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Rossetto D, Cvjetan N, Walde P, Mansy SS. Protocellular Heme and Iron-Sulfur Clusters. Acc Chem Res 2024; 57:2293-2302. [PMID: 39099316 PMCID: PMC11339926 DOI: 10.1021/acs.accounts.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/10/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
ConspectusCentral to the quest of understanding the emergence of life is to uncover the role of metals, particularly iron, in shaping prebiotic chemistry. Iron, as the most abundant of the accessible transition metals on the prebiotic Earth, played a pivotal role in early biochemical processes and continues to be indispensable to modern biology. Here, we discuss our recent contributions to probing the plausibility of prebiotic complexes with iron, including heme and iron-sulfur clusters, in mediating chemistry beneficial to a protocell. Laboratory experiments and spectroscopic findings suggest plausible pathways, often facilitated by UV light, for the synthesis of heme and iron-sulfur clusters. Once formed, heme displays catalytic, peroxidase-like activity when complexed with amphiphiles. This activity could have been beneficial in two ways. First, heme could have catalytically removed a molecule (H2O2) that could have had degradative effects on a protocell. Second, heme could have helped in the synthesis of the building blocks of life by coupling the reduction of H2O2 with the oxidation of organic substrates. The necessity of amphiphiles to avoid the formation of inactive complexes of heme is telling, as the modern-day electron transport chain possesses heme embedded within a lipid membrane. Conversely, prebiotic iron-sulfur peptides have yet to be reported to partition into lipid membranes, nor have simple iron-sulfur peptides been found to be capable of participating in the synthesis of organic molecules. Instead, iron-sulfur peptides span a wide range of reduction potentials complementary to the reduction potentials of hemes. The reduction potential of iron-sulfur peptides can be tuned by the type of iron-sulfur cluster formed, e.g., [2Fe-2S] versus [4Fe-4S], or by the substitution of ligands to the metal center. Since iron-sulfur clusters easily form upon stochastic encounters between iron ions, hydrosulfide, and small organic molecules possessing a thiolate, including peptides, the likelihood of soluble iron-sulfur clusters seems to be high. What remains challenging to determine is if iron-sulfur peptides participated in early prebiotic chemistry or were recruited later when protocellular membranes evolved that were compatible with the exploitation of electron transfer for the storage of energy as a proton gradient. This problem mirrors in some ways the difficulty in deciphering the origins of metabolism as a whole. Chemistry that resembles some facets of extant metabolism must have transpired on the prebiotic Earth, but there are few clues as to how and when such chemistry was harnessed to support a (proto)cell. Ultimately, unraveling the roles of hemes and iron-sulfur clusters in prebiotic chemistry promises to deepen our understanding of the origins of life on Earth and aids the search for life elsewhere in the universe.
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Affiliation(s)
- Daniele Rossetto
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AlbertaT6G 2G2, Canada
- D-CIBIO, University of Trento, via Sommarive 9, Trento 38123, Italy
| | - Nemanja Cvjetan
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AlbertaT6G 2G2, Canada
- Department
of Materials, ETH Zürich, Leopold-Ruzicka-Weg 4, Zürich 8093, Switzerland
| | - Peter Walde
- Department
of Materials, ETH Zürich, Leopold-Ruzicka-Weg 4, Zürich 8093, Switzerland
| | - Sheref S. Mansy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AlbertaT6G 2G2, Canada
- D-CIBIO, University of Trento, via Sommarive 9, Trento 38123, Italy
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Rodriguez LE, Weber JM, Barge LM. Evaluating Pigments as a Biosignature: Abiotic/Prebiotic Synthesis of Pigments and Pigment Mimics in Planetary Environments. ASTROBIOLOGY 2024; 24:767-782. [PMID: 38768415 DOI: 10.1089/ast.2023.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Pigments serve a multitude of functions in biology including light harvesting for photosynthesis, radiation protection, membrane support, and defense. The ubiquity of pigments-especially within extremophiles found in high-radiation, high-salinity, and dry environments-and their detectability via mission-ready techniques have elevated these molecules as promising targets in the search for evidence of life elsewhere. Moreover, the detection of pigments has been proposed as a "smoking gun" for extraterrestrial life as it has been suggested that these molecules cannot be generated abiotically. However, while pigments may hold promise as a biosignature, current understanding of their possible prebiotic origins remains understudied and uncertain. Better understanding of the abiotic synthesis of pigments is critical for evaluating the biogenicity of any pigment detected during missions, including by the Mars Perseverance rover or from returned samples. Compounding this uncertainty is the broad definition of pigment as it includes any compound capable of absorbing visible light and by itself does not specify a particular chemical motif. While not experimentally verified, there are promising prebiotic routes for generating pigments including hemes, chlorophylls, and carotenoids. Herein, we review the biochemistry of pigments, the inherent assumptions made when searching for these molecules in the field, their abiotic synthesis in industry and prebiotic reactions, prebiotically relevant molecules that can mimic their spectral signatures, and implications/recommendations for future work.
