1
|
Aydin O, Passaro AP, Raman R, Spellicy SE, Weinberg RP, Kamm RD, Sample M, Truskey GA, Zartman J, Dar RD, Palacios S, Wang J, Tordoff J, Montserrat N, Bashir R, Saif MTA, Weiss R. Principles for the design of multicellular engineered living systems. APL Bioeng 2022; 6:010903. [PMID: 35274072 PMCID: PMC8893975 DOI: 10.1063/5.0076635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell-cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the "black box" of living cells.
Collapse
Affiliation(s)
| | - Austin P. Passaro
- Regenerative Bioscience Center, University of Georgia, Athens, Georgia 30602, USA
| | - Ritu Raman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Robert P. Weinberg
- School of Pharmacy, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts 02115, USA
| | | | - Matthew Sample
- Center for Ethics and Law in the Life Sciences, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sebastian Palacios
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jesse Tordoff
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nuria Montserrat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | | | - M. Taher A. Saif
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ron Weiss
- Author to whom correspondence should be addressed:
| |
Collapse
|
2
|
Fairbanks BD, Culver HR, Mavila S, Bowman CN. Towards High-Efficiency Synthesis of Xenonucleic Acids. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
3
|
Nurse P, Hayles J. Using genetics to understand biology. Heredity (Edinb) 2019; 123:4-13. [PMID: 31189902 PMCID: PMC6781147 DOI: 10.1038/s41437-019-0209-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Paul Nurse
- The Francis Crick Institute, 1, Midland Road, London, NW1 1AT, UK
| | | |
Collapse
|
4
|
Cannon JGD, Sherman RM, Wang VMY, Newman GA. Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding. Sci Rep 2015; 5:18054. [PMID: 26656258 PMCID: PMC4674897 DOI: 10.1038/srep18054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/02/2015] [Indexed: 01/01/2023] Open
Abstract
The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We observed significant matching between an amino acid’s nucleobase affinity and corresponding codon content in both the standard genetic code and mitochondrial variants. Furthermore, we showed that knowledge of nucleobase preferences allows statistically significant prediction of protein primary sequence from mRNA using purely physiochemical information. Interestingly, ribosomal primary sequences were more accurately predicted than non-ribosomal sequences, suggesting a potential role for direct amino acid-nucleobase interactions in the genesis of amino acid-based ribosomal components. Finally, we observed matching between amino acid-nucleobase affinities and corresponding mRNA sequences in 35 evolutionarily diverse proteomes. We believe these results have important implications for the study of the evolutionary origins of the genetic code and protein-mRNA cross-regulation.
Collapse
Affiliation(s)
- John G D Cannon
- Department of Biology, Carleton College, 1 College Street, Northfield MN, 55057, United States
| | - Rachel M Sherman
- Department of Biology, Harvey Mudd College, 301 Platt Blvd, Claremont CA 91711, United States.,Department of Computer Science, Harvey Mudd College, 301 Platt Blvd, Claremont CA 91711, United States
| | - Victoria M Y Wang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Grace A Newman
- Department of Mathematics, Carleton College, 1 College Street, Northfield MN, 55057, United States
| |
Collapse
|
5
|
|
6
|
|
7
|
Biro JC. Coding nucleic acids are chaperons for protein folding: a novel theory of protein folding. Gene 2012; 515:249-57. [PMID: 23266645 DOI: 10.1016/j.gene.2012.12.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 11/29/2022]
Abstract
The arguments for nucleic acid chaperons are reviewed and three new lines of evidence are added. (1) It was found that amino acids encoded by codons in short nucleic acid loops frequently form turns and helices in the corresponding protein structures. (2) The amino acids encoded by partially complementary (1st and 3rd nucleotides) codons are more frequently co-located in the encoded proteins than expected by chance. (3) There are significant correlations between thermodynamic changes (ddG) caused by codon mutations in nucleic acids and the thermodynamic changes caused by the corresponding amino acid mutations in the encoded proteins. We conclude that the concept of the Proteomic Code and nucleic acid chaperons seems correct from the bioinformatics point of view, and we expect to see direct biochemical experiments and evidence in the near future.
Collapse
Affiliation(s)
- Jan C Biro
- Karolinska Institute, Stockholm, Sweden.
| |
Collapse
|
8
|
Lobanov AV, Turanov AA, Hatfield DL, Gladyshev VN. Dual functions of codons in the genetic code. Crit Rev Biochem Mol Biol 2010; 45:257-65. [PMID: 20446809 DOI: 10.3109/10409231003786094] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3'-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code.
