1
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Hocher A, Warnecke T. Nucleosomes at the Dawn of Eukaryotes. Genome Biol Evol 2024; 16:evae029. [PMID: 38366053 PMCID: PMC10919886 DOI: 10.1093/gbe/evae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/09/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024] Open
Abstract
Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain opaque. Histone-fold proteins are also found in archaea, but the nucleosome we know-a hetero-octameric complex composed of histones with long, disordered tails-is a hallmark of eukaryotes. What were the properties of the earliest nucleosomes? Did ancestral histones inevitably assemble into nucleosomes? When and why did the four core histones evolve? This review will look at the evolution of the eukaryotic nucleosome from the vantage point of archaea, focusing on the key evolutionary transitions required to build a modern nucleosome. We will highlight recent work on the closest archaeal relatives of eukaryotes, the Asgardarchaea, and discuss what their histones can and cannot tell us about the early evolution of eukaryotic chromatin. We will also discuss how viruses have become an unexpected source of information about the evolutionary path toward the nucleosome. Finally, we highlight the properties of early nucleosomes as an area where new tools and data promise tangible progress in the not-too-distant future.
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Affiliation(s)
- Antoine Hocher
- Medical Research Council Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tobias Warnecke
- Medical Research Council Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Trinity College, University of Oxford, Oxford, UK
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2
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Calvó-Tusell C, Maria-Solano MA, Osuna S, Feixas F. Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase. J Am Chem Soc 2022; 144:7146-7159. [PMID: 35412310 PMCID: PMC9052757 DOI: 10.1021/jacs.1c12629] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Deciphering the molecular
mechanisms of enzymatic allosteric regulation
requires the structural characterization of functional states and
also their time evolution toward the formation of the allosterically
activated ternary complex. The transient nature and usually slow millisecond
time scale interconversion between these functional states hamper
their experimental and computational characterization. Here, we combine
extensive molecular dynamics simulations, enhanced sampling techniques,
and dynamical networks to describe the allosteric activation of imidazole
glycerol phosphate synthase (IGPS) from the substrate-free form to
the active ternary complex. IGPS is a heterodimeric bienzyme complex
whose HisH subunit is responsible for hydrolyzing glutamine and delivering
ammonia for the cyclase activity in HisF. Despite significant advances
in understanding the underlying allosteric mechanism, essential molecular
details of the long-range millisecond allosteric activation of IGPS
remain hidden. Without using a priori information
of the active state, our simulations uncover how IGPS, with the allosteric
effector bound in HisF, spontaneously captures glutamine in a catalytically
inactive HisH conformation, subsequently attains a closed HisF:HisH
interface, and finally forms the oxyanion hole in HisH for efficient
glutamine hydrolysis. We show that the combined effector and substrate
binding dramatically decreases the conformational barrier associated
with oxyanion hole formation, in line with the experimentally observed
4500-fold activity increase in glutamine hydrolysis. The allosteric
activation is controlled by correlated time-evolving dynamic networks
connecting the effector and substrate binding sites. This computational
strategy tailored to describe millisecond events can be used to rationalize
the effect of mutations on the allosteric regulation and guide IGPS
engineering efforts.
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Affiliation(s)
- Carla Calvó-Tusell
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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3
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Del Duca S, Puglia AM, Calderone V, Bazzicalupo M, Fani R. Effect of Non-Lethal Selection on Spontaneous Revertants of Frameshift Mutations: The Escherichia coli hisF Case. Microorganisms 2022; 10:692. [PMID: 35456744 PMCID: PMC9032791 DOI: 10.3390/microorganisms10040692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/25/2023] Open
Abstract
Microorganisms possess the potential to adapt to fluctuations in environmental parameters, and their evolution is driven by the continuous generation of mutations. The reversion of auxotrophic mutations has been widely studied; however, little is known about the reversion of frameshift mutations resulting in amino acid auxotrophy and on the structure and functioning of the protein encoded by the revertant mutated gene. The aims of this work were to analyze the appearance of reverse mutations over time and under different selective pressures and to investigate revertant enzymes' three-dimensional structures and their correlation with a different growth ability. Escherichia coli FB182 strain, carrying the hisF892 single nucleotide deletion resulting in histidine auxotrophy, was subjected to different selective pressures, and revertant mutants were isolated and characterized. The obtained results allowed us to identify different indels of different lengths located in different positions in the hisF gene, and relations with the incubation time and the selective pressure applied were observed. Moreover, the structure of the different mutant proteins was consistent with the respective revertant ability to grow in absence of histidine, highlighting a correlation between the mutations and the catalytic activity of the mutated HisF enzyme.
