1
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Cohen ZR, Todd ZR, Maibaum L, Catling DC, Black RA. Stabilization of Prebiotic Vesicles by Peptides Depends on Sequence and Chirality: A Mechanism for Selection of Protocell-Associated Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8971-8980. [PMID: 38629792 DOI: 10.1021/acs.langmuir.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Cells require oligonucleotides and polypeptides with specific, homochiral sequences to perform essential functions, but it is unclear how such oligomers were selected from random sequences at the origin of life. Cells were probably preceded by simple compartments such as fatty acid vesicles, and oligomers that increased the stability, growth, or division of vesicles could have thereby increased in frequency. We therefore tested whether prebiotic peptides alter the stability or growth of vesicles composed of a prebiotic fatty acid. We find that three of 15 dipeptides tested reduce salt-induced flocculation of vesicles. All three contain leucine, and increasing their length increases the efficacy. Also, leucine-leucine but not alanine-alanine increases the size of vesicles grown by multiple additions of micelles. In a molecular simulation, leucine-leucine docks to the membrane, with the side chains inserted into the hydrophobic core of the bilayer, while alanine-alanine fails to dock. Finally, the heterochiral forms of leucine-leucine, at a high concentration, rapidly shrink the vesicles and make them leakier and less stable to high pH than the homochiral forms do. Thus, prebiotic peptide-membrane interactions influence the flocculation, growth, size, leakiness, and pH stability of prebiotic vesicles, with differential effects due to sequence, length, and chirality. These differences could lead to a population of vesicles enriched for peptides with beneficial sequence and chirality, beginning selection for the functional oligomers that underpin life.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R Todd
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David C Catling
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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2
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Guo X, Su M. The Origin of Translation: Bridging the Nucleotides and Peptides. Int J Mol Sci 2022; 24:ijms24010197. [PMID: 36613641 PMCID: PMC9820756 DOI: 10.3390/ijms24010197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To reveal how the translation emerged in the prebiotic context, we start with the structure and dissection of tRNA, followed by the theory and hypothesis of tRNA and amino acid recognition. Last, we review how amino acids assemble on the tRNA and further form peptides. Understanding the origin of life will also promote our knowledge of artificial living systems.
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Affiliation(s)
- Xuyuan Guo
- School of Genetics and Microbiology, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, D02 PN40 Dublin, Ireland
| | - Meng Su
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Correspondence:
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3
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Xiong N, Xie D, Dong Y, Xue YP, Zheng YG. Efficient biosynthesis of 1-cyanocyclohexaneacetic acid using a highly soluble nitrilase by N-terminus modification of novel peptide tags. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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4
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Xue M, Black RA, Cohen ZR, Roehrich A, Drobny GP, Keller SL. Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids. J Phys Chem B 2021; 125:7933-7939. [PMID: 34283913 DOI: 10.1021/acs.jpcb.1c01485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes. For amino acids, the side chains and carboxylate contribute to the interaction. For dipeptides, the extent of binding is generally less than that of the constituent amino acids, implying that other mechanisms would be necessary to drive molecular evolution. Nevertheless, our results are consistent with a scheme in which the building blocks of the biological polymers colocalized with protocells prior to the emergence of RNA and proteins.
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Affiliation(s)
- Mengjun Xue
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
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5
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Tretyachenko V, Voráček V, Souček R, Fujishima K, Hlouchová K. CoLiDe: Combinatorial Library Design tool for probing protein sequence space. Bioinformatics 2021; 37:482-489. [PMID: 32956450 PMCID: PMC8088326 DOI: 10.1093/bioinformatics/btaa804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/28/2020] [Accepted: 09/07/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Current techniques of protein engineering focus mostly on re-designing small targeted regions or defined structural scaffolds rather than constructing combinatorial libraries of versatile compositions and lengths. This is a missed opportunity because combinatorial libraries are emerging as a vital source of novel functional proteins and are of interest in diverse research areas. RESULTS Here, we present a computational tool for Combinatorial Library Design (CoLiDe) offering precise control over protein sequence composition, length and diversity. The algorithm uses evolutionary approach to provide solutions to combinatorial libraries of degenerate DNA templates. We demonstrate its performance and precision using four different input alphabet distribution on different sequence lengths. In addition, a model design and experimental pipeline for protein library expression and purification is presented, providing a proof-of-concept that our protocol can be used to prepare purified protein library samples of up to 1011-1012 unique sequences. CoLiDe presents a composition-centric approach to protein design towards different functional phenomena. AVAILABILITYAND IMPLEMENTATION CoLiDe is implemented in Python and freely available at https://github.com/voracva1/CoLiDe. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vyacheslav Tretyachenko
- Department of Cell Biology, Faculty of Science, Charles University, Biocev, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, 128 00 Prague 2, Czech Republic
| | - Václav Voráček
- Department of Cybernetics, Center for Machine Perception, Faculty of Electrical Engineering, Czech Technical University in Prague, 166 27 Prague, Czech Republic
| | - Radko Souček
- Institute of Organic Chemistry and Biochemistry IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
| | - Klára Hlouchová
- Department of Cell Biology, Faculty of Science, Charles University, Biocev, Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
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6
