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Bailleul G, Nicoll CR, Mascotti ML, Mattevi A, Fraaije MW. Ancestral reconstruction of mammalian FMO1 enables structural determination, revealing unique features that explain its catalytic properties. J Biol Chem 2020; 296:100221. [PMID: 33759784 PMCID: PMC7948450 DOI: 10.1074/jbc.ra120.016297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/09/2022] Open
Abstract
Mammals rely on the oxidative flavin-containing monooxygenases (FMOs) to detoxify numerous and potentially deleterious xenobiotics; this activity extends to many drugs, giving FMOs high pharmacological relevance. However, our knowledge regarding these membrane-bound enzymes has been greatly impeded by the lack of structural information. We anticipated that ancestral-sequence reconstruction could help us identify protein sequences that are more amenable to structural analysis. As such, we hereby reconstructed the mammalian ancestral protein sequences of both FMO1 and FMO4, denoted as ancestral flavin-containing monooxygenase (AncFMO)1 and AncFMO4, respectively. AncFMO1, sharing 89.5% sequence identity with human FMO1, was successfully expressed as a functional enzyme. It displayed typical FMO activities as demonstrated by oxygenating benzydamine, tamoxifen, and thioanisole, drug-related compounds known to be also accepted by human FMO1, and both NADH and NADPH cofactors could act as electron donors, a feature only described for the FMO1 paralogs. AncFMO1 crystallized as a dimer and was structurally resolved at 3.0 Å resolution. The structure harbors typical FMO aspects with the flavin adenine dinucleotide and NAD(P)H binding domains and a C-terminal transmembrane helix. Intriguingly, AncFMO1 also contains some unique features, including a significantly porous and exposed active site, and NADPH adopting a new conformation with the 2’-phosphate being pushed inside the NADP+ binding domain instead of being stretched out in the solvent. Overall, the ancestrally reconstructed mammalian AncFMO1 serves as the first structural model to corroborate and rationalize the catalytic properties of FMO1.
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Affiliation(s)
- Gautier Bailleul
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | - Callum R Nicoll
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - María Laura Mascotti
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands.
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María Hernández-Domínguez E, Sofía Castillo-Ortega L, García-Esquivel Y, Mandujano-González V, Díaz-Godínez G, Álvarez-Cervantes J. Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins. Comput Biol Chem 2020. [DOI: 10.5772/intechopen.89594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This chapter deals with the topic of bioinformatics, computational, mathematics, and statistics tools applied to biology, essential for the analysis and characterization of biological molecules, in particular proteins, which play an important role in all cellular and evolutionary processes of the organisms. In recent decades, with the next generation sequencing technologies and bioinformatics, it has facilitated the collection and analysis of a large amount of genomic, transcriptomic, proteomic, and metabolomic data from different organisms that have allowed predictions on the regulation of expression, transcription, translation, structure, and mechanisms of action of proteins as well as homology, mutations, and evolutionary processes that generate structural and functional changes over time. Although the information in the databases is greater every day, all bioinformatics tools continue to be constantly modified to improve performance that leads to more accurate predictions regarding protein functionality, which is why bioinformatics research remains a great challenge.
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53
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Kropp C, Straub K, Linde M, Babinger P. Hexamerization and thermostability emerged very early during geranylgeranylglyceryl phosphate synthase evolution. Protein Sci 2020; 30:583-596. [PMID: 33342010 PMCID: PMC7888582 DOI: 10.1002/pro.4016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
A large number of archaea live in hyperthermophilic environments. In consequence, their proteins need to adopt to these harsh conditions, including the enzymes that catalyze the synthesis of their membrane ether lipids. The enzyme that catalyzes the formation of the first ether bond in these lipids, geranylgeranylglyceryl phosphate synthase (GGGPS), exists as a hexamer in many hyperthermophilic archaea, and a recent study suggested that hexamerization serves for a fine‐tuning of the flexibility – stability trade‐off under hyperthermophilic conditions. We have recently reconstructed the sequences of ancestral group II GGGPS enzymes and now present a detailed biochemical characterization of nine of these predecessors, which allowed us to trace back the evolution of hexameric GGGPS and to draw conclusions about the properties of extant GGGPS branches that were not accessible to experiments up to now. Almost all ancestral GGGPS proteins formed hexamers, which demonstrates that hexamerization is even more widespread among the GGGPS family than previously assumed. Furthermore, all experimentally studied ancestral proteins showed high thermostability. Our results indicate that the hexameric oligomerization state and thermostability were present very early during the evolution of group II GGGPS, while the fine tuning of the flexibility – stability trade‐off developed very late, independent of the emergence of hexamerization.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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54
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Motoyama T, Hiramatsu N, Asano Y, Nakano S, Ito S. Protein Sequence Selection Method That Enables Full Consensus Design of Artificial l-Threonine 3-Dehydrogenases with Unique Enzymatic Properties. Biochemistry 2020; 59:3823-3833. [PMID: 32945652 DOI: 10.1021/acs.biochem.0c00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exponentially increasing protein sequence data enables artificial enzyme design using sequence-based protein design methods, including full-consensus protein design (FCD). The success of artificial enzyme design is strongly dependent on the nature of the sequences used. Hence, sequences must be selected from databases and curated libraries prepared to enable a successful design by FCD. In this study, we proposed a selection approach regarding several key residues as sequence motifs. We used l-threonine 3-dehydrogenase (TDH) as a model to test the validity of this approach. In the classification, four residues (143, 174, 188, and 214) were used as key residues. We classified thousands of TDH homologous sequences into five groups containing hundreds of sequences. Utilizing sequences in the libraries, we designed five artificial TDHs by FCD. Among the five, we successfully expressed four in soluble form. Biochemical analysis of artificial TDHs indicated that their enzymatic properties vary; half of the maximum measured enzyme activity (t1/2) and activation energies were distributed from 53 to 65 °C and from 38 to 125 kJ/mol, respectively. The artificial TDHs had unique kinetic parameters, distinct from one another. Structural analysis indicates that consensus mutations are mainly introduced in the secondary or outer shell. The functional diversity of the artificial TDHs is due to the accumulation of mutations that affect their physicochemical properties. Taken together, our findings indicate that our proposed approach can help generate artificial enzymes with unique enzymatic properties.
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Affiliation(s)
- Tomoharu Motoyama
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Nozomi Hiramatsu
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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55
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Furukawa R, Toma W, Yamazaki K, Akanuma S. Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties. Sci Rep 2020; 10:15493. [PMID: 32968141 PMCID: PMC7511310 DOI: 10.1038/s41598-020-72418-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/31/2020] [Indexed: 11/09/2022] Open
Abstract
Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.
