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Sutherland‐Smith AJ, Carbone V, Schofield LR, Cronin B, Duin EC, Ronimus RS. The crystal structure of methanogen McrD, a methyl-coenzyme M reductase-associated protein. FEBS Open Bio 2024; 14:1222-1229. [PMID: 38877345 PMCID: PMC11301259 DOI: 10.1002/2211-5463.13848] [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: 03/14/2024] [Revised: 05/16/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
Methyl-coenzyme M reductase (MCR) is a multi-subunit (α2β2γ2) enzyme responsible for methane formation via its unique F430 cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high-resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin-like domain assembled into an α + β barrel-like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.
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Affiliation(s)
| | | | | | - Bryan Cronin
- Department of Chemistry and BiochemistryAuburn UniversityALUSA
| | - Evert C. Duin
- Department of Chemistry and BiochemistryAuburn UniversityALUSA
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2
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Watterson JG. The cluster model of energy transduction in biological systems. Biosystems 2024; 240:105213. [PMID: 38616011 DOI: 10.1016/j.biosystems.2024.105213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.
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3
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Huang XL. Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics. iScience 2024; 27:109555. [PMID: 38638571 PMCID: PMC11024932 DOI: 10.1016/j.isci.2024.109555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.
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Affiliation(s)
- Xiao-Lan Huang
- Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-6044, USA
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4
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Fontecilla-Camps JC. Reflections on the Origin of Coded Protein Biosynthesis. Biomolecules 2024; 14:518. [PMID: 38785925 PMCID: PMC11117964 DOI: 10.3390/biom14050518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.
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5
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Zheng Z, Goncearenco A, Berezovsky IN. Back in time to the Gly-rich prototype of the phosphate binding elementary function. Curr Res Struct Biol 2024; 7:100142. [PMID: 38655428 PMCID: PMC11035071 DOI: 10.1016/j.crstbi.2024.100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.
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Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Igor N. Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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6
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Huang XL, Harmer JR, Schenk G, Southam G. Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology. Front Chem 2024; 12:1349020. [PMID: 38389729 PMCID: PMC10881703 DOI: 10.3389/fchem.2024.1349020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. These nanocolloids exhibit intrinsic redox activity and possess direct electron transfer capacities comparable to their biological counterparts. The unique metal ion architecture of these nanocolloids, including electron configurations, coordination environment, electron conductivity, and the ability to promote spontaneous electron hopping, contributes to their transfer capabilities. Nano-size inorganic colloids are believed to be among the earliest 'oxidoreductases' to have 'evolved' on early Earth, playing critical roles in biological systems. Representing a distinct type of biocatalysts alongside metalloproteins, these nanoparticles offer an early alternative to protein-based oxidoreductase activity. While the roles of inorganic nano-sized catalysts in current Earth ecosystems are intuitively significant, they remain poorly understood and underestimated. Their contribution to chemical reactions and biogeochemical cycles likely helped shape and maintain the balance of our planet's ecosystems. However, their potential applications in biomedical, agricultural, and environmental protection sectors have not been fully explored or exploited. This review examines the structure, properties, and mechanisms of such catalysts from a material's evolutionary standpoint, aiming to raise awareness of their potential to provide innovative solutions to some of Earth's sustainability challenges.
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Affiliation(s)
- Xiao-Lan Huang
- NYS Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Jeffrey R Harmer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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7
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McGuinness KN, Fehon N, Feehan R, Miller M, Mutter AC, Rybak LA, Nam J, AbuSalim JE, Atkinson JT, Heidari H, Losada N, Kim JD, Koder RL, Lu Y, Silberg JJ, Slusky JSG, Falkowski PG, Nanda V. The energetics and evolution of oxidoreductases in deep time. Proteins 2024; 92:52-59. [PMID: 37596815 DOI: 10.1002/prot.26563] [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: 05/16/2023] [Accepted: 07/06/2023] [Indexed: 08/20/2023]
Abstract
The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation-reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation-reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.