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Affiliation(s)
- Sara Del Duca
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (S.D.D.); (M.B.)
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy;
| | - Vito Calderone
- Magnetic Resonance Center (CERM)/Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (S.D.D.); (M.B.)
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (S.D.D.); (M.B.)
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4
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Dubey KD, Singh W. Simulations reveal the key role of Arg15 in the promiscuous activity in the HisA enzyme. Org Biomol Chem 2021; 19:10652-10661. [PMID: 34854451 DOI: 10.1039/d1ob02029c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HisA enzyme catalyzes the first step of histidine biosynthesis via the Amadori rearrangement of the substrate ProFAR. Since it possesses the most conserved and ancient TIM-barrel fold, it provides an ideal framework for bioengineering of a new function from ancestral enzymes. In the present study, first, the catalytic mechanism of HisA biosynthesis was elucidated using hybrid Quantum Mechanical/Molecular Mechanical calculations, and thereafter, key residues contributing towards the promiscuity for TrpF activity were revealed using several MD simulations of a wild type enzyme and its variant with the native (ProFAR) and promiscuous (PRA) substrates. Our study reveals that the two loops (βα)1 and (βα)5 on the catalytic site of the HisA enzyme have incredible adaptability for the native and promiscuous substrates. The conformational interplay between these two loops is substrate driven and precise bioengineering targeting these loops is key to the emergence of new functions. Furthermore, the study reveals a key role of the Arg 15 residue which is close to the catalytic center of the enzyme in the bifunctionality of the HisA enzyme by increasing the loop flexibility. Therefore, our study provides crucial information for future bioengineering work to use the HisA enzyme as a scaffold for new enzymatic activity.
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Affiliation(s)
- Kshatresh Dutta Dubey
- Department of Chemistry and Center for Informatics, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh-201314, India.
| | - Warispreet Singh
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.,Hub for Biotechnology in Build Environment, Newcastle upon Tyne, NE1 8ST, UK
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5
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A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family. Proc Natl Acad Sci U S A 2021; 118:2019571118. [PMID: 33875592 PMCID: PMC8092565 DOI: 10.1073/pnas.2019571118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Orthologous proteins from the three superkingdoms have conserved their structures and functions over evolutionary time. We ask whether their folding mechanisms and the structures of their partially folded states are similarly conserved, using bacterial and archaeal representatives of the IGPS TIM barrel enzyme. Comparison of circular dichroism and fluorescence spectroscopic studies reveal a highly conserved mechanism, and hydrogen–deuterium exchange mass spectrometry analyses highlight similar cores of stability in regions dominated by clusters of branched aliphatic side chains. A bioinformatics analysis of hundreds of IGPS sequences from each superkingdom shows a very highly conserved sequence, V/ILLI, that nucleates the formation of a misfolded, microsecond intermediate and has existed since the last universal common ancestor of the IGPS family of proteins. The amino acid sequences of proteins have evolved over billions of years, preserving their structures and functions while responding to evolutionary forces. Are there conserved sequence and structural elements that preserve the protein folding mechanisms? The functionally diverse and ancient (βα)1–8 TIM barrel motif may answer this question. We mapped the complex six-state folding free energy surface of a ∼3.6 billion y old, bacterial indole-3-glycerol phosphate synthase (IGPS) TIM barrel enzyme by equilibrium and kinetic hydrogen–deuterium exchange mass spectrometry (HDX-MS). HDX-MS on the intact protein reported exchange in the native basin and the presence of two thermodynamically distinct on- and off-pathway intermediates in slow but dynamic equilibrium with each other. Proteolysis revealed protection in a small (α1β2) and a large cluster (β5α5β6α6β7) and that these clusters form cores of stability in Ia and Ibp. The strongest protection in both states resides in β4α4 with the highest density of branched aliphatic side chain contacts in the folded structure. Similar correlations were observed previously for an evolutionarily distinct archaeal IGPS, emphasizing a key role for hydrophobicity in stabilizing common high-energy folding intermediates. A bioinformatics analysis of IGPS sequences from the three superkingdoms revealed an exceedingly high hydrophobicity and surprising α-helix propensity for β4, preceded by a highly conserved βα-hairpin clamp that links β3 and β4. The conservation of the folding mechanisms for archaeal and bacterial IGPS proteins reflects the conservation of key elements of sequence and structure that first appeared in the last universal common ancestor of these ancient proteins.