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Affiliation(s)
- Ryutaro Furukawa
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Wakako Toma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Koji Yamazaki
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
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56
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Antelo GT, Vila AJ, Giedroc DP, Capdevila DA. Molecular Evolution of Transition Metal Bioavailability at the Host-Pathogen Interface. Trends Microbiol 2020; 29:441-457. [PMID: 32951986 DOI: 10.1016/j.tim.2020.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/01/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
The molecular evolution of the adaptive response at the host-pathogen interface has been frequently referred to as an 'arms race' between the host and bacterial pathogens. The innate immune system employs multiple strategies to starve microbes of metals. Pathogens, in turn, develop successful strategies to maintain access to bioavailable metal ions under conditions of extreme restriction of transition metals, or nutritional immunity. However, the processes by which evolution repurposes or re-engineers host and pathogen proteins to perform or refine new functions have been explored only recently. Here we review the molecular evolution of several human metalloproteins charged with restricting bacterial access to transition metals. These include the transition metal-chelating S100 proteins, natural resistance-associated macrophage protein-1 (NRAMP-1), transferrin, lactoferrin, and heme-binding proteins. We examine their coevolution with bacterial transition metal acquisition systems, involving siderophores and membrane-spanning metal importers, and the biological specificity of allosteric transcriptional regulatory proteins tasked with maintaining bacterial metallostasis. We also discuss the evolution of metallo-β-lactamases; this illustrates how rapid antibiotic-mediated evolution of a zinc metalloenzyme obligatorily occurs in the context of host-imposed nutritional immunity.
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Affiliation(s)
- Giuliano T Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, S2002LRK Rosario, Argentina; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
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57
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Emlaw JR, Burkett KM, daCosta CJB. Contingency between Historical Substitutions in the Acetylcholine Receptor Pore. ACS Chem Neurosci 2020; 11:2861-2868. [PMID: 32786311 DOI: 10.1021/acschemneuro.0c00410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human adult muscle-type acetylcholine receptors incorporating a reconstructed ancestral β-subunit exhibit reduced single-channel conductance when compared to wild-type. The ancestral and wild-type β-subunits differ by 132 amino acids, including substitution of residues that line the lumen of the channel pore, near its narrowest constriction. Here we show that a single historical substitution in this region of the ancestral β-subunit accounts for the difference in conductance. Furthermore, the contribution of the substituted residue to conductance is dependent upon its ancestral or wild-type background, and it can be modulated by a neighboring residue that has also evolved throughout the β-subunit history. Using an expanded molecular phylogeny, we track the order in which these two mutations occurred and then show that the order in which they are installed upon the ancestral, but not the human, background determines their individual contribution to conductance. Our results show how the contribution of amino acids to acetylcholine receptor conductance is contingent upon their evolutionary history and that the order in which substitutions occurred was important for shaping conductance in the modern-day receptor.
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58
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Sternke M, Tripp KW, Barrick D. The use of consensus sequence information to engineer stability and activity in proteins. Methods Enzymol 2020; 643:149-179. [PMID: 32896279 DOI: 10.1016/bs.mie.2020.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The goal of protein design is to create proteins that are stable, soluble, and active. Here we focus on one approach to protein design in which sequence information is used to create a "consensus" sequence. Such consensus sequences comprise the most common residue at each position in a multiple sequence alignment (MSA). After describing some general ideas that relate MSA and consensus sequences and presenting a statistical thermodynamic framework that relates consensus and non-consensus sequences to stability, we detail the process of designing a consensus sequence and survey reports of consensus design and characterization from the literature. Many of these consensus proteins retain native biological activities including ligand binding and enzyme activity. Remarkably, in most cases the consensus protein shows significantly higher stability than extant versions of the protein, as measured by thermal or chemical denaturation, consistent with the statistical thermodynamic model. To understand this stability increase, we compare various features of consensus sequences with the extant MSA sequences from which they were derived. Consensus sequences show enrichment in charged residues (most notably glutamate and lysine) and depletion of uncharged polar residues (glutamine, serine, and asparagine). Surprisingly, a survey of stability changes resulting from point substitutions show little correlation with residue frequencies at the corresponding positions within the MSA, suggesting that the high stability of consensus proteins may result from interactions among residue pairs or higher-order clusters. Whatever the source, the large number of reported successes demonstrates that consensus design is a viable route to generating active and in many cases highly stabilized proteins.
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Affiliation(s)
- Matt Sternke
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Katherine W Tripp
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States.
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59
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Oliva A, Pulicani S, Lefort V, Bréhélin L, Gascuel O, Guindon S. Accounting for ambiguity in ancestral sequence reconstruction. Bioinformatics 2020; 35:4290-4297. [PMID: 30977781 DOI: 10.1093/bioinformatics/btz249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/29/2019] [Accepted: 04/06/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference. RESULTS The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned. AVAILABILITY AND IMPLEMENTATION The software package PhyML (https://github.com/stephaneguindon/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.
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Affiliation(s)
- A Oliva
- Department of Computer Science, LIRMM, CNRS & Université de Montpellier, Montpellier, France
- Australian Centre for Ancient DNA, Adelaide, Australia
| | - S Pulicani
- Department of Computer Science, LIRMM, CNRS & Université de Montpellier, Montpellier, France
| | - V Lefort
- Department of Computer Science, LIRMM, CNRS & Université de Montpellier, Montpellier, France
| | - L Bréhélin
- Department of Computer Science, LIRMM, CNRS & Université de Montpellier, Montpellier, France
| | - O Gascuel
- Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - S Guindon
- Department of Computer Science, LIRMM, CNRS & Université de Montpellier, Montpellier, France
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60
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Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
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Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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61
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Exploring the therapeutic potential of modern and ancestral phenylalanine/tyrosine ammonia-lyases as supplementary treatment of hereditary tyrosinemia. Sci Rep 2020; 10:1315. [PMID: 31992763 PMCID: PMC6987202 DOI: 10.1038/s41598-020-57913-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/07/2020] [Indexed: 12/01/2022] Open
Abstract
Phenylalanine/tyrosine ammonia-lyases (PAL/TALs) have been approved by the FDA for treatment of phenylketonuria and may harbour potential for complementary treatment of hereditary tyrosinemia Type I. Herein, we explore ancestral sequence reconstruction as an enzyme engineering tool to enhance the therapeutic potential of PAL/TALs. We reconstructed putative ancestors from fungi and compared their catalytic activity and stability to two modern fungal PAL/TALs. Surprisingly, most putative ancestors could be expressed as functional tetramers in Escherichia coli and thus retained their ability to oligomerize. All ancestral enzymes displayed increased thermostability compared to both modern enzymes, however, the increase in thermostability was accompanied by a loss in catalytic turnover. One reconstructed ancestral enzyme in particular could be interesting for further drug development, as its ratio of specific activities is more favourable towards tyrosine and it is more thermostable than both modern enzymes. Moreover, long-term stability assessment showed that this variant retained substantially more activity after prolonged incubation at 25 °C and 37 °C, as well as an increased resistance to incubation at 60 °C. Both of these factors are indicative of an extended shelf-life of biopharmaceuticals. We believe that ancestral sequence reconstruction has potential for enhancing the properties of enzyme therapeutics, especially with respect to stability. This work further illustrates that resurrection of putative ancestral oligomeric proteins is feasible and provides insight into the extent of conservation of a functional oligomerization surface area from ancestor to modern enzyme.