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Quantifying the Mutational Robustness of Protein-Coding Genes. J Mol Evol 2021; 89:357-369. [PMID: 33934169 DOI: 10.1007/s00239-021-10009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
We use large-scale mutagenesis data and computer simulations to quantify the mutational robustness of protein-coding genes by taking into account constraints arising from protein function and the genetic code. Analyses of the distribution of amino acid substitutions from 18 mutagenesis studies revealed an average of 45% of neutral variants; while mutagenesis data of 12 proteins artificially designed under no other constraints but stability, reach an average of 60%. Simulations using a lattice protein model allow us to contrast these estimates to the expected mutational robustness of protein families by generating unbiased samples of foldable sequences, which we find to have 30% of neutral variants. In agreement with mutagenesis data of designed proteins, the model shows that maximally robust protein families might access up to twice the amount of neutral variants observed in the unbiased samples (i.e. 60%). A biophysical model of protein-ligand binding suggests that constraints associated to molecular function have only a moderate impact on robustness of approximately 5 to 10% of neutral variants; and that the direction of this effect depends on the relation between functional performance and thermodynamic stability. Although the genetic code constraints the access of a gene's nucleotide sequence to only 30% of the full distribution of amino acid mutations, it provides an extra 15 to 20% of neutral variants to the estimations above, such that the expected, observed, and maximal robustness of protein-coding genes are approximately 50, 65, and 75%, respectively. We discuss our results in the light of three main hypothesis put forward to explain the existence of mutationally robust genes.
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7
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Tong CL, Lee KH, Seelig B. De novo proteins from random sequences through in vitro evolution. Curr Opin Struct Biol 2021; 68:129-134. [PMID: 33517151 DOI: 10.1016/j.sbi.2020.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022]
Abstract
Natural proteins are the result of billions of years of evolution. The earliest predecessors of today's proteins are believed to have emerged from random polypeptides. While we have no means to determine how this process exactly happened, there is great interest in understanding how it reasonably could have happened. We are reviewing how researchers have utilized in vitro selection and molecular evolution methods to investigate plausible scenarios for the emergence of early functional proteins. The studies range from analyzing general properties and structural features of unevolved random polypeptides to isolating de novo proteins with specific functions from synthetic randomized sequence libraries or generating novel proteins by combining evolution with rational design. While the results are exciting, more work is needed to fully unravel the mechanisms that seeded protein-dominated biology.
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Affiliation(s)
- Cher Ling Tong
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Kun-Hwa Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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8
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Lan T, Dong Y, Zheng M, Jiang L, Zhang Y, Sui X. Complexation between soy peptides and epigallocatechin-3-gallate (EGCG): Formation mechanism and morphological characterization. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109990] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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9
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Kelly B, Pearce EL. Amino Assets: How Amino Acids Support Immunity. Cell Metab 2020; 32:154-175. [PMID: 32649859 DOI: 10.1016/j.cmet.2020.06.010] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/06/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022]
Abstract
Amino acids are fundamental building blocks supporting life. Their role in protein synthesis is well defined, but they contribute to a host of other intracellular metabolic pathways, including ATP generation, nucleotide synthesis, and redox balance, to support cellular and organismal function. Immune cells critically depend on such pathways to acquire energy and biomass and to reprogram their metabolism upon activation to support growth, proliferation, and effector functions. Amino acid metabolism plays a key role in this metabolic rewiring, and it supports various immune cell functions beyond increased protein synthesis. Here, we review the mechanisms by which amino acid metabolism promotes immune cell function, and how these processes could be targeted to improve immunity in pathological conditions.
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Affiliation(s)
- Beth Kelly
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Erika L Pearce
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg 79108, Germany.
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10
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Houben B, Michiels E, Ramakers M, Konstantoulea K, Louros N, Verniers J, van der Kant R, De Vleeschouwer M, Chicória N, Vanpoucke T, Gallardo R, Schymkowitz J, Rousseau F. Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues. EMBO J 2020; 39:e102864. [PMID: 32237079 PMCID: PMC7265246 DOI: 10.15252/embj.2019102864] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
Many chaperones favour binding to hydrophobic sequences that are flanked by basic residues while disfavouring acidic residues. However, the origin of this bias in protein quality control remains poorly understood. Here, we show that while acidic residues are the most efficient aggregation inhibitors, they are also less compatible with globular protein structure than basic amino acids. As a result, while acidic residues allow for chaperone-independent control of aggregation, their use is structurally limited. Conversely, we find that, while being more compatible with globular structure, basic residues are not sufficient to autonomously suppress protein aggregation. Using Hsp70, we show that chaperones with a bias towards basic residues are structurally adapted to prioritize aggregating sequences whose structural context forced the use of the less effective basic residues. The hypothesis that emerges from our analysis is that the bias of many chaperones for basic residues results from fundamental thermodynamic and kinetic constraints of globular structure. This also suggests the co-evolution of basic residues and chaperones allowed for an expansion of structural variety in the protein universe.