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Affiliation(s)
- Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Nguyen KU, Zhang Y, Liu Q, Zhang R, Jin X, Taniguchi M, Miller ES, Lindsey JS. Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review. Molecules 2023; 28:6132. [PMID: 37630384 PMCID: PMC10459692 DOI: 10.3390/molecules28166132] [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: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium-microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known-each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or -OH or -OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.
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Affiliation(s)
- Kathy-Uyen Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Yunlong Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Qihui Liu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Xiaohe Jin
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Eric S. Miller
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA;
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
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Pleyer HL, Moeller R, Fujimori A, Fox S, Strasdeit H. Chemical, Thermal, and Radiation Resistance of an Iron Porphyrin: A Model Study of Biosignature Stability. ASTROBIOLOGY 2022; 22:776-799. [PMID: 35647896 PMCID: PMC9298530 DOI: 10.1089/ast.2021.0144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/22/2022] [Indexed: 06/15/2023]
Abstract
Metal complexes of porphyrins and porphyrin-type compounds are ubiquitous in all three domains of life, with hemes and chlorophylls being the best-known examples. Their diagenetic transformation products are found as geoporphyrins, in which the characteristic porphyrin core structure is retained and which can be up to 1.1 billion years old. Because of this, and their relative ease of detection, metalloporphyrins appear attractive as chemical biosignatures in the search for extraterrestrial life. In this study, we investigated the stability of solid chlorido(2,3,7,8,12,13,17,18-octaethylporphyrinato)iron(III) [FeCl(oep)], which served as a model for heme-like molecules and iron geoporphyrins. [FeCl(oep)] was exposed to a variety of astrobiologically relevant extreme conditions, namely: aqueous acids and bases, oxidants, heat, and radiation. Key results are: (1) the [Fe(oep)]+ core is stable over the pH range 0.0-13.5 even at 80°C; (2) the oxidizing power follows the order ClO- > H2O2 > ClO3- > HNO3 > ClO4-; (3) in an inert atmosphere, the iron porphyrin is thermally stable to near 250°C; (4) at high temperatures, carbon dioxide gas is not inert but acts as an oxidant, forming carbon monoxide; (5) a decomposition layer is formed on ultraviolet irradiation and protects the [FeCl(oep)] underneath; (6) an NaCl/NaHCO3 salt mixture has a protective effect against X-rays; and (7) no such effect is observed when [FeCl(oep)] is exposed to iron ion particle radiation. The relevance to potential iron porphyrin biosignatures on Mars, Europa, and Enceladus is discussed.
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Affiliation(s)
- Hannes Lukas Pleyer
- Department of Bioinorganic Chemistry and Chemical Evolution, Institute of Chemistry, University of Hohenheim, Stuttgart, Germany
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Akira Fujimori
- Molecular and Cellular Radiation Biology Group, Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, Chiba, Japan
| | - Stefan Fox
- Department of Bioinorganic Chemistry and Chemical Evolution, Institute of Chemistry, University of Hohenheim, Stuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry and Chemical Evolution, Institute of Chemistry, University of Hohenheim, Stuttgart, Germany
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5
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Barge LM, Rodriguez LE, Weber JM, Theiling BP. Determining the "Biosignature Threshold" for Life Detection on Biotic, Abiotic, or Prebiotic Worlds. ASTROBIOLOGY 2022; 22:481-493. [PMID: 34898272 DOI: 10.1089/ast.2021.0079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.