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62
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Arenas M, Bastolla U. ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13341] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology University of Vigo Vigo Spain
- Biomedical Research Center (CINBIO) University of Vigo Vigo Spain
| | - Ugo Bastolla
- Bioinformatics Unit Centre for Molecular Biology Severo Ochoa (CSIC) Madrid Spain
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63
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Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction. Proc Natl Acad Sci U S A 2019; 117:346-354. [PMID: 31871208 DOI: 10.1073/pnas.1912132117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tryptophan synthase (TS) is a heterotetrameric αββα complex. It is characterized by the channeling of the reaction intermediate indole and the mutual activation of the α-subunit TrpA and the β-subunit TrpB via a complex allosteric network. We have analyzed this allosteric network by means of ancestral sequence reconstruction (ASR), which is an in silico method to resurrect extinct ancestors of modern proteins. Previously, the sequences of TrpA and TrpB from the last bacterial common ancestor (LBCA) have been computed by means of ASR and characterized. LBCA-TS is similar to modern TS by forming a αββα complex with indole channeling taking place. However, LBCA-TrpA allosterically decreases the activity of LBCA-TrpB, whereas, for example, the modern ncTrpA from Neptuniibacter caesariensis allosterically increases the activity of ncTrpB. To identify amino acid residues that are responsible for this inversion of the allosteric effect, all 6 evolutionary TrpA and TrpB intermediates that stepwise link LBCA-TS with ncTS were characterized. Remarkably, the switching from TrpB inhibition to TrpB activation by TrpA occurred between 2 successive TS intermediates. Sequence comparison of these 2 intermediates and iterative rounds of site-directed mutagenesis allowed us to identify 4 of 413 residues from TrpB that are crucial for its allosteric activation by TrpA. The effect of our mutational studies was rationalized by a community analysis based on molecular dynamics simulations. Our findings demonstrate that ancestral sequence reconstruction can efficiently identify residues contributing to allosteric signal propagation in multienzyme complexes.
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64
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Nakano S, Minamino Y, Hasebe F, Ito S. Deracemization and Stereoinversion to Aromatic d-Amino Acid Derivatives with Ancestral l-Amino Acid Oxidase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03418] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yuki Minamino
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Fumihito Hasebe
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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65
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Jones DR, McLean R, Hobbs JK, Abbott DW. A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase. J Struct Biol 2019; 207:279-286. [PMID: 31200020 DOI: 10.1016/j.jsb.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Yersinia enterocolitica is a pectinolytic zoonotic foodborne pathogen, the genome of which contains pectin-binding proteins and several different classes of pectinases, including polysaccharide lyases (PLs) and an exopolygalacturonase. These proteins operate within a coordinated pathway to completely saccharify homogalacturonan (HG). Polysaccharide lyase family 2 (PL2) is divided into two major subfamilies that are broadly-associated with contrasting 'endolytic' (PL2A) or 'exolytic' (PL2B) activities on HG. In the Y. enterocolitica genome, the PL2A gene is adjacent to an independent carbohydrate binding module from family 32 (YeCBM32), which possesses a N-terminal secretion tag and is known to specifically bind HG. Independent CBMs are rare in nature and, most commonly, are fused to enzymes in order to potentiate catalysis. The unconventional gene architecture of YePL2A and YeCBM32, therefore, may represent an ancestral relic of a fission event that decoupled PL2A from its cognate CBM. To provide further insight into the evolution of this pectinolytic locus and the molecular basis of HG depolymerisation within Y. enterocolitica, we have resurrected a YePL2A-YeCBM32 chimera and demonstrated that the extant PL2A digests HG more efficiently. In addition, we have engineered a tryptophan from the active site of the exolytic YePL2B into YePL2A (YePL2A-K291W) and demonstrated, using X-ray crystallography of substrate complexes, that it is a structural determinant of exo-activity within the PL2 family. In this manner, surrogate structural platforms may assist in the study of phylogenetic relationships informed by extant and resurrected sequences, and can be used to overcome challenging structural problems within carbohydrate active enzyme families.
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Affiliation(s)
- Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
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66
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Garcia AK, Kaçar B. How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free Radic Biol Med 2019; 140:260-269. [PMID: 30951835 DOI: 10.1016/j.freeradbiomed.2019.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/11/2019] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Astronomy and Steward Observatory, University of Arizona, Tucson, AZ, 85721, USA.
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67
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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68
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Barruetabeña N, Alonso-Lerma B, Galera-Prat A, Joudeh N, Barandiaran L, Aldazabal L, Arbulu M, Alcalde M, De Sancho D, Gavira JA, Carrion-Vazquez M, Perez-Jimenez R. Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis. Commun Chem 2019. [DOI: 10.1038/s42004-019-0176-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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69
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Palacios-Pérez M, José MV. The evolution of proteome: From the primeval to the very dawn of LUCA. Biosystems 2019; 181:1-10. [DOI: 10.1016/j.biosystems.2019.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 10/27/2022]
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70
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Vialle RA, Tamuri AU, Goldman N. Alignment Modulates Ancestral Sequence Reconstruction Accuracy. Mol Biol Evol 2019; 35:1783-1797. [PMID: 29618097 PMCID: PMC5995191 DOI: 10.1093/molbev/msy055] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying ancient proteins and comparing biochemical properties between parental or extinct species and their extant relatives. It relies on multiple sequence alignment (MSA) which may introduce biases, and it remains unknown how MSA methodological approaches impact ancestral sequence reconstruction (ASR). Here, we investigate how MSA methodology modulates ASR using a simulation study of various evolutionary scenarios. We evaluate the accuracy of ancestral protein sequence reconstruction for simulated data and compare reconstruction outcomes using different alignment methods. Our results reveal biases introduced not only by aligner algorithms and assumptions, but also tree topology and the rate of insertions and deletions. Under many conditions we find no substantial differences between the MSAs. However, increasing the difficulty for the aligners can significantly impact ASR. The MAFFT consistency aligners and PRANK variants exhibit the best performance, whereas FSA displays limited performance. We also discover a bias towards reconstructed sequences longer than the true ancestors, deriving from a preference for inferring insertions, in almost all MSA methodological approaches. In addition, we find measures of MSA quality generally correlate highly with reconstruction accuracy. Thus, we show MSA methodological differences can affect the quality of reconstructions and propose MSA methods should be selected with care to accurately determine ancestral states with confidence.