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Affiliation(s)
- Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Katerina Konstantoulea
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Joffré Verniers
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Matthias De Vleeschouwer
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Nuno Chicória
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Thomas Vanpoucke
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
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11
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Determining amino acid scores of the genetic code table: Complementarity, structure, function and evolution. Biosystems 2020; 187:104026. [DOI: 10.1016/j.biosystems.2019.104026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 11/22/2022]
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12
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Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes. Proc Natl Acad Sci U S A 2019; 116:17239-17244. [PMID: 31405964 DOI: 10.1073/pnas.1900275116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The membranes of the first protocells on the early Earth were likely self-assembled from fatty acids. A major challenge in understanding how protocells could have arisen and withstood changes in their environment is that fatty acid membranes are unstable in solutions containing high concentrations of salt (such as would have been prevalent in early oceans) or divalent cations (which would have been required for RNA catalysis). To test whether the inclusion of amino acids addresses this problem, we coupled direct techniques of cryoelectron microscopy and fluorescence microscopy with techniques of NMR spectroscopy, centrifuge filtration assays, and turbidity measurements. We find that a set of unmodified, prebiotic amino acids binds to prebiotic fatty acid membranes and that a subset stabilizes membranes in the presence of salt and Mg2+ Furthermore, we find that final concentrations of the amino acids need not be high to cause these effects; membrane stabilization persists after dilution as would have occurred during the rehydration of dried or partially dried pools. In addition to providing a means to stabilize protocell membranes, our results address the challenge of explaining how proteins could have become colocalized with membranes. Amino acids are the building blocks of proteins, and our results are consistent with a positive feedback loop in which amino acids bound to self-assembled fatty acid membranes, resulting in membrane stabilization and leading to more binding in turn. High local concentrations of molecular building blocks at the surface of fatty acid membranes may have aided the eventual formation of proteins.
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13
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Newton MS, Morrone DJ, Lee KH, Seelig B. Genetic Code Evolution Investigated through the Synthesis and Characterisation of Proteins from Reduced-Alphabet Libraries. Chembiochem 2019; 20:846-856. [PMID: 30511381 DOI: 10.1002/cbic.201800668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Indexed: 11/08/2022]
Abstract
The universal genetic code of 20 amino acids is the product of evolution. It is believed that earlier versions of the code had fewer residues. Many theories for the order in which amino acids were integrated into the code have been proposed, considering factors ranging from prebiotic chemistry to codon capture. Several meta-analyses combined these theories to yield a feasible consensus chronology of the genetic code's evolution, but there is a dearth of experimental data to test the hypothesised order. We used combinatorial chemistry to synthesise libraries of random polypeptides that were based on different subsets of the 20 standard amino acids, thus representing different stages of a plausible history of the alphabet. Four libraries were comprised of the five, nine, and 16 most ancient amino acids, and all 20 extant residues for a direct side-by-side comparison. We characterised numerous variants from each library for their solubility and propensity to form secondary, tertiary or quaternary structures. Proteins from the two most ancient libraries were more likely to be soluble than those from the extant library. Several individual protein variants exhibited inducible protein folding and other traits typical of intrinsically disordered proteins. From these libraries, we can infer how primordial protein structure and function might have evolved with the genetic code.
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Affiliation(s)
- Matilda S Newton
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.,BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, 140 Gortner Laboratory, St. Paul, MN, 55108-6106, USA
| | - Dana J Morrone
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.,BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, 140 Gortner Laboratory, St. Paul, MN, 55108-6106, USA
| | - Kun-Hwa Lee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.,BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, 140 Gortner Laboratory, St. Paul, MN, 55108-6106, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.,BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, 140 Gortner Laboratory, St. Paul, MN, 55108-6106, USA
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14
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Blanco LP, Payne BL, Feyertag F, Alvarez-Ponce D. Proteins of generalist and specialist pathogens differ in their amino acid composition. Life Sci Alliance 2018; 1:e201800017. [PMID: 30456362 PMCID: PMC6238412 DOI: 10.26508/lsa.201800017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
Pathogens differ in their host specificities, with species infecting a unique host (specialist pathogens) and others having a wide host range (generalists). Molecular determinants of pathogen's host range remain poorly understood. Secreted proteins of generalist pathogens are expected to have a broader range of intermolecular interactions (i.e., higher promiscuity) compared with their specialist counterparts. We hypothesize that this increased promiscuity of generalist secretomes may be based on an elevated content of primitive amino acids and intrinsically disordered regions, as these features are known to increase protein flexibility and interactivity. Here, we measure the proportion of primitive amino acids and percentage of intrinsically disordered residues in secreted, membrane, and cytoplasmic proteins from pathogens with different host specificity. Supporting our prediction, there is a significant general enrichment for primitive amino acids and intrinsically disordered regions in proteins from generalists compared to specialists, particularly among secreted proteins in prokaryotes. Our findings support our hypothesis that secreted proteins' amino acid composition and disordered content influence the pathogens' host range.
