNA folds co-transcriptionally and must refold following the passage of ribosome. The mRNAs can be entrapped in metastable structures during these folding events. In the present study, we evaluated the conformational dynamics of the kinetically favored, metastable, and hairpin-like structure, which disturbs the thermodynamically favored G-quadruplex structure, and its effect on co-transcriptional translation in prokaryotic cells. We found that nascent mRNA forms a metastable hairpin-like structure during co-transcriptional folding instead of the G-quadruplex structure. When the translation progressed co-transcriptionally before the metastable hairpin-like structure transition to the G-quadruplex, function of the G-quadruplex as a roadblock of the ribosome was sequestered. This suggested that kinetically formed RNA structures had a dominant effect on gene expression in prokaryotes. The results of this study indicate that it is critical to consider the conformational dynamics of RNA-folding to understand the contributions of the mRNA structures in controlling gene expression.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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89
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Stano P. Gene Expression Inside Liposomes: From Early Studies to Current Protocols. Chemistry 2019; 25:7798-7814. [DOI: 10.1002/chem.201806445] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA)University of Salento, Ecotekne 73100 Lecce Italy
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90
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Blanken D, van Nies P, Danelon C. Quantitative imaging of gene-expressing liposomes reveals rare favorable phenotypes. Phys Biol 2019; 16:045002. [PMID: 30978176 DOI: 10.1088/1478-3975/ab0c62] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The biosynthesis of proteins from genomic DNA is a universal process in every living organism. Building a synthetic cell using separate biological parts hence implies to reconstitute a minimal gene expression apparatus and to compartmentalize it in a cell-mimicking environment. Previous studies have demonstrated that the PURE (Protein synthesis Using Recombinant Elements) system could be functionally encapsulated inside lipid vesicles. However, quantitative insights on functional consequences of spatial confinement of PURE system reactions remain scarce, which has hampered the full exploitation of gene-expressing liposomes as the fundamental unit to build an artificial cell. We report on direct imaging of tens of thousands of gene-expressing liposomes per sample allowing us to assess sub-population features in a statistically relevant manner. Both the vesicle size (diameter <10 μm) and lipid composition (mixture of phospholipids with zwitterionic and negatively charged headgroups, including cardiolipin) are compatible with the properties of bacterial cells. Therefore, our liposomes provide a suitable chassis to host the Escherichia coli-derived PURE translation machinery and other bacterial processes in future developments. The potential of high-content imaging to identify rare phenotypes is demonstrated by the fact that a subset of the liposome population exhibits a remarkably high yield of synthesized protein or a prolonged expression lifespan that surpasses the performance of ensemble liposome-averaged and bulk reactions. Among the three commercial PURE systems tested, PUREfrex2.0 offers the most favorable phenotypes displaying both high yield and long protein synthesis lifespan. Moreover, probing membrane permeability reveals a large heterogeneity amongst liposomes. In situ expression and membrane embedding of the pore-forming connexin leads to a characteristic permeability time profile, while increasing the fraction of permeable liposomes in the population. We see diversity in gene expression dynamics and membrane permeability as an opportunity to complement a rational design approach aiming at further implementing biological functions in liposome-based synthetic cells.
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Affiliation(s)
- Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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91
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Kumar S, Dangi AK, Shukla P, Baishya D, Khare SK. Thermozymes: Adaptive strategies and tools for their biotechnological applications. BIORESOURCE TECHNOLOGY 2019; 278:372-382. [PMID: 30709766 DOI: 10.1016/j.biortech.2019.01.088] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 05/10/2023]
Abstract
In today's scenario of global climate change, there is a colossal demand for sustainable industrial processes and enzymes from thermophiles. Plausibly, thermozymes are an important toolkit, as they are known to be polyextremophilic in nature. Small genome size and diverse molecular conformational modifications have been implicated in devising adaptive strategies. Besides, the utilization of chemical technology and gene editing attributions according to mechanical necessities are the additional key factor for efficacious bioprocess development. Microbial thermozymes have been extensively used in waste management, biofuel, food, paper, detergent, medicinal and pharmaceutical industries. To understand the strength of enzymes at higher temperatures different models utilize X-ray structures of thermostable proteins, machine learning calculations, neural networks, but unified adaptive measures are yet to be totally comprehended. The present review provides a recent updates on thermozymes and various interdisciplinary applications including the aspects of thermophiles bioengineering utilizing synthetic biology and gene editing tools.