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Affiliation(s)
- Ricardo Assunção Vialle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Department of Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Asif U Tamuri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Research IT Services, University College London, London, United Kingdom
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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71
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Following the Evolutionary Track of a Highly Specific l-Arginine Oxidase by Reconstruction and Biochemical Analysis of Ancestral and Native Enzymes. Appl Environ Microbiol 2019; 85:AEM.00459-19. [PMID: 30979835 DOI: 10.1128/aem.00459-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 03/27/2019] [Indexed: 02/02/2023] Open
Abstract
Following the evolutionary track of enzymes can help elucidate how enzymes attain their characteristic functions, such as thermal adaptation and substrate selectivity, during the evolutionary process. Ancestral sequence reconstruction (ASR) is effective for following evolutionary processes if sufficient sequence data are available. Selecting sequences from the data to generate a curated sequence library is necessary for the successful design of artificial proteins by ASR. In this study, we tried to follow the evolutionary track of l-arginine oxidase (AROD), a flavin adenine dinucleotide (FAD)-dependent amino acid oxidase (LAAO) that exhibits high specificity for l-arginine. The library was generated by selecting sequences in which the 15th, 50th, 332nd, and 580th residues are Gly, Ser, Trp, and Thr, respectively. We excluded sequences that are either extremely short or long and those with a low degree of sequence identity. Three ancestral ARODs (AncARODn0, AncARODn1, and AncARODn2) were designed using the library. Subsequently, we expressed the ancestral ARODs as well as native Oceanobacter kriegii AROD (OkAROD) in bacteria. AncARODn0 is phylogenetically most remote from OkAROD, whereas AncARODn2 is most similar to OkAROD. Thermal stability was gradually increased by extending AROD sequences back to the progenitor, while the temperature at which the residual activity is half of the maximum measured activity (T 1/2) of AncARODn0 was >20°C higher than that of OkAROD. Remarkably, only AncARODn0 exhibited broad substrate selectivity similar to that of conventional promiscuous LAAO. Taken together, our findings led us to infer that AROD may have evolved from a highly thermostable and promiscuous LAAO.IMPORTANCE In this study, we attempted to infer the molecular evolution of a recently isolated FAD-dependent l-arginine oxidase (AROD) that oxidizes l-arginine to 2-ketoarginine. Utilizing 10 candidate AROD sequences, we obtained a total of three ancestral ARODs. In addition, one native AROD was obtained by cloning one of the candidate ARODs. The candidate sequences were selected utilizing a curation method defined in this study. All the ARODs were successfully expressed in Escherichia coli for analysis of their biochemical functions. The catalytic activity of our bacterially expressed ancestral ARODs suggests that our ASR was successful. The ancestral AROD that is phylogenetically most remote from a native AROD has the highest thermal stability and substrate promiscuity. Our findings led us to infer that AROD evolved from a highly thermostable and promiscuous LAAO. As an application, we can design artificial ARODs with improved functions compared with those of native ones.
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72
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Zhong Z, Liu CC. Probing pathways of adaptation with continuous evolution. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 14:18-24. [PMID: 31608311 PMCID: PMC6788780 DOI: 10.1016/j.coisb.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ziwei Zhong
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
- Lead Contact
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73
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Kuzminkova AA, Sokol AD, Ushakova KE, Popadin KY, Gunbin KV. mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria. BMC Evol Biol 2019; 19:47. [PMID: 30813887 PMCID: PMC6391778 DOI: 10.1186/s12862-019-1371-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Heterotachy is the variation in the evolutionary rate of aligned sites in different parts of the phylogenetic tree. It occurs mainly due to epistatic interactions among the substitutions, which are highly complex and make it difficult to study protein evolution. The vast majority of computational evolutionary approaches for studying these epistatic interactions or their evolutionary consequences in proteins require high computational time. However, recently, it has been shown that the evolution of residue solvent accessibility (RSA) is tightly linked with changes in protein fitness and intra-protein epistatic interactions. This provides a computationally fast alternative, based on comparison of evolutionary rates of amino acid replacements with the rates of RSA evolutionary changes in order to recognize any shifts in epistatic interaction. RESULTS Based on RSA information, data randomization and phylogenetic approaches, we constructed a software pipeline, which can be used to analyze the evolutionary consequences of intra-protein epistatic interactions with relatively low computational time. We analyzed the evolution of 512 protein families tightly linked to mitochondrial function in Vertebrates and created "mtProtEvol", the web resource with data on protein evolution. In strict agreement with lifespan and metabolic rate data, we demonstrated that different functional categories of mitochondria-related proteins subjected to selection on accelerated and decelerated RSA rates in rodents and primates. For example, accelerated RSA evolution in rodents has been shown for Krebs cycle enzymes, respiratory chain and reactive oxygen species metabolism, while in primates these functions are stress-response, translation and mtDNA integrity. Decelerated RSA evolution in rodents has been demonstrated for translational machinery and oxidative stress response components. CONCLUSIONS mtProtEvol is an interactive resource focused on evolutionary analysis of epistatic interactions in protein families involved in Vertebrata mitochondria function and available at http://bioinfodbs.kantiana.ru/mtProtEvol /. This resource and the devised software pipeline may be useful tool for researchers in area of protein evolution.
