1
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Kirschning A. Why pyridoxal phosphate could be a functional predecessor of thiamine pyrophosphate and speculations on a primordial metabolism. RSC Chem Biol 2024; 5:508-517. [PMID: 38846080 PMCID: PMC11151856 DOI: 10.1039/d4cb00016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 06/09/2024] Open
Abstract
The account attempts to substantiate the hypothesis that, from an evolutionary perspective, the coenzyme couple pyridoxal phosphate and pyridoxamine phosphate preceded the coenzyme thiamine pyrophosphate and acted as its less efficient chemical analogue in some form of early metabolism. The analysis combines mechanism-based chemical reactivity with biosynthetic arguments and provides evidence that vestiges of "TPP-like reactivity" are still found for PLP today. From these thoughts, conclusions can be drawn about the key elements of a primordial form of metabolism, which includes the citric acid cycle, amino acid biosynthesis and the pentose phosphate pathway.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B 30167 Hannover Germany
- Uppsala Biomedical Center (BMC), University Uppsala, Husargatan 3 752 37 Uppsala Sweden
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2
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Ju Y, Zhang H, Jiang Y, Wang W, Kan G, Yu K, Wang X, Liu J, Jiang J. Aqueous microdroplets promote C-C bond formation and sequences in the reverse tricarboxylic acid cycle. Nat Ecol Evol 2023; 7:1892-1902. [PMID: 37679455 DOI: 10.1038/s41559-023-02193-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/08/2023] [Indexed: 09/09/2023]
Abstract
The reverse tricarboxylic acid cycle (rTCA) is a central anabolic network that uses carbon dioxide (CO2) and may have provided complex carbon substrates for life before the advent of RNA or enzymes. However, non-enzymatic promotion of the rTCA cycle, in particular carbon fixation, remains challenging, even with primordial metal catalysis. Here, we report that the fixation of CO2 by reductive carboxylation of succinate and α-ketoglutarate was achieved in aqueous microdroplets under ambient conditions without the use of catalysts. Under identical conditions, the aqueous microdroplets also facilitated the sequences in the rTCA cycle, including reduction, hydration, dehydration and retro-aldol cleavage and linked with the glyoxylate cycle. These reactions of the rTCA cycle were compatible with the aqueous microdroplets, as demonstrated with two-reaction and four-reaction sequences. A higher selectivity giving higher product yields was also observed. Our results suggest that the microdroplets provide an energetically favourable microenvironment and facilitate a non-enzymatic version of the rTCA cycle in prebiotic carbon anabolism.
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Affiliation(s)
- Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China.
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Wenxin Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
| | - Jilin Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China.
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China.
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3
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Zhang X, Paoletti MM, Izon G, Fournier GP, Summons RE. Late acquisition of the rTCA carbon fixation pathway by Chlorobi. Nat Ecol Evol 2023; 7:1398-1407. [PMID: 37537385 DOI: 10.1038/s41559-023-02147-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
The reverse tricarboxylic acid (rTCA) cycle is touted as a primordial mode of carbon fixation due to its autocatalytic propensity and oxygen intolerance. Despite this inferred antiquity, however, the earliest rock record affords scant supporting evidence. In fact, based on the chimeric inheritance of rTCA cycle steps within the Chlorobiaceae, even the use of the chemical fossil record of this group is now subject to question. While the 1.64-billion-year-old Barney Creek Formation contains chemical fossils of the earliest known putative Chlorobiaceae-derived carotenoids, interferences from the accompanying hydrocarbon matrix have hitherto precluded the carbon isotope measurements necessary to establish the physiology of the organisms that produced them. Overcoming this obstacle, here we report a suite of compound-specific carbon isotope measurements identifying a cyanobacterially dominated ecosystem featuring heterotrophic bacteria. We demonstrate chlorobactane is 13C-depleted when compared to contemporary equivalents, showing only slight 13C-enrichment over co-existing cyanobacterial carotenoids. The absence of this diagnostic isotopic fingerprint, in turn, confirms phylogenomic hypotheses that call for the late assembly of the rTCA cycle and, thus, the delayed acquisition of autotrophy within the Chlorobiaceae. We suggest that progressive oxygenation of the Earth System caused an increase in the marine sulfate inventory thereby providing the selective pressure to fuel the Neoproterozoic shift towards energy-efficient photoautotrophy within the Chlorobiaceae.
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Affiliation(s)
- Xiaowen Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
| | - Madeline M Paoletti
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gareth Izon
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Ernst L, Barayeu U, Hädeler J, Dick TP, Klatt JM, Keppler F, Rebelein JG. Methane formation driven by light and heat prior to the origin of life and beyond. Nat Commun 2023; 14:4364. [PMID: 37528079 PMCID: PMC10394037 DOI: 10.1038/s41467-023-39917-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Methane is a potent greenhouse gas, which likely enabled the evolution of life by keeping the early Earth warm. Here, we demonstrate routes towards abiotic methane and ethane formation under early-earth conditions from methylated sulfur and nitrogen compounds with prebiotic origin. These compounds are demethylated in Fenton reactions governed by ferrous iron and reactive oxygen species (ROS) produced by light and heat in aqueous environments. After the emergence of life, this phenomenon would have greatly intensified in the anoxic Archean by providing methylated sulfur and nitrogen substrates. This ROS-driven Fenton chemistry can occur delocalized from serpentinization across Earth's humid realm and thereby substantially differs from previously suggested methane formation routes that are spatially restricted. Here, we report that Fenton reactions driven by light and heat release methane and ethane and might have shaped the chemical evolution of the atmosphere prior to the origin of life and beyond.