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Affiliation(s)
- Luz P Blanco
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bryan L Payne
- Department of Biology, University of Nevada, Reno, NV, USA
| | - Felix Feyertag
- Department of Biology, University of Nevada, Reno, NV, USA
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15
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Grohmann U, Mondanelli G, Belladonna ML, Orabona C, Pallotta MT, Iacono A, Puccetti P, Volpi C. Amino-acid sensing and degrading pathways in immune regulation. Cytokine Growth Factor Rev 2017; 35:37-45. [PMID: 28545736 DOI: 10.1016/j.cytogfr.2017.05.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 02/07/2023]
Abstract
Indoleamine 2,3-dioxygenases (IDOs) - belonging in the heme dioxygenase family and degrading tryptophan - are responsible for the de novo synthesis of nicotinamide adenine dinucleotide (NAD+). As such, they are expressed by a variety of invertebrate and vertebrate species. In mammals, IDO1 has remarkably evolved to expand its functions, so to become a prominent homeostatic regulator, capable of modulating infection and immunity in multiple ways, including local tryptophan deprivation, production of biologically active tryptophan catabolites, and non-enzymatic cell-signaling activity. Much like IDO1, arginase 1 (Arg1) is an immunoregulatory enzyme that catalyzes the degradation of arginine. Here, we discuss the possible role of amino-acid degradation as related to the evolution of the immune systems and how the functions of those enzymes are linked by an entwined pathway selected by phylogenesis to meet the newly arising needs imposed by an evolving environment.
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Affiliation(s)
- Ursula Grohmann
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy.
| | - Giada Mondanelli
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Maria L Belladonna
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Ciriana Orabona
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Maria T Pallotta
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Alberta Iacono
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Paolo Puccetti
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Claudia Volpi
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
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16
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Wieczorek R, Adamala K, Gasperi T, Polticelli F, Stano P. Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine. Life (Basel) 2017; 7:E19. [PMID: 28397774 PMCID: PMC5492141 DOI: 10.3390/life7020019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.
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Affiliation(s)
- Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Katarzyna Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
| | - Fabio Polticelli
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
- National Institute of Nuclear Physics, Roma Tre Section, Via della Vasca Navale 84, 00146 Rome, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Campus Ecotekne (S.P. 6 Lecce-Monteroni), 73100 Lecce, Italy.
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17
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Doig AJ. Frozen, but no accident – why the 20 standard amino acids were selected. FEBS J 2017; 284:1296-1305. [DOI: 10.1111/febs.13982] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew J. Doig
- Department of Chemistry Manchester Institute of Biotechnology University of Manchester UK
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18
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Kumachi S, Husimi Y, Nemoto N. An RNA Binding Peptide Consisting of Four Types of Amino Acid by in Vitro Selection Using cDNA Display. ACS OMEGA 2016; 1:52-57. [PMID: 30023471 PMCID: PMC6044570 DOI: 10.1021/acsomega.6b00015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/17/2016] [Indexed: 05/06/2023]
Abstract
RNA-protein interactions have a central role in the living world. In this article, we examined whether primitive peptides (30 residues) consisting of four types of amino acid (Gly, Ala, Asp, and Val) could interact with tRNA as a model of primitive RNAs in the RNA world. By in vitro selection of binding peptides using the cDNA display method, a characteristic peptide was selected from a random peptide library and assayed by electrophoretic mobility shift and pull-down assays. Interestingly, the selected peptide bound to a single-stranded region including a loop structure of an RNA molecule with some sequence specificity.
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Affiliation(s)
- Shigefumi Kumachi
- Graduate
School of Science and Engineering, Saitama
University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yuzuru Husimi
- SOKENDAI
(The Graduate University for Advanced Studies), Shonan International Village, Hayama, Kanagawa 240-0193, Japan
| | - Naoto Nemoto
- Graduate
School of Science and Engineering, Saitama
University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
- E-mail: . Fax: +81-48-858-3531. Tel: +81-48-858-3531
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19
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Uversky VN. Paradoxes and wonders of intrinsic disorder: Complexity of simplicity. INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1135015. [PMID: 28232895 DOI: 10.1080/21690707.2015.1135015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 10/18/2015] [Indexed: 01/20/2023]
Abstract
At first glance it may seem that intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are simpler than ordered proteins and domains on multiple levels. However, such multilevel simplicity equips these proteins with the ability to have very complex behavior.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Faculty of Science, Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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20
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Solis AD. Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins. Proteins 2015; 83:2198-216. [DOI: 10.1002/prot.24936] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/04/2015] [Accepted: 09/04/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Armando D. Solis
- Biological Sciences Department, New York City College of Technology; the City University of New York (CUNY); Brooklyn New York 11201
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21
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Kang SK, Chen BX, Tian T, Jia XS, Chu XY, Liu R, Dong PF, Yang QY, Zhang HY. ATP selection in a random peptide library consisting of prebiotic amino acids. Biochem Biophys Res Commun 2015; 466:400-5. [PMID: 26365351 DOI: 10.1016/j.bbrc.2015.09.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
Abstract
Based upon many theoretical findings on protein evolution, we proposed a ligand-selection model for the origin of proteins, in which the most ancient proteins originated from ATP selection in a pool of random peptides. To test this ligand-selection model, we constructed a random peptide library consisting of 15 types of prebiotic amino acids and then used cDNA display to perform six rounds of in vitro selection with ATP. By means of next-generation sequencing, the most prevalent sequence was defined. Biochemical and biophysical characterization of the selected peptide showed that it was stable and foldable and had ATP-hydrolysis activity as well.