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Affiliation(s)
- Kenneth N McGuinness
- Department of Natural Sciences, Caldwell University, Caldwell, New Jersey, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Nolan Fehon
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ryan Feehan
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA
| | - Michelle Miller
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Andrew C Mutter
- Department of Physics, The City College of New York, New York, New York, USA
| | - Laryssa A Rybak
- Department of Physics, The City College of New York, New York, New York, USA
| | - Justin Nam
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Jenna E AbuSalim
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Joshua T Atkinson
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Natalie Losada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - J Dongun Kim
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York, USA
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Jonathan J Silberg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Joanna S G Slusky
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
- Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
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8
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Feng X, Schut GJ, Adams MWW, Li H. Structures and Electron Transport Paths in the Four Families of Flavin-Based Electron Bifurcation Enzymes. Subcell Biochem 2024; 104:383-408. [PMID: 38963493 DOI: 10.1007/978-3-031-58843-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Oxidoreductases facilitating electron transfer between molecules are pivotal in metabolic pathways. Flavin-based electron bifurcation (FBEB), a recently discovered energy coupling mechanism in oxidoreductases, enables the reversible division of electron pairs into two acceptors, bridging exergonic and otherwise unfeasible endergonic reactions. This chapter explores the four distinct FBEB complex families and highlights a decade of structural insights into FBEB complexes. In this chapter, we discuss the architecture, electron transfer routes, and conformational changes across all FBEB families, revealing the structural foundation that facilitate these remarkable functions.
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Affiliation(s)
- Xiang Feng
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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9
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Magalon A. History of Maturation of Prokaryotic Molybdoenzymes-A Personal View. Molecules 2023; 28:7195. [PMID: 37894674 PMCID: PMC10609526 DOI: 10.3390/molecules28207195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
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Affiliation(s)
- Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
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10
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Freire MÁ. The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios. Biosystems 2023; 226:104873. [PMID: 36906114 DOI: 10.1016/j.biosystems.2023.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Photosynthesis is the predominant biochemical process of carbon dioxide assimilation in the biosphere. To reduce carbon dioxide into organic compounds, photosynthetic organisms have one or two distinct photochemical reaction centre complexes with which they capture solar energy and generate ATP and reducing power. The core polypeptides of the photosynthetic reaction centres show low homologies but share overlapping structural folds, overall architecture, similar functional properties and highly conserved positions in protein sequences suggesting a common ancestry. However, the other biochemical components of photosynthetic apparatus appear to be a mosaic resulting from different evolutionary trajectories. The current proposal focusses on the nature and biosynthetic pathways of some organic redox cofactors that participate in the photosynthetic systems: quinones, chlorophyll and heme rings and their attached isoprenoid side chains, as well as on the coupled proton motive forces and associated carbon fixation pathways. This perspective highlights clues about the involvement of the phosphorus and sulphur chemistries that would have shaped the different types of photosynthetic systems.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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11
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Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway. Life (Basel) 2023; 13:life13030731. [PMID: 36983886 PMCID: PMC10053121 DOI: 10.3390/life13030731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.
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12
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Aithal A, Dagar S, Rajamani S. Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins. ACS OMEGA 2023; 8:5197-5208. [PMID: 36816708 PMCID: PMC9933472 DOI: 10.1021/acsomega.2c07635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 06/07/2023]
Abstract
Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.