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Affiliation(s)
- Leonard Ernst
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), 35032, Marburg, Germany.
| | - Uladzimir Barayeu
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Jonas Hädeler
- Institute of Earth Sciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Judith M Klatt
- Center for Synthetic Microbiology (SYNMIKRO), 35032, Marburg, Germany
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology & Philipps University Marburg, 35032, Marburg, Germany
- Biogeochemistry Group, Department for Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, 69120, Heidelberg, Germany
- Heidelberg Center for the Environment HCE, Heidelberg University, 69120, Heidelberg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), 35032, Marburg, Germany.
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5
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Chopra M, Kumar V, Singh M, Aggarwal NK. An overview about the approaches used in the production of alpha-ketoglutaric acid with their applications. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2022-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Alpha ketoglutaric acid is a biological compound found naturally in the human body. It plays an important role in the cell metabolism and has a role in various metabolic pathways including Kreb’s cycle, protein metabolism and so on. Keto glutaric acid is chemically prepared from succinic acid and oxalic acid. It is a direct precursor of glutamic acid and triazines. It can be produced by oxidative decarboxylation of isocitrate by isocitrate dehydrogenase. The yeast Yarrowia lipolytica is used as a prospective producer of alpha ketoglutaric acid from ethanol. The capability to synthesize Keto glutaric acid has so far been investigated for many microorganisms such as Pseudomonas fluoroscens
, Bacillus subtilis
etc. P. fluoroscens have the ability to synthesize a huge amount of alpha ketoglutaric acid in a glycerol medium supplemented with manganese (Mn). The Mangnese has a significant impact on glycerol metabolism resulting in the buildup of alpha ketoglutaric acid. The metabolism of succinate may result in the production of alpha ketoglutarate. Despite its importance in TCA cycle, alpha ketoglutaric acid buildup as an intermediate product of bacterial glucose oxidation. Along with chemical synthesis and microbial fermentation, enzymatic transformation can also be used to produce alpha ketoglutaric acid. Biodiesel waste is considered as cheap and renewable carbon source for the development of alpha ketoglutaric acid. Alpha ketoglutarate is used for kidney disease, intestinal and stomach disorders and many other conditions. It also plays an important role in the food industry as food and nutrient enhancers. The review is covering all the aspects related with the Alpha ketoglutaric acid production, utilization and product recovery.
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Affiliation(s)
- Monika Chopra
- Department of Biotechnology , Maharishi Markandeshwar (Deemed to be University), Mullana , Ambala , 133207 , India
| | - Vikas Kumar
- Department of Biotechnology , Maharishi Markandeshwar (Deemed to be University), Mullana , Ambala , 133207 , India
| | - Manoj Singh
- Department of Biotechnology , Maharishi Markandeshwar (Deemed to be University), Mullana , Ambala , 133207 , India
| | - Neeraj K. Aggarwal
- Department of Microbiology , Kurukshetra University , Kurukshetra , 136119 , India
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6
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Santos Correa S, Schultz J, Lauersen KJ, Soares Rosado A. Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways. J Adv Res 2022; 47:75-92. [PMID: 35918056 PMCID: PMC10173188 DOI: 10.1016/j.jare.2022.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms. AIM OF REVIEW In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field. KEY SCIENTIFIC CONCEPTS OF REVIEW Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.
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Affiliation(s)
- Sulamita Santos Correa
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Junia Schultz
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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7
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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8
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [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] [Received: 08/08/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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9
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Ritson DJ. A cyanosulfidic origin of the Krebs cycle. SCIENCE ADVANCES 2021; 7:7/33/eabh3981. [PMID: 34389542 PMCID: PMC8363140 DOI: 10.1126/sciadv.abh3981] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
The centrality of the Krebs cycle in metabolism has long been interpreted as evidence of its antiquity, and consequently, questions regarding its provenance, and whether it initially functioned as a cycle or not, have received much attention. The present report shows that prebiotic oxidation of α-hydroxy carboxylates can be achieved by UV photolysis of a simple geochemical species (HS-), which leads to α-oxo carboxylates that feature in the Krebs cycle and glyoxylate shunt. Further reaction of these products leads to almost all intermediates of the Krebs cycle proper, succinate semialdehyde bypass, and glyoxylate shunt. Fumarate, the missing Krebs cycle component, and the required α-hydroxy carboxylates can be provided by a highly related hydrogen cyanide chemistry, which also provides precursors for amino acids, nucleotides, and phospholipids.