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Affiliation(s)
- Shou-Kai Kang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Bai-Xue Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Tian Tian
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xi-Shuai Jia
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin-Yi Chu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Rong Liu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Peng-Fei Dong
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qing-Yong Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hong-Yu Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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22
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Abstract
It is pointed out that one of the main reasons of lack of real conceptual progress in the field may lie in the fact that questions concerning the biogenesis of macromolecules have never been asked or addressed in a proper way. We should start again research on the origin of life starting from "ground zero" and focusing on the prebiotic synthesis of ordered sequences of proteins and nucleic acids.
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Affiliation(s)
- Pier Luigi Luisi
- University of Rome3, Viale Guglielmo Marconi 446, Rome, 00146, Italy,
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23
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Ferrada E. The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets. PLoS Comput Biol 2014; 10:e1003946. [PMID: 25473967 PMCID: PMC4256021 DOI: 10.1371/journal.pcbi.1003946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
The correspondence between protein sequences and structures, or sequence-structure map, relates to fundamental aspects of structural, evolutionary and synthetic biology. The specifics of the mapping, such as the fraction of accessible sequences and structures, or the sequences' ability to fold fast, are dictated by the type of interactions between the monomers that compose the sequences. The set of possible interactions between monomers is encapsulated by the potential energy function. In this study, I explore the impact of the relative forces of the potential on the architecture of the sequence-structure map. My observations rely on simple exact models of proteins and random samples of the space of potential energy functions of binary alphabets. I adopt a graph perspective and study the distribution of viable sequences and the structures they produce, as networks of sequences connected by point mutations. I observe that the relative proportion of attractive, neutral and repulsive forces defines types of potentials, that induce sequence-structure maps of vastly different architectures. I characterize the properties underlying these differences and relate them to the structure of the potential. Among these properties are the expected number and relative distribution of sequences associated to specific structures and the diversity of structures as a function of sequence divergence. I study the types of binary potentials observed in natural amino acids and show that there is a strong bias towards only some types of potentials, a bias that seems to characterize the folding code of natural proteins. I discuss implications of these observations for the architecture of the sequence-structure map of natural proteins, the construction of random libraries of peptides, and the early evolution of the natural amino acid alphabet.
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Affiliation(s)
- Evandro Ferrada
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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24
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Longo LM, Tenorio CA, Kumru OS, Middaugh CR, Blaber M. A single aromatic core mutation converts a designed "primitive" protein from halophile to mesophile folding. Protein Sci 2014; 24:27-37. [PMID: 25297559 DOI: 10.1002/pro.2580] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 10/06/2014] [Indexed: 11/06/2022]
Abstract
The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate "cradle" for proteogenesis. In this viewpoint, a subsequent halophile-to-mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original "prebiotic" set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile-to-mesophile transition by hydrophobic core-packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a "primitive" designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)-having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a "primitive" polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile-to-mesophile protein folding adaptation-identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.
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Affiliation(s)
- Liam M Longo
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, 32306-4300
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25
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26
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Abstract
Although both the most popular form of synthetic biology (SB) and chemical synthetic biology (CSB) share the biotechnologically useful aim of making new forms of life, SB does so by using genetic manipulation of extant microorganism, while CSB utilises classic chemical procedures in order to obtain biological structures which are non-existent in nature. The main query concerning CSB is the philosophical question: why did nature do this, and not that? The idea then is to synthesise alternative structures in order to understand why nature operated in such a particular way. We briefly present here some various examples of CSB, including those cases of nucleic acids synthesised with pyranose instead of ribose, and proteins with a reduced alphabet of amino acids; also we report the developing research on the "never born proteins" (NBP) and "never born RNA" (NBRNA), up to the minimal cell project, where the issue is the preparation of semi-synthetic cells that can perform the basic functions of biological cells.
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Affiliation(s)
| | - Pier Luigi Luisi
- Department of Materials, Swiss Federal Institute of Technology Zurich (ETHZ), University of Roma Tre, Italy
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27
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Chiarabelli C, Stano P, Luisi PL. Chemical synthetic biology: a mini-review. Front Microbiol 2013; 4:285. [PMID: 24065964 PMCID: PMC3779815 DOI: 10.3389/fmicb.2013.00285] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/04/2013] [Indexed: 01/08/2023] Open
Abstract
Chemical synthetic biology (CSB) is a branch of synthetic biology (SB) oriented toward the synthesis of chemical structures alternative to those present in nature. Whereas SB combines biology and engineering with the aim of synthesizing biological structures or life forms that do not exist in nature – often based on genome manipulation, CSB uses and assembles biological parts, synthetic or not, to create new and alternative structures. A short epistemological note will introduce the theoretical concepts related to these fields, whereas the text will be largely devoted to introduce and comment two main projects of CSB, carried out in our laboratory in the recent years. The “Never Born Biopolymers” project deals with the construction and the screening of RNA and peptide sequences that are not present in nature, whereas the “Minimal Cell” project focuses on the construction of semi-synthetic compartments (usually liposomes) containing the minimal and sufficient number of components to perform the basic function of a biological cell. These two topics are extremely important for both the general understanding of biology in terms of function, organization, and development, and for applied biotechnology.