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6
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Chioccioli S, Del Duca S, Vassallo A, Castronovo LM, Fani R. Exploring the role of the histidine biosynthetic hisF gene in cellular metabolism and in the evolution of (ancestral) genes: from LUCA to the extant (micro)organisms. Microbiol Res 2020; 240:126555. [PMID: 32673985 DOI: 10.1016/j.micres.2020.126555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 01/14/2023]
Abstract
Histidine biosynthesis is an ancestral pathway that was assembled before the appearance of the Last Universal Common Ancestor; afterwards, it remained unaltered in all the extant histidine-synthesizing (micro)organisms. It is a metabolic cross-road interconnecting histidine biosynthesis to nitrogen metabolism and the de novo synthesis of purines. This interconnection is due to the reaction catalyzed by the products of hisH and hisF genes. The latter gene is an excellent model to study which trajectories have been followed by primordial cells to build the first metabolic routes, since its evolution is the result of different molecular rearrangement events, i.e. gene duplication, gene fusion, gene elongation, and domain shuffling. Additionally, this review summarizes data concerning the involvement of hisF and its product in other different cellular processes, revealing that HisF very likely plays a role also in cell division control and involvement in virulence and nodule development in different bacteria. From the metabolic viewpoint, these results suggest that HisF plays a central role in cellular metabolism, highlighting the interconnections of different metabolic pathways.
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Affiliation(s)
- Sofia Chioccioli
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Alberto Vassallo
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | | | - Renato Fani
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
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7
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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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8
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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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9
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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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10
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Abstract
The prevalence of purifying selection in the nature suggests that larger organisms bear a higher number of slightly deleterious mutations because of smaller populations and therefore weaker selection. In this work redistribution of purifying selection in favor of information genes, pathways and processes was found in primates compared with treeshrew and rodents on the ground of genome-wide analysis. The genes which are more favored in primates belong mainly to regulation of gene expression and development, in treeshrew and rodents, to metabolism, transport, energetics, reproduction and olfaction. The former occur predominantly in the nucleus, the latter, in the cytoplasm and membranes. Thus, although purifying selection is on average weaker in the primates, it is stronger concentrated on the "information technology" of life (regulation of gene expression and development). Increased accuracy of information processes probably allows escaping "error catastrophes" in spite of more complex organization, larger body size and higher longevity.
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11
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Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering. Biochem J 2017; 474:1-19. [PMID: 28008088 DOI: 10.1042/bcj20160507] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022]
Abstract
A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular complexes. Recently, however, ASR has developed from a tool for testing hypotheses about protein evolution to a useful means for designing novel proteins. The strength of this approach lies in the ability to infer ancestral sequences encoding proteins that have desirable properties compared with contemporary forms, particularly thermostability and broad substrate range, making them good starting points for laboratory evolution. Developments in technologies for DNA sequencing and synthesis and computational phylogenetic analysis have led to an escalation in the number of ancient proteins resurrected in the last decade and greatly facilitated the use of ASR in the burgeoning field of synthetic biology. However, the primary challenge of ASR remains in accurately inferring ancestral states, despite the uncertainty arising from evolutionary models, incomplete sequences and limited phylogenetic trees. This review will focus, firstly, on the use of ASR to uncover links between sequence and phenotype and, secondly, on the practical application of ASR in protein engineering.