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Affiliation(s)
- Anuraag Aithal
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Shikha Dagar
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
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13
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Glass JB, Elbon CE, Williams LD. Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration. Trends Microbiol 2023; 31:135-141. [PMID: 36058785 DOI: 10.1016/j.tim.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Aerobic respiration evolved by bricolage, with modules cobbled together as microbial biochemistry coevolved with Earth's geochemistry. The mitochondrial electron transport chain represents a patchwork of respiratory modules inherited from microbial methanogenesis, iron oxidation, anoxygenic photosynthesis, and denitrification pathways, and preserves a biochemical record of Earth's redox environment over its four-billion-year history. Imprints of the anoxic early Earth are recognizable in Complex I's numerous iron-sulfur cofactors and vestigial binding sites for ferredoxin, nickel-iron, and molybdopterin, whereas the more recent advent of oxygen as a terminal electron acceptor necessitated use of heme and copper cofactors by Complex IV. Bricolage of respiratory complexes resulted in supercomplexes for improved electron transfer efficiency in some bacteria and archaea, and in many eukaryotes. Accessory subunits evolved to wrap mitochondrial supercomplexes for improved assembly and stability. Environmental microbes with 'fossil' proteins that are similar to ancestral forms of the respiratory complexes deserve further scrutiny and may reveal new insights on the evolution of aerobic respiration.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Claire E Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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14
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Römling U. Is biofilm formation intrinsic to the origin of life? Environ Microbiol 2023; 25:26-39. [PMID: 36655713 PMCID: PMC10086821 DOI: 10.1111/1462-2920.16179] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 01/21/2023]
Abstract
Biofilms are multicellular, often surface-associated, communities of autonomous cells. Their formation is the natural mode of growth of up to 80% of microorganisms living on this planet. Biofilms refractory towards antimicrobial agents and the actions of the immune system due to their tolerance against multiple environmental stresses. But how did biofilm formation arise? Here, I argue that the biofilm lifestyle has its foundation already in the fundamental, surface-triggered chemical reactions and energy preserving mechanisms that enabled the development of life on earth. Subsequently, prototypical biofilm formation has evolved and diversified concomitantly in composition, cell morphology and regulation with the expansion of prokaryotic organisms and their radiation by occupation of diverse ecological niches. This ancient origin of biofilm formation thus mirrors the harnessing environmental conditions that have been the rule rather than the exception in microbial life. The subsequent emergence of the association of microbes, including recent human pathogens, with higher organisms can be considered as the entry into a nutritional and largely stress-protecting heaven. Nevertheless, basic mechanisms of biofilm formation have surprisingly been conserved and refunctionalized to promote sustained survival in new environments.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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15
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McGuinness KN, Klau GW, Morrison SM, Moore EK, Seipp J, Falkowski PG, Nanda V. Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution. ORIGINS LIFE EVOL B 2022; 52:263-275. [DOI: 10.1007/s11084-022-09630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
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16
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Ma L, Shao Z, Li L, Huang J, Wang S, Lin Q, Li J, Gong M, Nandi AK. Heuristics and metaheuristics for biological network alignment: A review. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2021.08.156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Fontecilla-Camps JC, Volbeda A. Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis. Chem Rev 2022; 122:12110-12131. [PMID: 35536891 DOI: 10.1021/acs.chemrev.1c00869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activation energy barrier of biochemical reactions is normally lowered by an enzyme catalyst, which directly helps the weakening of the bond(s) to be broken. In many metalloenzymes, this is a first coordination sphere effect. Besides having a direct catalytic action, enzymes can fix their reactive groups and substrates so that they are optimally positioned and also modify the water activity in the system. They can either activate substrates prior to their reaction or bind preactivated substrates, thereby drastically reducing local entropic effects. The latter type is well represented by some bisubstrate reactions, where they have been defined as "entropic traps". These can be described as "second coordination sphere" processes, but enzymes can also control the reactivity beyond this point through local conformational changes belonging to an "outer coordinate sphere" that can be modulated by substrate binding. We have chosen the [4Fe-4S] cluster-dependent enzyme quinolinate synthase to illustrate each one of these processes. In addition, this very old metalloenzyme shows low in vitro substrate binding specificity, atypical reactivity that produces dead-end products, and a unique modulation of its active site volume.
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Affiliation(s)
| | - Anne Volbeda
- Université Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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18
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Dagar S, Sarkar S, Rajamani S. Porphyrin in prebiotic catalysis: Ascertaining a route for the emergence of early metalloporphyrins. Chembiochem 2022; 23:e202200013. [PMID: 35233914 DOI: 10.1002/cbic.202200013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/15/2022] [Indexed: 11/09/2022]
Abstract
Metal ions are known to catalyze certain prebiotic reactions. However, the transition from metal ions to extant metalloenzymes remains unclear. Porphyrins are found ubiquitously in the catalytic core of many ancient metalloenzymes. In this study, we evaluated the influence of porphyrin-based organic scaffold, on the catalysis, emergence and putative molecular evolution of prebiotic metalloporphyrins. We studied the effect of porphyrins on the transition metal ion-mediated oxidation of hydroquinone (HQ). We report a change in the catalytic activity of the metal ions in the presence of porphyrin. This was observed to be facilitated by the coordination between metal ions and porphyrins or by the formation of non-coordinated complexes. The metal-porphyrin complexes also oxidized NADH, underscoring its versatility at oxidizing more than one substrate. Our study highlights the selective advantage that some of the metal ions would have had in the presence of porphyrin, underscoring their role in shaping the evolution of protometalloenzymes.