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28
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Uversky VN. A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci 2013; 22:693-724. [PMID: 23553817 PMCID: PMC3690711 DOI: 10.1002/pro.2261] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 03/23/2013] [Accepted: 03/25/2013] [Indexed: 12/28/2022]
Abstract
The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically "freeze" while their "pictures are taken." However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA.
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29
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Yanagawa H. Exploration of the Origin and Evolution of Globular Proteins by mRNA Display. Biochemistry 2013; 52:3841-51. [DOI: 10.1021/bi301704x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hiroshi Yanagawa
- Department of Biosciences and Informatics,
Faculty
of Sciences and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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30
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Pollack JD, Gerard D, Pearl DK. Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth. ORIGINS LIFE EVOL B 2013; 43:161-87. [PMID: 23715690 DOI: 10.1007/s11084-013-9331-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 04/04/2013] [Indexed: 11/27/2022]
Abstract
The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.
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Affiliation(s)
- J Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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31
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Longo LM, Lee J, Blaber M. Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proc Natl Acad Sci U S A 2013; 110:2135-9. [PMID: 23341608 PMCID: PMC3568330 DOI: 10.1073/pnas.1219530110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.
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Affiliation(s)
- Liam M. Longo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306-4300
| | | | - Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306-4300
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32
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33
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Unusual biophysics of intrinsically disordered proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:932-51. [PMID: 23269364 DOI: 10.1016/j.bbapap.2012.12.008] [Citation(s) in RCA: 409] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/21/2012] [Accepted: 12/12/2012] [Indexed: 02/08/2023]
Abstract
Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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34
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Artificial proteins from combinatorial approaches. Trends Biotechnol 2012; 30:512-20. [DOI: 10.1016/j.tibtech.2012.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/01/2012] [Accepted: 06/06/2012] [Indexed: 11/21/2022]
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35
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Longo LM, Blaber M. Protein design at the interface of the pre-biotic and biotic worlds. Arch Biochem Biophys 2012; 526:16-21. [DOI: 10.1016/j.abb.2012.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/23/2012] [Indexed: 12/01/2022]
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36
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Approaches to chemical synthetic biology. FEBS Lett 2012; 586:2138-45. [DOI: 10.1016/j.febslet.2012.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 01/10/2012] [Indexed: 11/24/2022]
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37
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Su J, Cao X, Wang K. A novel degradation signal derived from distal C-terminal frameshift mutations of KCNQ2 protein which cause neonatal epilepsy. J Biol Chem 2011; 286:42949-58. [PMID: 21937445 DOI: 10.1074/jbc.m111.287268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Benign familial neonatal convulsions is an autosomal-dominant idiopathic form of epilepsy primarily caused by gene mutations of the voltage-gated Kv7.2/KCNQ2/M-channel that exert only partial dominant-negative effects. However, the mechanism underlying the incomplete dominance of channel mutations, which cause epilepsy in infancy, remains unknown. Using mutagenesis and biochemistry combined with electrophysiology, we identified a novel degradation signal derived from distal C-terminal frameshift mutations, which impairs channel function. This degradation signal, transferable to non-channel CD4, can lead to accelerated degradation of mutant proteins through ubiquitin-independent proteasome machinery but does not affect mRNA quantity and protein trafficking. Functional dissection of this signal has revealed a key five-amino acid (RCXRG) motif critical for degradation. Taken together, our findings reveal a mechanism by which proteins that carry this signal are subject to degradation, leading to M-current dysfunction, which causes epilepsy.
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Affiliation(s)
- Jun Su
- Department of Neurobiology, Neuroscience Research Institute, Peking University Health Science Center, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
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38
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Labean TH, Butt TR, Kauffman SA, Schultes EA. Protein folding absent selection. Genes (Basel) 2011; 2:608-26. [PMID: 24710212 PMCID: PMC3927614 DOI: 10.3390/genes2030608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 08/05/2011] [Accepted: 08/11/2011] [Indexed: 11/16/2022] Open
Abstract
Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.
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Affiliation(s)
- Thomas H Labean
- Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA.
| | - Tauseef R Butt
- LifeSensors Inc., 271 Great Valley Parkway, Suite 100, Malvern, PA 19355, USA.
| | - Stuart A Kauffman
- Complex Systems Center University of Vermont, 200C Farrell Hall, 210 Colchester Ave., Burlington, VT 05405, USA.
| | - Erik A Schultes
- Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA.