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Affiliation(s)
- Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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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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Abstract
The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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8
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Kirschning A. The coenzyme/protein pair and the molecular evolution of life. Nat Prod Rep 2020; 38:993-1010. [PMID: 33206101 DOI: 10.1039/d0np00037j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Zentrum für Biomolekulare Wirkstoffchemie (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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9
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
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do Nascimento Vieira A, Kleinermanns K, Martin WF, Preiner M. The ambivalent role of water at the origins of life. FEBS Lett 2020; 594:2717-2733. [PMID: 32416624 DOI: 10.1002/1873-3468.13815] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022]
Abstract
Life as we know it would not exist without water. However, water molecules not only serve as a solvent and reactant but can also promote hydrolysis, which counteracts the formation of essential organic molecules. This conundrum constitutes one of the central issues in origin of life. Hydrolysis is an important part of energy metabolism for all living organisms but only because, inside cells, it is a controlled reaction. How could hydrolysis have been regulated under prebiotic settings? Lower water activities possibly provide an answer: geochemical sites with less free and more bound water can supply the necessary conditions for protometabolic reactions. Such conditions occur in serpentinising systems, hydrothermal sites that synthesise hydrogen gas via rock-water interactions. Here, we summarise the parallels between biotic and abiotic means of controlling hydrolysis in order to narrow the gap between biochemical and geochemical reactions and briefly outline how hydrolysis could even have played a constructive role at the origin of molecular self-organisation.
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Affiliation(s)
| | | | - William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, Germany
| | - Martina Preiner
- Institute for Molecular Evolution, University of Düsseldorf, Germany
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Pleyer HL, Strasdeit H, Fox S. A Possible Prebiotic Ancestry of Porphyrin-Type Protein Cofactors. ORIGINS LIFE EVOL B 2018; 48:347-371. [PMID: 30547367 DOI: 10.1007/s11084-018-9567-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/31/2018] [Indexed: 10/27/2022]
Abstract
In previous experiments that simulated conditions on primordial volcanic islands, we demonstrated the abiotic formation of hydrophobic porphyrins. The present study focused on the question whether such porphyrins can be metalated by prebiotically plausible metal ion sources. We used water-insoluble octaethylporphyrin (H2oep) as a model compound. Experiments were conducted in a nitrogen atmosphere under cyclic wet-dry conditions in order to simulate the fluctuating environment in prebiotic rock pools. Wetting-drying proved to be a crucial factor. Significant yields of the metalloporphyrins (20-78% with respect to H2oep) were obtained from the soluble salts MCl2 (M = Mg, Fe, Co, Ni and Cu) in freshwater. Even almost insoluble minerals and rocks metalated the porphyrin. Basalt (an iron source, 11% yield), synthetic jaipurite (CoS, 33%) and synthetic covellite (CuS, 57%) were most efficient. Basalt, magnetite and FeCl2 gave considerably higher yields in artificial seawater than in freshwater. From iron sources, the highest yields, however, were obtained in an acidic medium (hydrochloric acid with an initial pH of 2.1). Under these conditions, iron meteorites also metalated the porphyrin. Acidic conditions were considered because they are known to occur during eruptions on volcanic islands. Octaethylporphyrinatomagnesium(II) did not form in acidic medium and was unstable towards dissolved Fe2+. It is therefore questionable whether magnesium porphyrins, i.e. possible ancestors of chlorophyll, could have accumulated in primordial rock pools. However, abiotically formed ancestors of the modern cofactors heme (Fe), B12 (Co), and F430 (Ni) may have been available to hypothetical protometabolisms and early organisms.
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Affiliation(s)
- Hannes Lukas Pleyer
- Department of Bioinorganic Chemistry and Chemical Evolution, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry and Chemical Evolution, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Stefan Fox
- Department of Bioinorganic Chemistry and Chemical Evolution, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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Taniguchi M, Lindsey JS. Database of Absorption and Fluorescence Spectra of >300 Common Compounds for use in Photochem
CAD. Photochem Photobiol 2018; 94:290-327. [DOI: 10.1111/php.12860] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/22/2017] [Indexed: 12/11/2022]
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Taniguchi M, Ptaszek M, Chandrashaker V, Lindsey JS. The Porphobilinogen Conundrum in Prebiotic Routes to Tetrapyrrole Macrocycles. ORIGINS LIFE EVOL B 2017; 47:93-119. [PMID: 27207103 DOI: 10.1007/s11084-016-9506-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/01/2016] [Indexed: 02/05/2023]
Abstract
Attempts to develop a credible prebiotic route to tetrapyrroles have relied on enzyme-free recapitulation of the extant biosynthesis, but this process has foundered from the inability to form the pyrrole porphobilinogen (PBG) in good yield by self-condensation of the precursor δ-aminolevulinic acid (ALA). PBG undergoes robust oligomerization in aqueous solution to give uroporphyrinogen (4 isomers) in good yield. ALA, PBG, and uroporphyrinogen III are universal precursors to all known tetrapyrrole macrocycles. The enzymic formation of PBG entails carbon-carbon bond formation between the less stable enolate/enamine of one ALA molecule (3-position) and the carbonyl/imine (4-position) of the second ALA molecule; without enzymes, the first ALA reacts at the more stable enolate/enamine (5-position) and gives the pyrrole pseudo-PBG. pseudo-PBG cannot self-condense, yet has one open α-pyrrole position and is proposed to be a terminator of oligopyrromethane chain-growth from PBG. Here, 23 analogues of ALA have been subjected to density functional theoretical (DFT) calculations, but no motif has been identified that directs reaction at the 3-position. Deuteriation experiments suggested 5-(phosphonooxy)levulinic acid would react preferentially at the 3- versus 5-position, but a hybrid condensation with ALA gave no observable uroporphyrin. The results suggest efforts toward a biomimetic, enzyme-free route to tetrapyrroles from ALA should turn away from structure-directed reactions and focus on catalysts that orient the two aminoketones to form PBG in a kinetically controlled process, thereby avoiding formation of pseudo-PBG.