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Affiliation(s)
- Anastasia A. Kuzminkova
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Anastasia D. Sokol
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Kristina E. Ushakova
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Konstantin Yu. Popadin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Konstantin V. Gunbin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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74
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Straub K, Linde M, Kropp C, Blanquart S, Babinger P, Merkl R. Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. Biol Chem 2019; 400:367-381. [PMID: 30763032 DOI: 10.1515/hsz-2018-0344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/07/2018] [Indexed: 11/15/2022]
Abstract
For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool. The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction. A common approach for sequence selection consists of several rounds of manual recompilation that is driven by embedded phylogenetic analyses of the varied sequence sets. For ASR of a geranylgeranylglyceryl phosphate synthase, we additionally utilized FitSS4ASR, which replaces this time-consuming protocol with an efficient and more rational approach. FitSS4ASR applies orthogonal filters to a set of homologs to eliminate outlier sequences and those bearing only a weak phylogenetic signal. To demonstrate the usefulness of FitSS4ASR, we determined experimentally the oligomerization state of eight predecessors, which is a delicate and taxon-specific property. Corresponding ancestors deduced in a manual approach and by means of FitSS4ASR had the same dimeric or hexameric conformation; this concordance testifies to the efficiency of FitSS4ASR for sequence selection. FitSS4ASR-based results of two other ASR experiments were added to the Supporting Information. Program and documentation are available at https://gitlab.bioinf.ur.de/hek61586/FitSS4ASR.
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Affiliation(s)
- Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Samuel Blanquart
- University of Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
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75
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Doroshkov AV, Konstantinov DK, Afonnikov DA, Gunbin KV. The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development. BMC PLANT BIOLOGY 2019; 19:53. [PMID: 30813891 PMCID: PMC6393967 DOI: 10.1186/s12870-019-1640-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND The variation in structure and function of gene regulatory networks (GRNs) participating in organisms development is a key for understanding species-specific evolutionary strategies. Even the tiniest modification of developmental GRN might result in a substantial change of a complex morphogenetic pattern. Great variety of trichomes and their accessibility makes them a useful model for studying the molecular processes of cell fate determination, cell cycle control and cellular morphogenesis. Nowadays, a large number of genes regulating the morphogenesis of A. thaliana trichomes are described. Here we aimed at a study the evolution of the GRN defining the trichome formation, and evaluation its importance in other developmental processes. RESULTS In study of the evolution of trichomes formation GRN we combined classical phylogenetic analysis with information on the GRN topology and composition in major plants taxa. This approach allowed us to estimate both times of evolutionary emergence of the GRN components which are mainly proteins, and the relative rate of their molecular evolution. Various simplifications of protein structure (based on the position of amino acid residues in protein globula, secondary structure type, and structural disorder) allowed us to demonstrate the evolutionary associations between changes in protein globules and speciations/duplications events. We discussed their potential involvement in protein-protein interactions and GRN function. CONCLUSIONS We hypothesize that the divergence and/or the specialization of the trichome-forming GRN is linked to the emergence of plant taxa. Information about the structural targets of the protein evolution in the GRN may predict switching points in gene networks functioning in course of evolution. We also propose a list of candidate genes responsible for the development of trichomes in a wide range of plant species.
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Affiliation(s)
- Alexey V. Doroshkov
- The Siberian Branch of the Russian Academy of Sciences (IC&G SB RAS), The Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University (NSU), Novosibirsk, Russia
| | - Dmitrii K. Konstantinov
- The Siberian Branch of the Russian Academy of Sciences (IC&G SB RAS), The Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University (NSU), Novosibirsk, Russia
| | - Dmitrij A. Afonnikov
- The Siberian Branch of the Russian Academy of Sciences (IC&G SB RAS), The Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University (NSU), Novosibirsk, Russia
| | - Konstantin V. Gunbin
- Novosibirsk State University (NSU), Novosibirsk, Russia
- School of Life Science, Immanuel Kant Federal Baltic University, Kaliningrad, Russia
- Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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Schulte‐Sasse M, Pardo‐Ávila F, Pulido‐Mayoral NO, Vázquez‐Lobo A, Costas M, García‐Hernández E, Rodríguez‐Romero A, Fernández‐Velasco DA. Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function. FEBS J 2019; 286:882-900. [DOI: 10.1111/febs.14741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/01/2018] [Accepted: 12/23/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Mariana Schulte‐Sasse
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Fátima Pardo‐Ávila
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Nancy O. Pulido‐Mayoral
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Alejandra Vázquez‐Lobo
- Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica Departamento de Fisicoquímica Facultad de Química Universidad Nacional Autónoma de México Mexico
| | | | | | - Daniel Alejandro Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
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77
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Straub K, Merkl R. Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation. Methods Mol Biol 2019; 1851:171-182. [PMID: 30298397 DOI: 10.1007/978-1-4939-8736-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ancestral sequence reconstruction (ASR) is a powerful tool to infer primordial sequences from contemporary, i.e., extant ones. An essential element of ASR is the computation of a phylogenetic tree whose leaves are the chosen extant sequences. Most often, the reconstructed sequence related to the root of this tree is of greatest interest: It represents the common ancestor (CA) of the sequences under study. If this sequence encodes a protein, one can "resurrect" the CA by means of gene synthesis technology and study biochemical properties of this extinct predecessor with the help of wet-lab experiments.However, ASR deduces also sequences for all internal nodes of the tree, and the well-considered analysis of these "intermediates" can help to elucidate evolutionary processes. Moreover, one can identify key mutations that alter proteins or protein complexes and are responsible for the differing properties of extant proteins. As an illustrative example, we describe the protocol for the rapid identification of hotspots determining the binding of the two subunits within the heteromeric complex imidazole glycerol phosphate synthase.
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Affiliation(s)
- Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.
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78
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The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. Methods Mol Biol 2019; 1851:215-231. [PMID: 30298399 DOI: 10.1007/978-1-4939-8736-8_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Phylogenetic inference from protein data is traditionally based on empirical substitution models of evolution that assume that protein sites evolve independently of each other and under the same substitution process. However, it is well known that the structural properties of a protein site in the native state affect its evolution, in particular the sequence entropy and the substitution rate. Starting from the seminal proposal by Halpern and Bruno, where structural properties are incorporated in the evolutionary model through site-specific amino acid frequencies, several models have been developed to tackle the influence of protein structure on sequence evolution. Here we describe stability-constrained substitution (SCS) models that explicitly consider the stability of the native state against both unfolded and misfolded states. One of them, the mean-field model, provides an independent sites approximation that can be readily incorporated in maximum likelihood methods of phylogenetic inference, including ancestral sequence reconstruction. Next, we describe its validation with simulated and real proteins and its limitations and advantages with respect to empirical models that lack site specificity. We finally provide guidelines and recommendations to analyze protein data accounting for stability constraints, including computer simulations and inferences of protein evolution based on maximum likelihood. Some practical examples are included to illustrate these procedures.