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39
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Tanaka J, Yanagawa H, Doi N. Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display. PLoS One 2011; 6:e18034. [PMID: 21445307 PMCID: PMC3061877 DOI: 10.1371/journal.pone.0018034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 02/23/2011] [Indexed: 11/18/2022] Open
Abstract
Although modern proteins consist of 20 different amino acids, it has been proposed that primordial proteins consisted of a small set of amino acids, and additional amino acids have gradually been recruited into the genetic code. This hypothesis has recently been supported by comparative genome sequence analysis, but no direct experimental approach has been reported. Here, we utilized a novel experimental approach to test a hypothesis that native-like globular proteins might be easily simplified by a set of putative primitive amino acids with retention of its structure and function than by a set of putative new amino acids. We performed in vitro selection of a functional SH3 domain as a model from partially randomized libraries with different sets of amino acids using mRNA display. Consequently, a library rich in putative primitive amino acids included a larger number of functional SH3 sequences than a library rich in putative new amino acids. Further, the functional SH3 sequences were enriched from the primitive library slightly earlier than from a randomized library with the full set of amino acids, while the function and structure of the selected SH3 proteins with the primitive alphabet were comparable with those from the 20 amino acid alphabet. Application of this approach to various combinations of codons in protein sequences may be useful not only for clarifying the precise order of the amino acid expansion in the early stages of protein evolution but also for efficiently creating novel functional proteins in the laboratory.
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Affiliation(s)
- Junko Tanaka
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Hiroshi Yanagawa
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
- * E-mail:
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Tanaka J, Doi N, Takashima H, Yanagawa H. Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids. Protein Sci 2010; 19:786-95. [PMID: 20162614 DOI: 10.1002/pro.358] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Screening of functional proteins from a random-sequence library has been used to evolve novel proteins in the field of evolutionary protein engineering. However, random-sequence proteins consisting of the 20 natural amino acids tend to aggregate, and the occurrence rate of functional proteins in a random-sequence library is low. From the viewpoint of the origin of life, it has been proposed that primordial proteins consisted of a limited set of amino acids that could have been abundantly formed early during chemical evolution. We have previously found that members of a random-sequence protein library constructed with five primitive amino acids show high solubility (Doi et al., Protein Eng Des Sel 2005;18:279-284). Although such a library is expected to be appropriate for finding functional proteins, the functionality may be limited, because they have no positively charged amino acid. Here, we constructed three libraries of 120-amino acid, random-sequence proteins using alphabets of 5, 12, and 20 amino acids by preselection using mRNA display (to eliminate sequences containing stop codons and frameshifts) and characterized and compared the structural properties of random-sequence proteins arbitrarily chosen from these libraries. We found that random-sequence proteins constructed with the 12-member alphabet (including five primitive amino acids and positively charged amino acids) have higher solubility than those constructed with the 20-member alphabet, though other biophysical properties are very similar in the two libraries. Thus, a library of moderate complexity constructed from 12 amino acids may be a more appropriate resource for functional screening than one constructed from 20 amino acids.
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Affiliation(s)
- Junko Tanaka
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
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Abstract
The quantitative underpinning of the information content of biosequences represents an elusive goal and yet also an obvious prerequisite to the quantitative modeling and study of biological function and evolution. Several past studies have addressed the question of what distinguishes biosequences from random strings, the latter being clearly unpalatable to the living cell. Such studies typically analyze the organization of biosequences in terms of their constituent characters or substrings and have, in particular, consistently exposed a tenacious lack of compressibility on behalf of biosequences. This article attempts, perhaps for the first time, an assessement of the structure and randomness of polypeptides in terms on newly introduced parameters that relate to the vocabulary of their (suitably constrained) subsequences rather than their substrings. It is shown that such parameters grasp structural/functional information, and are related to each other under a specific set of rules that span biochemically diverse polypeptides. Measures on subsequences separate few amino acid strings from their random permutations, but show that the random permutations of most polypeptides amass along specific linear loci.
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Affiliation(s)
- Alberto Apostolico
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30318, USA.
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Chiarabelli C, Stano P, Luisi PL. Chemical approaches to synthetic biology. Curr Opin Biotechnol 2009; 20:492-7. [DOI: 10.1016/j.copbio.2009.08.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 08/07/2009] [Accepted: 08/10/2009] [Indexed: 11/17/2022]
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Higgs PG, Pudritz RE. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. ASTROBIOLOGY 2009; 9:483-90. [PMID: 19566427 DOI: 10.1089/ast.2008.0280] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Of the 20 amino acids used in proteins, 10 were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these 10 early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.
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Affiliation(s)
- Paul G Higgs
- Origins Institute and Department of Physics and Astronomy, McMaster University, Ontario, Canada.