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Affiliation(s)
- Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Marcin Ptaszek
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250-0001, USA
| | | | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA.
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Deans RM, Taniguchi M, Chandrashaker V, Ptaszek M, Chambers DR, Soares ARM, Lindsey JS. Complexity in structure-directed prebiotic chemistry. Unexpected compositional richness from competing reactants in tetrapyrrole formation. NEW J CHEM 2016. [DOI: 10.1039/c6nj00543h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acyclic reactants afford “partially defective” pyrroles that interfere with chain growth of “normal” pyrroles on the path to tetrapyrrole macrocycles.
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Affiliation(s)
- Richard M. Deans
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | | | | | - Marcin Ptaszek
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Dana R. Chambers
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Ana R. M. Soares
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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Taniguchi M, Deans RM, Chandrashaker V, Ptaszek M, Lindsey JS. Scope and limitations of two model prebiotic routes to tetrapyrrole macrocycles. NEW J CHEM 2016. [DOI: 10.1039/c6nj01423b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aqueous reaction (35 °C, 72 h) of two acyclic compounds, an α-aminoketone + β-ketoester or β-diketone (not shown), affords a pyrrole that self-condenses to give the porphyrinogen.
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Affiliation(s)
| | - Richard M. Deans
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | | | - Marcin Ptaszek
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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16
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Chandrashaker V, Ptaszek M, Taniguchi M, Lindsey JS. Synthesis of diverse acyclic precursors to pyrroles for studies of prebiotic routes to tetrapyrrole macrocycles. NEW J CHEM 2016. [DOI: 10.1039/c6nj02048h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some 50 ketones, β-diketones, β-ketoesters and α-aminoketones have been prepared for studies of the formation of trisubstituted pyrroles equipped for self-condensation leading to tetrapyrrole macrocycles.
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Affiliation(s)
| | - Marcin Ptaszek
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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17
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Deans RM, Taniguchi M, Chandrashaker V, Ptaszek M, Lindsey JS. Complexity in structure-directed prebiotic chemistry. Reaction bifurcation from a β-diketone in tetrapyrrole formation. NEW J CHEM 2016. [DOI: 10.1039/c6nj00545d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An unsymmetrical β-diketone with δ-aminolevulinic acid affords both a “defective” and a “normal” pyrrole; upon combinatorial reaction the former terminates chain-growth of the latter on the path to tetrapyrrole macrocycles.
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Affiliation(s)
- Richard M. Deans
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | | | | | - Marcin Ptaszek
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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18
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Deans RM, Chandrashaker V, Taniguchi M, Lindsey JS. Complexity in structure-directed prebiotic chemistry. Effect of a defective competing reactant in tetrapyrrole formation. NEW J CHEM 2015. [DOI: 10.1039/c5nj01474c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A reactive but defective pyrrole, derived from the simple β-diketone acetylacetone, terminates chain-growth in a quantitative combinatorial manner in tetrapyrrole formation.
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Affiliation(s)
- Richard M. Deans
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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19
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Alexy EJ, Hintz CW, Hughes HM, Taniguchi M, Lindsey JS. Paley's watchmaker analogy and prebiotic synthetic chemistry in surfactant assemblies. Formaldehyde scavenging by pyrroles leading to porphyrins as a case study. Org Biomol Chem 2015; 13:10025-31. [DOI: 10.1039/c5ob01409c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Facile exchange of micromolar dialkylpyrrolic constituents among a Poisson distribution of aqueous micelles overcomes immense statistical odds against reaction.
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Affiliation(s)
- Eric J. Alexy
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Carl W. Hintz
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Hubert M. Hughes
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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