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Affiliation(s)
- Sumit Kumar
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Arun K Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Institute of Science and Technology, Gauhati University, Guwahati 781014, Assam, India
| | - Sunil K Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India.
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92
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Bilal M, Iqbal HM. Microbial-derived biosensors for monitoring environmental contaminants: Recent advances and future outlook. PROCESS SAFETY AND ENVIRONMENTAL PROTECTION 2019. [DOI: 10.1016/j.psep.2019.01.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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93
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Gregorio NE, Levine MZ, Oza JP. A User's Guide to Cell-Free Protein Synthesis. Methods Protoc 2019; 2:E24. [PMID: 31164605 PMCID: PMC6481089 DOI: 10.3390/mps2010024] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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94
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Kai L, Schwille P. Cell-Free Protein Synthesis and Its Perspectives for Assembling Cells from the Bottom-Up. ACTA ACUST UNITED AC 2019; 3:e1800322. [PMID: 32648712 DOI: 10.1002/adbi.201800322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Indexed: 12/20/2022]
Abstract
The underlying idea of synthetic biology is that biological reactions/modules/systems can be precisely engineered and controlled toward desired products. Numerous efforts in the past decades in deciphering the complexity of biological systems in vivo have led to a variety of tools for synthetic biology, especially based on recombinant DNA. However, one generic limitation of all living systems is that the vast majority of energy input is dedicated to maintain the system as a whole, rather than the small part of interest. Cell-free synthetic biology is aiming at exactly this fundamental limitation, providing the next level of flexibility for engineering and designing biological systems in vitro. New technology has continuously inspired cell-free biology and extended its applications, including gene circuits, spatiotemporally controlled pathways, coactivated catalysts systems, and rationally designed multienzyme pathways, in particular, minimal cell construction. In the context of this special issue, discussing work being carried out in the "MaxSynBio" consortium, the advances in characterizing stochasticity and dynamics of cell-free protein synthesis within cell-sized compartments, as well as the molecular crowding effect, are discussed. The organization of spatial heterogeneity is the key prerequisite for achieving hierarchy and stepwise assembly of minimal cells from the bottom-up.
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Affiliation(s)
- Lei Kai
- School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, 221116, Xuzhou, P. R. China.,Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
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95
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Doerr A, de Reus E, van Nies P, van der Haar M, Wei K, Kattan J, Wahl A, Danelon C. Modelling cell-free RNA and protein synthesis with minimal systems. Phys Biol 2019; 16:025001. [DOI: 10.1088/1478-3975/aaf33d] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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96
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Tsiamantas C, Otero-Ramirez ME, Suga H. Discovery of Functional Macrocyclic Peptides by Means of the RaPID System. Methods Mol Biol 2019; 2001:299-315. [PMID: 31134577 DOI: 10.1007/978-1-4939-9504-2_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flexizymes, highly flexible tRNA aminoacylation ribozymes, have enabled charging of virtually any amino acid (including non-proteogenic ones) onto tRNA molecules. Coupling to a custom-made in vitro translation system, namely the flexible in vitro translation (FIT) system, has unveiled the remarkable tolerance of the ribosome toward molecules, remote from what nature has selected to carry out its elaborate functions. Among the very diverse molecules and chemistries that have been ribosomally incorporated, a plethora of entities capable of mediating intramolecular cyclization have revolutionized the design and discovery of macrocyclic peptides. These macrocyclization reactions (which can be spontaneous, chemical, or enzymatic) have all served as tools for the discovery of peptides with natural-like structures and properties. Coupling of the FIT system and mRNA display techniques, known as the random non-standard peptide integrated discovery (RaPID) system, has in turn allowed for the simultaneous screening of trillions of macrocyclic peptides against challenging biological targets. The macrocyclization methodologies are chosen depending on the structural and functional characteristics of the desired molecule. Thus, they can emanate from the peptide's N-terminus or its side chains, attributing flexibility or rigidity, or even result in the installation of fluorescent probes.
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Affiliation(s)
- Christos Tsiamantas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Manuel E Otero-Ramirez
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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97
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Stano P. Is Research on "Synthetic Cells" Moving to the Next Level? Life (Basel) 2018; 9:E3. [PMID: 30587790 PMCID: PMC6463193 DOI: 10.3390/life9010003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/15/2022] Open
Abstract
"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento; Ecotekne-S.P. Lecce-Monteroni, I-73100 Lecce, Italy.