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Prak K, Utsumi S. Production of a bioactive peptide (IIAEK) in Escherichia coli using soybean proglycinin A1ab1b as a carrier. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:3792-3799. [PMID: 19298043 DOI: 10.1021/jf8034258] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To produce large amounts of a peptide of fewer than 10 amino acid residues, construction of a gene encoding multimers of the small peptide is necessary. For this study a method was developed to facilitate the gene construction of high multimers of a small peptide with one step of cloning. A hypocholesterolemic peptide, IIAEK, from cow's milk beta-lactoglobulin was used as a model peptide for the construction of a gene encoding multimers of IIAEK and for the production of the peptide. Two systems for direct expression of 28-mers of IIAEK sequences (28IIAEK) and expression of 34 IIAEK sequences (4 IIAEK sequences in each of the disordered regions I, II, and III and 14 and 8 IIAEK sequences in disordered regions IV and V, respectively) in a mutant of soybean proglycinin A1aB1b lacking 31 residues in disordered region IV [A1aB1b(Delta31)-34IIAEK] were used. The protein produced from both systems formed inclusion bodies. The expression level of A1aB1b(Delta31)-34IIAEK was 29.9% of the total cell proteins and that of the 28IIAEK was 2.0%. The insoluble A1aB1b(Delta31)-34IIAEK was digested by trypsin without any help from urea or chemicals, and the produced IIAEK was purified using an octadecyl silica column. The yield of IIAEK was 58.6%. The results showed that A1aB1b as a carrier of multiple peptides and use of an Escherichia coli expression system are suitable for production of bioactive peptide.
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Affiliation(s)
- Krisna Prak
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Reetz MT, Kahakeaw D, Sanchis J. Shedding light on the efficacy of laboratory evolution based on iterative saturation mutagenesis. ACTA ACUST UNITED AC 2009; 5:115-22. [DOI: 10.1039/b814862g] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Dryden DTF, Thomson AR, White JH. How much of protein sequence space has been explored by life on Earth? J R Soc Interface 2008; 5:953-6. [PMID: 18426772 PMCID: PMC2459213 DOI: 10.1098/rsif.2008.0085] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.
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Affiliation(s)
- David T F Dryden
- School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK.
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Reetz MT, Kahakeaw D, Lohmer R. Addressing the Numbers Problem in Directed Evolution. Chembiochem 2008; 9:1797-804. [DOI: 10.1002/cbic.200800298] [Citation(s) in RCA: 334] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Identification and Classification of G-protein coupled receptors (GPCRs) using protein sequences is an important computational challenge, given that experimental screening of thousands of ligands is an expensive proposition. There are two distinct but complementary approaches to GPCR classification --machine learning and sequence motif analysis. Machine learning methodologies typically suffer from problems of class imbalance and lack of multi-class classification. Many sequence motif methods, meanwhile, are too dependent on the similarity of the primary sequence alignments. It is desirable to have a motif discovery and application methodology that is not strongly dependent on primary sequence similarity. It should also overcome limitations of machine learning. We propose and evaluate the effectiveness of a simple methodology that uses a reduced protein functional alphabet representation, where similar functional residues have similar symbols. Regular expression motifs can then be obtained by ClustalW based multiple sequence alignment, using an identity matrix. Since evolutionary matrices like BLOSUM, PAM are not used, this method can be useful for any set of sequences that do not necessarily share a common ancestry. Reduced alphabet motifs can accurately classify known GPCR proteins and the results are comparable to PRINTS and PROSITE. For well known GPCR proteins from SWISSPROT, there were no false negatives and only a few false positives. This methodology covers most currently known classes of GPCRs, even if there are very few representative sequences. It also predicts more than one class for certain sequences, thus overcoming the limitation of machine learning methods. We also annotated, 695 orphan receptors, and 121 were identified as belonging to Family A. A simple JavaScript based web interface has been developed to predict GPCR families and subfamilies (www.insilico-consulting.com/gpcrmotif.html).
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Affiliation(s)
- Rajeev Gangal
- Insilico Consulting, 402, Citi Centre, 39/2, Erandwane, Karve Road, Pune, Maharashtra, India
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Buchete NV, Straub JE, Thirumalai D. Dissecting contact potentials for proteins: relative contributions of individual amino acids. Proteins 2008; 70:119-30. [PMID: 17640067 DOI: 10.1002/prot.21538] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Knowledge-based contact potentials are routinely used in fold recognition, binding of peptides to proteins, structure prediction, and coarse-grained models to probe protein folding kinetics. The dominant physical forces embodied in the contact potentials are revealed by eigenvalue analysis of the matrices, whose elements describe the strengths of interaction between amino acid side chains. We propose a general method to rank quantitatively the importance of various inter-residue interactions represented in the currently popular pair contact potentials. Eigenvalue analysis and correlation diagrams are used to rank the inter-residue pair interactions with respect to the magnitude of their relative contributions to the contact potentials. The amino acid ranking is shown to be consistent with a mean field approximation that is used to reconstruct the original contact potentials from the most relevant amino acids for several contact potentials. By providing a general, relative ranking score for amino acids, this method permits a detailed, quantitative comparison of various contact interaction schemes. For most contact potentials, between 7 and 9 amino acids of varying chemical character are needed to accurately reconstruct the full matrix. By correlating the identified important amino acid residues in contact potentials and analysis of about 7800 structural domains in the CATH database we predict that it is important to model accurately interactions between small hydrophobic residues. In addition, only potentials that take interactions involving the protein backbone into account can predict dense packing in protein structures.
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Affiliation(s)
- N-V Buchete
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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Reetz MT, Wu S. Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. Chem Commun (Camb) 2008:5499-501. [DOI: 10.1039/b813388c] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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