Collapse
Affiliation(s)
- Alexey V Lobanov
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
9
|
PESTKA S, MARSHALL R, NIRENBERG M. RNA CODEWORDS AND PROTEIN SYNTHESIS. V. EFFECT OF STREPTOMYCIN ON THE FORMATION OF RIBOSOME-SRNA COMPLEXES. Proc Natl Acad Sci U S A 1996; 53:639-46. [PMID: 14338246 PMCID: PMC336990 DOI: 10.1073/pnas.53.3.639] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
10
|
BERNFIELD MR, NIRENBERG MW. RNA CODEWORDS AND PROTEIN SYNTHESIS. THE NUCLEOTIDE SEQUENCES OF MULTIPLE CODEWORDS FOR PHENYLALANINE, SERINE, LEUCINE, AND PROLINE. Science 1996; 147:479-84. [PMID: 14237203 DOI: 10.1126/science.147.3657.479] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
11
|
Ihler G, Nakada D. Selective binding of ribosomes to initiation sites on single-stranded DNA from bacterial viruses. Nature 1970; 228:239-42. [PMID: 4920920 DOI: 10.1038/228239a0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
12
|
|
13
|
Mitchell WM. A model for protein biosynthesis predicated on the concept of metastable states: a postulated role for genetic code degeneracy. Proc Natl Acad Sci U S A 1968; 61:742-7. [PMID: 5246005 PMCID: PMC225222 DOI: 10.1073/pnas.61.2.742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|
14
|
|
15
|
Evidence for the Enzymatic Binding of Aminoacyl Transfer Ribonucleic Acid to Rat Liver Ribosomes. J Biol Chem 1968. [DOI: 10.1016/s0021-9258(19)81735-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
16
|
|
17
|
Marshall RE, Caskey CT, Nirenberg M. Fine structure of RNA codewords recognized by bacterial, amphibian, and mammalian transfer RNA. Science 1967; 155:820-6. [PMID: 5335001 DOI: 10.1126/science.155.3764.820] [Citation(s) in RCA: 128] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nucleotide sequences of 50 RNA codons recognized by amphibian and mammalian liver transfer RNA preparations were determined and compared with those recognized by Escherichia coli transfer RNA. Almost identical translations were obtained with transfer RNA from guinea pig liver, Xenopus laevis liver (South African clawed toad), and E. coli. However, guinea pig and Xenopus transfer RNA differ markedly from E. coli transfer RNA in relative response to certain trinucleotides. Transfer RNA from mammalian liver, amphibian liver, and amphibian muscle respond similarly to trinucleotide codons. Thus the genetic code is essentially universal, but transfer RNA from one organism may differ from that of another in relative response to some codons.
Collapse
|
18
|
|
19
|
Chang FN, Sih CJ, Weisblum B. Lincomycin, an inhibitor of aminoacyl sRNA binding to ribosomes. Proc Natl Acad Sci U S A 1966; 55:431-8. [PMID: 5328728 PMCID: PMC224162 DOI: 10.1073/pnas.55.2.431] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|
20
|
|
21
|
|
22
|
|
23
|
Guest JR, Yanofsky C. Amino acid replacements associated with reversion and recombination within a coding unit. J Mol Biol 1965; 12:793-804. [PMID: 5323485 DOI: 10.1016/s0022-2836(65)80328-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
24
|
Brenner S, Stretton AO, Kaplan S. Genetic code: the 'nonsense' triplets for chain termination and their suppression. Nature 1965; 206:994-8. [PMID: 5320272 DOI: 10.1038/206994a0] [Citation(s) in RCA: 313] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
25
|
Nash HA, Bradley DF. Interactions between trinucleotides: the electrostatic contribution and its possible relation to the mechanism of translation of the genetic code. Biopolymers 1965; 3:261-73. [PMID: 5889542 DOI: 10.1002/bip.360030304] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
26
|
Nirenberg M, Leder P, Bernfield M, Brimacombe R, Trupin J, Rottman F, O'Neal C. RNA codewords and protein synthesis, VII. On the general nature of the RNA code. Proc Natl Acad Sci U S A 1965; 53:1161-8. [PMID: 5330357 PMCID: PMC301388 DOI: 10.1073/pnas.53.5.1161] [Citation(s) in RCA: 196] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|