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12
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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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13
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14
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Busch F, Rajendran C, Heyn K, Schlee S, Merkl R, Sterner R. Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes. Cell Chem Biol 2016; 23:709-15. [DOI: 10.1016/j.chembiol.2016.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/26/2016] [Accepted: 05/05/2016] [Indexed: 11/29/2022]
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15
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Plach MG, Reisinger B, Sterner R, Merkl R. Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation. PLoS Genet 2016; 12:e1005836. [PMID: 26824644 PMCID: PMC4732765 DOI: 10.1371/journal.pgen.1005836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/09/2016] [Indexed: 01/10/2023] Open
Abstract
Modern enzymes are highly optimized biocatalysts that process their substrates with extreme efficiency. Many enzymes catalyze more than one reaction; however, the persistence of such ambiguities, their consequences and evolutionary causes are largely unknown. As a paradigmatic case, we study the history of bi-functionality for a time span of approximately two billion years for the sugar isomerase HisA from histidine biosynthesis. To look back in time, we computationally reconstructed and experimentally characterized three HisA predecessors. We show that these ancient enzymes catalyze not only the HisA reaction but also the isomerization of a similar substrate, which is commonly processed by the isomerase TrpF in tryptophan biosynthesis. Moreover, we found that three modern-day HisA enzymes from Proteobacteria and Thermotogae also possess low TrpF activity. We conclude that this bi-functionality was conserved for at least two billion years, most likely without any evolutionary pressure. Although not actively selected for, this trait can become advantageous in the case of a gene loss. Such exaptation is exemplified by the Actinobacteria that have lost the trpF gene but possess the bi-functional HisA homolog PriA, which adopts the roles of both HisA and TrpF. Our findings demonstrate that bi-functionality can perpetuate in the absence of selection for very long time-spans. The term exaptation describes the process by which a trait that is initially just a by-product of another function may become important in a later evolutionary phase. For example, feathers served to insulate dinosaurs before helping birds fly. On the level of enzymes, bi-functionality can contribute to microbial evolution through exaptation. However, bi-functional enzymes may cause metabolic conflicts, if they are involved in different metabolic pathways. By characterizing properties of modern and computationally reconstructed ancestral variants of the sugar isomerase HisA, we demonstrate that it has been a bi-functional enzyme for the last two billion years. Most likely, bi-functionality persisted because the remaining TrpF activity is not harmful or its elimination would concurrently compromise HisA activity. Moreover, this substrate ambiguity is advantageous, as it allows compensating a gene loss as exemplified by the Actinobacteria. These microbes have lost the isomerase TrpF but possess the bi-functional HisA homolog PriA, which takes over the roles of both HisA and TrpF. Our results argue to view bi-functionality not as an evolutionary disadvantage but rather as a contribution to the evolvability of novel functions via exaptation.
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Affiliation(s)
- Maximilian G. Plach
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Bernd Reisinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (RS); (RM)
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (RS); (RM)
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Fournier GP, Andam CP, Gogarten JP. Ancient horizontal gene transfer and the last common ancestors. BMC Evol Biol 2015; 15:70. [PMID: 25897759 PMCID: PMC4427996 DOI: 10.1186/s12862-015-0350-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 04/14/2015] [Indexed: 01/22/2023] Open
Abstract
Background The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased”. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0350-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Cheryl P Andam
- Department of Epidemiology, School of Public Health, Harvard University, Boston, MA, 02115, USA.
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, and the Institute for Systems Genomics, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269-3125, USA.
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