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Affiliation(s)
- Shikha Dagar
- IISER Pune: Indian Institute of Science Education Research Pune, Biology, IISER Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Pune, INDIA
| | - Susovan Sarkar
- IISER Pune: Indian Institute of Science Education Research Pune, Biology, Iiser Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Pune, INDIA
| | - Sudha Rajamani
- IISER Pune: Indian Institute of Science Education Research Pune, Biology, Dr. Homi Bhaba Rd, Pashan, Near NCL, 411008, Pune, INDIA
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19
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Dong Y, Zhang S, Zhao L. Unraveling the Structural Development of
Peptide‐Coordinated Iron‐Sulfur
Clusters: Prebiotic Evolution and Biosynthetic Strategies. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yijun Dong
- School of Life Sciences, Tsinghua University Beijing 100084 China
| | - Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
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20
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Bromberg Y, Aptekmann AA, Mahlich Y, Cook L, Senn S, Miller M, Nanda V, Ferreiro DU, Falkowski PG. Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. SCIENCE ADVANCES 2022; 8:eabj3984. [PMID: 35030025 PMCID: PMC8759750 DOI: 10.1126/sciadv.abj3984] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/22/2021] [Indexed: 06/07/2023]
Abstract
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago.Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life. [A. I. Oparin (1)]
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Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Ariel A. Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Yannick Mahlich
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Linda Cook
- Program in Applied and Computational Math, Princeton University, Princeton, NJ 08540, USA
| | - Stefan Senn
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Maximillian Miller
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, and Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Diego U. Ferreiro
- Protein Physiology Lab, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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21
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Huang XL. What are the inorganic nanozymes? Artificial or inorganic enzymes! NEW J CHEM 2022. [DOI: 10.1039/d2nj02088b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...
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22
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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23
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James JK, Nanda V. A Folding Insulator Defines Cryptic Domains in Tropomyosin. J Mol Biol 2021; 433:167281. [PMID: 34606830 DOI: 10.1016/j.jmb.2021.167281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
Multidomain proteins are the product of evolutionary selection for diversity of function through concatenation and repurposing of existing modular units of structures. In structures of proteins with multiple domains, components are often globular units stitched together with flexible linkers. Multidomain proteins often fold as multiple distinct order-disorder transitions. However, the relationship between structure and folding is not always straightforward. Tropomyosin binds to actin in muscle and cytoskeletal filaments. The structure is that of a continuous ɑ-helix lacking domain boundaries, but unfolding shows distinct transitions suggesting at least three possible domains do exist. To explore how domains might occur in a continuous structure, we used Lifson-Roig helix-coil models with sequence domains of varying helical nucleation propensities. Of these models, ones with a central folding insulator, separating folding of N- and C-terminal domains, are most consistent with experimental folding studies. The positions of domain boundaries are identified by hydrogen-deuterium exchange mass spectrometry. The presence of structurally cryptic folding domains in tropomyosin could relate to its evolution and explain the uneven distribution of deleterious mutations that lead to various cardiomyopathies.
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Affiliation(s)
- Jose K James
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, NJ 08854, USA.
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24
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Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine. Nat Commun 2021; 12:5925. [PMID: 34635654 PMCID: PMC8505563 DOI: 10.1038/s41467-021-26158-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Iron-sulfur (FeS) proteins are ancient and fundamental to life, being involved in electron transfer and CO2 fixation. FeS clusters have structures similar to the unit-cell of FeS minerals such as greigite, found in hydrothermal systems linked with the origin of life. However, the prebiotic pathway from mineral surfaces to biological clusters is unknown. Here we show that FeS clusters form spontaneously through interactions of inorganic Fe2+/Fe3+ and S2- with micromolar concentrations of the amino acid cysteine in water at alkaline pH. Bicarbonate ions stabilize the clusters and even promote cluster formation alone at concentrations >10 mM, probably through salting-out effects. We demonstrate robust, concentration-dependent formation of [4Fe4S], [2Fe2S] and mononuclear iron clusters using UV-Vis spectroscopy, 57Fe-Mössbauer spectroscopy and 1H-NMR. Cyclic voltammetry shows that the clusters are redox-active. Our findings reveal that the structures responsible for biological electron transfer and CO2 reduction could have formed spontaneously from monomers at the origin of life.