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79
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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80
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Hendrikse NM, Charpentier G, Nordling E, Syrén PO. Ancestral diterpene cyclases show increased thermostability and substrate acceptance. FEBS J 2018; 285:4660-4673. [PMID: 30369053 DOI: 10.1111/febs.14686] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/07/2018] [Accepted: 10/25/2018] [Indexed: 11/26/2022]
Abstract
Bacterial diterpene cyclases are receiving increasing attention in biocatalysis and synthetic biology for the sustainable generation of complex multicyclic building blocks. Herein, we explore the potential of ancestral sequence reconstruction (ASR) to generate remodeled cyclases with enhanced stability, activity, and promiscuity. Putative ancestors of spiroviolene synthase, a bacterial class I diterpene cyclase, display an increased yield of soluble protein of up to fourfold upon expression in the model organism Escherichia coli. Two of the resurrected enzymes, with an estimated age of approximately 1.7 million years, display an upward shift in thermostability of 7-13 °C. Ancestral spiroviolene synthases catalyze cyclization of the natural C20 -substrate geranylgeranyl diphosphate (GGPP) and also accept C15 farnesyl diphosphate (FPP), which is not converted by the extant enzyme. In contrast, the consensus sequence generated from the corresponding multiple sequence alignment was found to be inactive toward both substrates. Mutation of a nonconserved position within the aspartate-rich motif of the reconstructed ancestral cyclases was associated with modest effects on activity and relative substrate specificity (i.e., kcat /KM for GGPP over kcat /KM for FPP). Kinetic analyses performed at different temperatures reveal a loss of substrate saturation, when going from the ancestor with highest thermostability to the modern enzyme. The kinetics data also illustrate how an increase in temperature optimum of biocatalysis is reflected in altered entropy and enthalpy of activation. Our findings further highlight the potential and limitations of applying ASR to biosynthetic machineries in secondary metabolism.
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Affiliation(s)
- Natalie M Hendrikse
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Swedish Orphan Biovitrum AB, Stockholm, Sweden
| | - Gwenaëlle Charpentier
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Swedish Orphan Biovitrum AB, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Protein Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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81
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Abstract
The sequence space of five protein superfamilies was investigated by constructing sequence networks. The nodes represent individual sequences, and two nodes are connected by an edge if the global sequence identity of two sequences exceeds a threshold. The networks were characterized by their degree distribution (number of nodes with a given number of neighbors) and by their fractal network dimension. Although the five protein families differed in sequence length, fold, and domain arrangement, their network properties were similar. The fractal network dimension Df was distance-dependent: a high dimension for single and double mutants (Df = 4.0), which dropped to Df = 0.7-1.0 at 90% sequence identity, and increased to Df = 3.5-4.5 below 70% sequence identity. The distance dependency of the network dimension is consistent with evolutionary constraints for functional proteins. While random single and double mutations often result in a functional protein, the accumulation of more than ten mutations is dominated by epistasis. The networks of the five protein families were highly inhomogeneous with few highly connected communities ("hub sequences") and a large number of smaller and less connected communities. The degree distributions followed a power-law distribution with similar scaling exponents close to 1. Because the hub sequences have a large number of functional neighbors, they are expected to be robust toward possible deleterious effects of mutations. Because of their robustness, hub sequences have the potential of high innovability, with additional mutations readily inducing new functions. Therefore, they form hotspots of evolution and are promising candidates as starting points for directed evolution experiments in biotechnology.
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82
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Nakano S, Motoyama T, Miyashita Y, Ishizuka Y, Matsuo N, Tokiwa H, Shinoda S, Asano Y, Ito S. Benchmark Analysis of Native and Artificial NAD +-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data. Biochemistry 2018; 57:3722-3732. [PMID: 29787243 DOI: 10.1021/acs.biochem.8b00339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full-consensus design (FCD) and ancestral-sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial l-threonine 3-dehydrogenases (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1, and AncTDH, using FCD and ASR, respectively. The artificial SDR-TDHs had excellent thermal stability and NAD+ recognition compared to native SDR-TDH from Cupriavidus necator (CnTDH); the melting temperatures of FcTDH-N1 and AncTDH were about 10 and 5 °C higher than that of CnTDH, respectively, and the dissociation constants toward NAD+ of FcTDH-N1 and AncTDH were 2- and 7-fold lower than that of CnTDH, respectively. Enzymatic efficiency of the artificial SDR-TDHs were comparable to that of CnTDH. Crystal structures of FcTDH-N1 and AncTDH were determined at 2.8 and 2.1 Å resolution, respectively. Structural and MD simulation analysis of the SDR-TDHs indicated that only the flexibility at specific regions was changed, suggesting that multiple mutations introduced in the artificial SDR-TDHs altered their flexibility and thereby affected their enzymatic properties. Benchmark analysis of the SDR-TDHs indicated that both FCD and ASR can generate highly functional proteins if a curated library is prepared appropriately.
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Affiliation(s)
- Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.,Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Tomoharu Motoyama
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Yurina Miyashita
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Yuki Ishizuka
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Naoya Matsuo
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Hiroaki Tokiwa
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Suguru Shinoda
- Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan.,Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Yasuhisa Asano
- Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan.,Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.,Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
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83
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Campbell EC, Correy GJ, Mabbitt PD, Buckle AM, Tokuriki N, Jackson CJ. Laboratory evolution of protein conformational dynamics. Curr Opin Struct Biol 2018; 50:49-57. [DOI: 10.1016/j.sbi.2017.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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84
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Risso VA, Sanchez-Ruiz JM, Ozkan SB. Biotechnological and protein-engineering implications of ancestral protein resurrection. Curr Opin Struct Biol 2018; 51:106-115. [PMID: 29660672 DOI: 10.1016/j.sbi.2018.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Approximations to the sequences of ancestral proteins can be derived from the sequences of their modern descendants. Proteins encoded by such reconstructed sequences can be prepared in the laboratory and subjected to experimental scrutiny. These 'resurrected' ancestral proteins often display remarkable properties, reflecting ancestral adaptations to intra-cellular and extra-cellular environments that differed from the environments hosting modern/extant proteins. Recent experimental and computational work has specifically discussed high stability, substrate and catalytic promiscuity, conformational flexibility/diversity and altered patterns of interaction with other sub-cellular components. In this review, we discuss these remarkable properties as well as recent attempts to explore their biotechnological and protein-engineering potential.
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Affiliation(s)
- Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain.
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, United States.
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85
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Buddrus L, Andrews ESV, Leak DJ, Danson MJ, Arcus VL, Crennell SJ. Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase. Acta Crystallogr F Struct Biol Commun 2018; 74:179-186. [PMID: 29497023 PMCID: PMC5947705 DOI: 10.1107/s2053230x18002819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/16/2018] [Indexed: 12/30/2022] Open
Abstract
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were Rwork = 0.246 (0.3671 in the highest resolution bin) and Rfree = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.