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98
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Beppu K, Izri Z, Maeda YT, Sakamoto R. Geometric Effect for Biological Reactors and Biological Fluids. Bioengineering (Basel) 2018; 5:E110. [PMID: 30551608 PMCID: PMC6316181 DOI: 10.3390/bioengineering5040110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 01/21/2023] Open
Abstract
As expressed "God made the bulk; the surface was invented by the devil" by W. Pauli, the surface has remarkable properties because broken symmetry in surface alters the material properties. In biological systems, the smallest functional and structural unit, which has a functional bulk space enclosed by a thin interface, is a cell. Cells contain inner cytosolic soup in which genetic information stored in DNA can be expressed through transcription (TX) and translation (TL). The exploration of cell-sized confinement has been recently investigated by using micron-scale droplets and microfluidic devices. In the first part of this review article, we describe recent developments of cell-free bioreactors where bacterial TX-TL machinery and DNA are encapsulated in these cell-sized compartments. Since synthetic biology and microfluidics meet toward the bottom-up assembly of cell-free bioreactors, the interplay between cellular geometry and TX-TL advances better control of biological structure and dynamics in vitro system. Furthermore, biological systems that show self-organization in confined space are not limited to a single cell, but are also involved in the collective behavior of motile cells, named active matter. In the second part, we describe recent studies where collectively ordered patterns of active matter, from bacterial suspensions to active cytoskeleton, are self-organized. Since geometry and topology are vital concepts to understand the ordered phase of active matter, a microfluidic device with designed compartments allows one to explore geometric principles behind self-organization across the molecular scale to cellular scale. Finally, we discuss the future perspectives of a microfluidic approach to explore the further understanding of biological systems from geometric and topological aspects.
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Affiliation(s)
- Kazusa Beppu
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan.
| | - Ziane Izri
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan.
| | - Yusuke T Maeda
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan.
| | - Ryota Sakamoto
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan.
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99
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Ziblat R, Weaver JC, Arriaga LR, Chong S, Weitz DA. Determining the lipid specificity of insoluble protein transmembrane domains. LAB ON A CHIP 2018; 18:3561-3569. [PMID: 30406786 DOI: 10.1039/c8lc00311d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
While the specificity of protein-lipid interactions is a key feature in the function of biological membranes, studying the specifics of these interactions is challenging because most membrane proteins are insoluble in water due to the hydrophobic nature of their transmembrane domains (TMDs). Here, we introduce a method that overcomes this solubility limitation and identifies the affinity profile of protein TMDs to specific lipid formulations. Using 5 human TMDs as a sample group, our results demonstrate that TMDs are highly selective and that these specific lipid-TMD interactions can involve either a single lipid, or the combination of multiple lipid species.
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Affiliation(s)
- R Ziblat
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
| | - J C Weaver
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - L R Arriaga
- Department of Physical Chemistry, Universidad Complutense, Madrid, 28040, Spain
| | - S Chong
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - D A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA. and Department of Physics, Harvard University, Cambridge, MA02138, USA
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100
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Petroll K, Kopp D, Care A, Bergquist PL, Sunna A. Tools and strategies for constructing cell-free enzyme pathways. Biotechnol Adv 2018; 37:91-108. [PMID: 30521853 DOI: 10.1016/j.biotechadv.2018.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/22/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Abstract
Single enzyme systems or engineered microbial hosts have been used for decades but the notion of assembling multiple enzymes into cell-free synthetic pathways is a relatively new development. The extensive possibilities that stem from this synthetic concept makes it a fast growing and potentially high impact field for biomanufacturing fine and platform chemicals, pharmaceuticals and biofuels. However, the translation of individual single enzymatic reactions into cell-free multi-enzyme pathways is not trivial. In reality, the kinetics of an enzyme pathway can be very inadequate and the production of multiple enzymes can impose a great burden on the economics of the process. We examine here strategies for designing synthetic pathways and draw attention to the requirements of substrates, enzymes and cofactor regeneration systems for improving the effectiveness and sustainability of cell-free biocatalysis. In addition, we comment on methods for the immobilisation of members of a multi-enzyme pathway to enhance the viability of the system. Finally, we focus on the recent development of integrative tools such as in silico pathway modelling and high throughput flux analysis with the aim of reinforcing their indispensable role in the future of cell-free biocatalytic pathways for biomanufacturing.
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Affiliation(s)
- Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Peter L Bergquist
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Department of Molecular Medicine & Pathology, University of Auckland, Auckland, New Zealand
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia.
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