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25
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Yagi S, Padhi AK, Vucinic J, Barbe S, Schiex T, Nakagawa R, Simoncini D, Zhang KYJ, Tagami S. Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. J Am Chem Soc 2021; 143:15998-16006. [PMID: 34559526 DOI: 10.1021/jacs.1c05367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The extant complex proteins must have evolved from ancient short and simple ancestors. The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.
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Affiliation(s)
- Sota Yagi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Aditya K Padhi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jelena Vucinic
- Université Fédérale de Toulouse, ANITI, INRAE-UR 875, 31000 Toulouse, France.,TBI, Université Fédérale de Toulouse, CNRS, INRAE, INSA, ANITI, 31000 Toulouse, France.,Université Fédérale de Toulouse, ANITI, IRIT-UMR 5505, 31000 Toulouse, France
| | - Sophie Barbe
- TBI, Université Fédérale de Toulouse, CNRS, INRAE, INSA, ANITI, 31000 Toulouse, France
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE-UR 875, 31000 Toulouse, France
| | - Reiko Nakagawa
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - David Simoncini
- Université Fédérale de Toulouse, ANITI, IRIT-UMR 5505, 31000 Toulouse, France
| | - Kam Y J Zhang
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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26
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Freire MÁ. Short non-coded peptides interacting with cofactors facilitated the integration of early chemical networks. Biosystems 2021; 211:104547. [PMID: 34547425 DOI: 10.1016/j.biosystems.2021.104547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/28/2021] [Accepted: 09/15/2021] [Indexed: 11/02/2022]
Abstract
Independently developed iron-sulphur/thioester- and phosphate-driven chemical reactions would have set up two distinct reaction networks prior to coupling in a proto-metabolic system supporting a minimal organisation closure. Each chemical system assisted initially by simple catalysts and then by more complex cofactors would have provided the precursors of the small metabolites and monomer units along with their respective polymers through dehydrating template-independent assemblies. For example, acylation reactions mediated by activated thioester groups produced peptides, fatty acids and polyhydroxyalkanoates, while phosphorylation reactions by phosphorylating agents allowed the synthesis of polysaccharides, polyribonucleotides and polyphosphates. Here, we address how these independent chemical systems might fit together and shaped a proto-metabolic system, focusing specifically on cofactors as molecular fossils of metabolism. As a result, the proposed overview suggests that non-coded peptides capable of binding a variety of ligands, but in particular with a redox active versatility and/or group transfer potential could have facilitated the chemical connections that led to a minimal closure with a proto-metabolism. Later developments would have made it possible to establish a cellular organisation with more complex and interdependent metabolic pathways.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC). Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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27
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Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Bridging Themes: Short Protein Segments Found in Different Architectures. Mol Biol Evol 2021; 38:2191-2208. [PMID: 33502503 PMCID: PMC8136508 DOI: 10.1093/molbev/msab017] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as "themes." At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-80 residues that are unexpectedly shared between domains considered to have emerged independently. Among these "bridging themes" are ones shared between the most ancient domains, for example, Rossmann, P-loop NTPase, TIM-barrel, flavodoxin, and ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.