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Affiliation(s)
- Lisa Buddrus
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, England
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Emma S. V. Andrews
- School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Michael J. Danson
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Vickery L. Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Susan J. Crennell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
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86
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Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins. Sci Rep 2018; 8:1227. [PMID: 29352156 PMCID: PMC5775292 DOI: 10.1038/s41598-018-19561-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/03/2018] [Indexed: 11/19/2022] Open
Abstract
Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study. We eventually found that two convergent sequences, each comprised of a 13-amino acid alphabet, folded into soluble, stable and catalytically active structures, even though their stabilities and activities were not as high as those of the parent protein. Notably, many but not all of the reduced-set amino acids coincide with those plausibly abundant in primitive Earth. The inconsistent amino acids appeared to be important for catalytic activity but not for stability. Therefore, our findings suggest that the prebiotically abundant amino acids were used for creating stable protein structures and other amino acids with functional side chains were recruited to achieve efficient catalysis.
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87
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Jones DR, Thomas D, Alger N, Ghavidel A, Inglis GD, Abbott DW. SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:27. [PMID: 29441125 PMCID: PMC5798181 DOI: 10.1186/s13068-018-1027-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/18/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Deposition of new genetic sequences in online databases is expanding at an unprecedented rate. As a result, sequence identification continues to outpace functional characterization of carbohydrate active enzymes (CAZymes). In this paradigm, the discovery of enzymes with novel functions is often hindered by high volumes of uncharacterized sequences particularly when the enzyme sequence belongs to a family that exhibits diverse functional specificities (i.e., polyspecificity). Therefore, to direct sequence-based discovery and characterization of new enzyme activities we have developed an automated in silico pipeline entitled: Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity (SACCHARIS). This pipeline streamlines the selection of uncharacterized sequences for discovery of new CAZyme or CBM specificity from families currently maintained on the CAZy website or within user-defined datasets. RESULTS SACCHARIS was used to generate a phylogenetic tree of a GH43, a CAZyme family with defined subfamily designations. This analysis confirmed that large datasets can be organized into sequence clusters of manageable sizes that possess related functions. Seeding this tree with a GH43 sequence from Bacteroides dorei DSM 17855 (BdGH43b, revealed it partitioned as a single sequence within the tree. This pattern was consistent with it possessing a unique enzyme activity for GH43 as BdGH43b is the first described α-glucanase described for this family. The capacity of SACCHARIS to extract and cluster characterized carbohydrate binding module sequences was demonstrated using family 6 CBMs (i.e., CBM6s). This CBM family displays a polyspecific ligand binding profile and contains many structurally determined members. Using SACCHARIS to identify a cluster of divergent sequences, a CBM6 sequence from a unique clade was demonstrated to bind yeast mannan, which represents the first description of an α-mannan binding CBM. Additionally, we have performed a CAZome analysis of an in-house sequenced bacterial genome and a comparative analysis of B. thetaiotaomicron VPI-5482 and B. thetaiotaomicron 7330, to demonstrate that SACCHARIS can generate "CAZome fingerprints", which differentiate between the saccharolytic potential of two related strains in silico. CONCLUSIONS Establishing sequence-function and sequence-structure relationships in polyspecific CAZyme families are promising approaches for streamlining enzyme discovery. SACCHARIS facilitates this process by embedding CAZyme and CBM family trees generated from biochemically to structurally characterized sequences, with protein sequences that have unknown functions. In addition, these trees can be integrated with user-defined datasets (e.g., genomics, metagenomics, and transcriptomics) to inform experimental characterization of new CAZymes or CBMs not currently curated, and for researchers to compare differential sequence patterns between entire CAZomes. In this light, SACCHARIS provides an in silico tool that can be tailored for enzyme bioprospecting in datasets of increasing complexity and for diverse applications in glycobiotechnology.
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Affiliation(s)
- Darryl R. Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - Dallas Thomas
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - Nicholas Alger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - Ata Ghavidel
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - G. Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - D. Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
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88
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Buchholz PCF, Fademrecht S, Pleiss J. Percolation in protein sequence space. PLoS One 2017; 12:e0189646. [PMID: 29261740 PMCID: PMC5738032 DOI: 10.1371/journal.pone.0189646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
The currently known protein sequences are not distributed equally in sequence space, but cluster into families. Analyzing the cluster size distribution gives a glimpse of the large and unknown extant protein sequence space, which has been explored during evolution. For six protein superfamilies with different fold and function, the cluster size distributions followed a power law with slopes between 2.4 and 3.3, which represent upper limits to the cluster distribution of extant sequences. The power law distribution of cluster sizes is in accordance with percolation theory and strongly supports connectedness of extant sequence space. Percolation of extant sequence space has three major consequences: (1) It transforms our view of sequence space as a highly connected network where each sequence has multiple neighbors, and each pair of sequences is connected by many different paths. A high degree of connectedness is a necessary condition of efficient evolution, because it overcomes the possible blockage by sign epistasis and reciprocal sign epistasis. (2) The Fisher exponent is an indicator of connectedness and saturation of sequence space of each protein superfamily. (3) All clusters are expected to be connected by extant sequences that become apparent as a higher portion of extant sequence space becomes known. Being linked to biochemically distinct homologous families, bridging sequences are promising enzyme candidates for applications in biotechnology because they are expected to have substrate ambiguity or catalytic promiscuity.
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Affiliation(s)
- Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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89
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Jan AH, Dubreucq E, Drone J, Subileau M. A glimpse into the specialization history of the lipases/acyltransferases family of CpLIP2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [DOI: 10.1016/j.bbapap.2017.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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90
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Akanuma S. Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere. Life (Basel) 2017; 7:life7030033. [PMID: 28783077 PMCID: PMC5617958 DOI: 10.3390/life7030033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 01/02/2023] Open
Abstract
Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth’s early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth’s surface temperature gradually decreased over time, from Archean to present.
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Affiliation(s)
- Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan.
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91
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Palombo M, Bonucci A, Etienne E, Ciurli S, Uversky VN, Guigliarelli B, Belle V, Mileo E, Zambelli B. The relationship between folding and activity in UreG, an intrinsically disordered enzyme. Sci Rep 2017; 7:5977. [PMID: 28729736 PMCID: PMC5519622 DOI: 10.1038/s41598-017-06330-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/12/2017] [Indexed: 12/02/2022] Open
Abstract
A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease. The effect of denaturants and osmolytes on protein structure and activity was analyzed using circular dichroism (CD), Site-Directed Spin Labeling (SDSL) coupled to EPR spectroscopy, and enzymatic assays. Our data show that SpUreG needs a "flexibility window" to be catalytically competent, with both too low and too high mobility being detrimental for its activity.
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Affiliation(s)
- Marta Palombo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna, 40127, Italy
| | - Alessio Bonucci
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Emilien Etienne
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna, 40127, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, MDC07, USA
| | - Bruno Guigliarelli
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Valérie Belle
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Elisabetta Mileo
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France.
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna, 40127, Italy.
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92
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Manteca A, Schönfelder J, Alonso-Caballero A, Fertin MJ, Barruetabeña N, Faria BF, Herrero-Galán E, Alegre-Cebollada J, De Sancho D, Perez-Jimenez R. Mechanochemical evolution of the giant muscle protein titin as inferred from resurrected proteins. Nat Struct Mol Biol 2017; 24:652-657. [PMID: 28671667 DOI: 10.1038/nsmb.3426] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/02/2017] [Indexed: 01/07/2023]
Abstract
The sarcomere-based structure of muscles is conserved among vertebrates; however, vertebrate muscle physiology is extremely diverse. A molecular explanation for this diversity and its evolution has not been proposed. We use phylogenetic analyses and single-molecule force spectroscopy (smFS) to investigate the mechanochemical evolution of titin, a giant protein responsible for the elasticity of muscle filaments. We resurrect eight-domain fragments of titin corresponding to the common ancestors to mammals, sauropsids, and tetrapods, which lived 105-356 Myr ago, and compare them with titin fragments from some of their modern descendants. We demonstrate that the resurrected titin molecules are rich in disulfide bonds and display high mechanical stability. These mechanochemical elements have changed over time, creating a paleomechanical trend that seems to correlate with animal body size, allowing us to estimate the sizes of extinct species. We hypothesize that mechanical adjustments in titin contributed to physiological changes that allowed the muscular development and diversity of modern tetrapods.
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Affiliation(s)
| | | | | | | | | | - Bruna F Faria
- Laboratory of Molecular Modeling, Federal University of São João del-Rei, São João del-Rei, Brazil
| | - Elias Herrero-Galán
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | | | - David De Sancho
- CIC nanoGUNE, San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Raul Perez-Jimenez
- CIC nanoGUNE, San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Evolution and Genomics Technologies, S. L. (Evolgene), San Sebastian, Spain
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93
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Dias R, Manny A, Kolaczkowski O, Kolaczkowski B. Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins. Mol Biol Evol 2017; 34:1429-1444. [PMID: 28333205 PMCID: PMC5435087 DOI: 10.1093/molbev/msx090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs-consisting of 2-3 tandem double-stranded RNA binding motifs (dsrms)-arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1-β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications.
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Affiliation(s)
- Raquel Dias
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Austin Manny
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL
- Genetics Institute, University of Florida, Gainesville, FL
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94
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Lumba S, Holbrook-Smith D, McCourt P. The perception of strigolactones in vascular plants. Nat Chem Biol 2017; 13:599-606. [DOI: 10.1038/nchembio.2340] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/15/2017] [Indexed: 11/09/2022]
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95
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Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance. Cell Rep 2017; 19:1247-1256. [DOI: 10.1016/j.celrep.2017.04.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/14/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022] Open
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96
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97
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Holinski A, Heyn K, Merkl R, Sterner R. Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 2017; 85:312-321. [PMID: 27936490 DOI: 10.1002/prot.25225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 01/20/2023]
Abstract
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues. Subsequent titration experiments with a reconstructed evolutionary intermediate linking LUCA-HisF and paHisF and inspection of the subunit interface of a contemporary ImGPS allowed us to narrow down the differences crucial for zmHisH binding to nine amino acids of HisF. Homology modeling and in silico mutagenesis studies suggested that at most two of these nine HisF residues are crucial for zmHisH binding. These computational results were verified by experimental site-directed mutagenesis, which finally enabled us to pinpoint a single amino acid residue in HisF that is decisive for high-affinity binding of zmHisH. Our work shows that the identification of protein interface hotspots can be very efficient when reconstructed proteins with different binding properties are included in the analysis. Proteins 2017; 85:312-321. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexandra Holinski
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
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98
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Barriuso J, Martínez MJ. Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures. BMC Genomics 2017; 18:12. [PMID: 28049436 PMCID: PMC5209871 DOI: 10.1186/s12864-016-3419-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/13/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Fungal "Versatile carboxylic ester hydrolases" are enzymes with great biotechnological interest. Here we carried out a bioinformatic screening to find these proteins in genomes from Agaricales, by means of searching for conserved motifs, sequence and phylogenetic analysis, and three-dimensional modeling. Moreover, we reconstructed the molecular evolution of these enzymes along the time by inferring and analyzing the sequence of ancestral intermediate forms. RESULTS The properties of the ancestral candidates are discussed on the basis of their three-dimensional structural models, the hydrophobicity of the lid, and the substrate binding intramolecular tunnel, revealing all of them featured properties of these enzymes. The evolutionary history of the putative lipases revealed an increase on the length and hydrophobicity of the lid region, as well as in the size of the substrate binding pocket, during evolution time. These facts suggest the enzymes' specialization towards certain substrates and their subsequent loss of promiscuity. CONCLUSIONS These results bring to light the presence of different pools of lipases in fungi with different habitats and life styles. Despite the consistency of the data gathered from reconstruction of ancestral sequences, the heterologous expression of some of these candidates would be essential to corroborate enzymes' activities.
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Affiliation(s)
- Jorge Barriuso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Department of Environmental Biology, Ramiro de Maeztu 9, Madrid, E-28040, Spain.
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Department of Environmental Biology, Ramiro de Maeztu 9, Madrid, E-28040, Spain.
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99
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Clifton BE, Whitfield JH, Sanchez-Romero I, Herde MK, Henneberger C, Janovjak H, Jackson CJ. Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors. Methods Mol Biol 2017; 1596:71-87. [PMID: 28293881 DOI: 10.1007/978-1-4939-6940-1_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Small molecule biosensors based on Förster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.
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Affiliation(s)
- Ben E Clifton
- Research School of Chemistry, The Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT, 2601, Australia
| | - Jason H Whitfield
- Research School of Chemistry, The Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT, 2601, Australia
| | | | - Michel K Herde
- Institute of Cellular Neurosciences, University of Bonn, Bonn, Germany
| | - Christian Henneberger
- Institute of Cellular Neurosciences, University of Bonn, Bonn, Germany
- German Centre for Neurodegenerative Diseases, Bonn, Germany
- University College of London, London, UK
| | - Harald Janovjak
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT, 2601, Australia.
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100
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