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Affiliation(s)
- Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | | | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
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28
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Zhao D, Bartlett S, Yung YL. Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes. Life (Basel) 2020; 10:life10120338. [PMID: 33321803 PMCID: PMC7764262 DOI: 10.3390/life10120338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/15/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023] Open
Abstract
Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate electron transfer reactions. An inherent difficulty with studying the catalytic potential of many metal compounds is the wide range of data and parameters to consider when searching for individual minerals and ligands of interest. Detecting mineral-ligand pairs that are structurally analogous enables more relevant selections of data to study, since structural affinity is a key indicator of comparable catalytic function. However, current structure-oriented approaches tend to be subjective and localized, and do not quantify observations or compare them with other potential targets. Here, we present a mathematical approach that compares structural similarities between various minerals and ligands using molecular similarity metrics. We use an iterative substructure search in the crystal lattice, paired with benchmark structural similarity methods. This structural comparison may be considered as a first stage in a more advanced analysis tool that will include a range of chemical and physical factors when computing mineral-ligand similarity. This approach will seek relationships between the mineral and enzyme worlds, with applications to the origins of life, ecology, catalysis, and astrobiology.
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Affiliation(s)
- Daniel Zhao
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; (D.Z.); (Y.L.Y.)
- Department of Mathematics, Harvard University, Massachusetts Hall, Cambridge, MA 02138, USA
| | - Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; (D.Z.); (Y.L.Y.)
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Correspondence:
| | - Yuk L. Yung
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; (D.Z.); (Y.L.Y.)
- NASA Jet Propulsion Laboratory, Oak Grove Dr, La Cañada Flintridge, CA 91011, USA
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29
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Mancini JA, Pike DH, Tyryshkin AM, Haramaty L, Wang MS, Poudel S, Hecht M, Nanda V. Design of a Fe 4 S 4 cluster into the core of a de novo four-helix bundle. Biotechnol Appl Biochem 2020; 67:574-585. [PMID: 32770861 DOI: 10.1002/bab.2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
We explore the capacity of the de novo protein, S824, to incorporate a multinuclear iron-sulfur cluster within the core of a single-chain four-helix bundle. This topology has a high intrinsic designability because sequences are constrained largely by the pattern of hydrophobic and hydrophilic amino acids, thereby allowing for the extensive substitution of individual side chains. Libraries of novel proteins based on these constraints have surprising functional potential and have been shown to complement the deletion of essential genes in E. coli. Our structure-based design of four first-shell cysteine ligands, one per helix, in S824 resulted in successful incorporation of a cubane Fe4 S4 cluster into the protein core. A number of challenges were encountered during the design and characterization process, including nonspecific metal-induced aggregation and the presence of competing metal-cluster stoichiometries. The introduction of buried iron-sulfur clusters into the helical bundle is an initial step toward converting libraries of designed structures into functional de novo proteins with catalytic or electron-transfer functionalities.
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Affiliation(s)
- Joshua A Mancini
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Douglas H Pike
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Alexei M Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Liti Haramaty
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Michael S Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Saroj Poudel
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Michael Hecht
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
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30
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Chu XY, Zhang HY. Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins. Chembiochem 2020; 21:3161-3168. [PMID: 32515532 DOI: 10.1002/cbic.202000027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Due to their early origin and extreme conservation, cofactors are valuable molecular fossils for tracing the origin and evolution of proteins. First, as the order of protein folds binding with cofactors roughly coincides with protein-fold chronology, cofactors are considered to have facilitated the origin of primitive proteins by selecting them from pools of random amino acid sequences. Second, in the subsequent evolution of proteins, cofactors still played an important role. More interestingly, as metallic cofactors evolved with geochemical variations, some geochemical events left imprints in the chronology of protein architecture; this provides further evidence supporting the coevolution of biochemistry and geochemistry. In this paper, we attempt to review the molecular fossils used in tracing the origin and evolution of proteins, with a special focus on cofactors.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
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31
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Sanden SA, Yi R, Hara M, McGlynn SE. Simultaneous synthesis of thioesters and iron–sulfur clusters in water: two universal components of energy metabolism. Chem Commun (Camb) 2020; 56:11989-11992. [DOI: 10.1039/d0cc04078a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Thioesters and peptide ligated [Fe–S] clusters can be synthesized simultaneously from thioacetic acid in an aqueous one-pot reaction.
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Affiliation(s)
- Sebastian A. Sanden
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- School of Materials and Chemical Technology
| | - Ruiqin Yi
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
| | - Masahiko Hara
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- School of Materials and Chemical Technology
| | - Shawn E. McGlynn
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- Center for Sustainable Resource Science
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