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Affiliation(s)
- Dougal J Ritson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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10
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Jaramillo EA, Ferreira Santos MS, Noell AC, Mora MF. Capillary electrophoresis method for analysis of inorganic and organic anions related to habitability and the search for life. Electrophoresis 2021; 42:1956-1964. [PMID: 34287988 DOI: 10.1002/elps.202100134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/08/2022]
Abstract
In situ missions of exploration require analytical methods that are capable of detecting a wide range of molecular targets in complex matrices without a priori assumptions of sample composition. Furthermore, these methods should minimize the number of reagents needed and any sample preparation steps. We have developed a method for the detection of metabolically relevant inorganic and organic anions that is suitable for implementation on in situ spaceflight missions. Using 55 mM acetic acid, 50 mM triethylamine, and 5% glycerol, more than 21 relevant anions are separated in less than 20 min. The method is robust to sample ionic strength, tolerating high concentrations of background salts (up to 900 mM NaCl and 300 mM MgSO4 ). This is an important feature for future missions to ocean worlds. The method was validated using a culture of Escherichia coli and with high salinity natural samples collected from Mono Lake, California.
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Affiliation(s)
| | | | - Aaron C Noell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Maria F Mora
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
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11
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Stubbs RT, Yadav M, Krishnamurthy R, Springsteen G. A plausible metal-free ancestral analogue of the Krebs cycle composed entirely of α-ketoacids. Nat Chem 2020; 12:1016-1022. [PMID: 33046840 PMCID: PMC8570912 DOI: 10.1038/s41557-020-00560-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 08/26/2020] [Indexed: 12/02/2022]
Abstract
Efforts to decipher the prebiotic roots of metabolic pathways have focused on recapitulating modern biological transformations, with metals typically serving in place of cofactors and enzymes. Here we show that the reaction of glyoxylate with pyruvate under mild aqueous conditions produces a series of α-ketoacid analogues of the reductive citric acid cycle without the need for metals or enzyme catalysts. The transformations proceed in the same sequence as the reverse Krebs cycle, resembling a protometabolic pathway, with glyoxylate acting as both the carbon source and reducing agent. Furthermore, the α-ketoacid analogues provide a natural route for the synthesis of amino acids by transamination with glycine, paralleling the extant metabolic mechanisms and obviating the need for metal-catalysed abiotic reductive aminations. This emerging sequence of prebiotic reactions could have set the stage for the advent of increasingly sophisticated pathways operating under catalytic control.
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Affiliation(s)
- R Trent Stubbs
- Department of Chemistry, Furman University, Greenville, SC, USA
- NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA
| | - Mahipal Yadav
- NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA.
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| | - Greg Springsteen
- Department of Chemistry, Furman University, Greenville, SC, USA.
- NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA.
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12
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A way to thioacetate esters compatible with non-oxidative prebiotic conditions. Sci Rep 2020; 10:14488. [PMID: 32879403 PMCID: PMC7467925 DOI: 10.1038/s41598-020-71524-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/17/2020] [Indexed: 11/22/2022] Open
Abstract
The centrality of pyruvate oxidative decarboxylation into acetyl-CoA in current biochemistry is a strong argument for proposing that a similar reaction have been necessary for the development of an effective protometabolism on the primitive Earth. However, such a decarboxylation requires the use of an oxidant and a catalyst, today enzymatic. Based on the mechanisms of the pyruvate dehydrogenase complex and pyruvate-ferredoxin oxidoreductase, we propose that the initial mechanism involved disulfides and occurred via radicals. A first disulfide is obtained by reacting glyoxylate with hydrogen sulfide. It is then possible to produce a wide variety of other disulfides by exchange reactions. When reacted with pyruvate under UV light they give thioesters. This process requires no oxidant and is therefore compatible with what is known of the redox conditions of the early Earth. Neither does it require any catalyst. It could be the first way to acetyl thioesters, a way that was later improved by the introduction of catalysts, first minerals, then enzymes.
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13
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Muchowska KB, Varma SJ, Moran J. Nonenzymatic Metabolic Reactions and Life's Origins. Chem Rev 2020; 120:7708-7744. [PMID: 32687326 DOI: 10.1021/acs.chemrev.0c00191] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.
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Affiliation(s)
| | - Sreejith J Varma
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
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14
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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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15
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Kitadai N, Nishiuchi K. Thermodynamic Impact of Mineral Surfaces on Amino Acid Polymerization: Aspartate Dimerization on Goethite. ASTROBIOLOGY 2019; 19:1363-1376. [PMID: 31539273 DOI: 10.1089/ast.2018.1967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This article presents a thermodynamic predictive scheme for amino acid polymerization in the presence of minerals as a function of various environmental parameters (pH, ionic strength, amino acid concentration, and the solid/water ratio) using l-aspartate (Asp) and goethite as a model combination. This prediction is enabled by the combination of the surface adsorption constants of amino acid and its polymer, determined from the extended triple layer model characterization of the corresponding experimental results, with the thermodynamic data of these organic compounds in water reported in the literature. Calculations for the Asp-goethite system showed that the goethite surface drastically shifts the Asp monomer-dipeptide equilibrium toward the dipeptide side; when the dimerization of 0.1 mM Asp was considered in the presence of 10 m2 L-1 of goethite, an Asp dipeptide concentration around 105 times larger was computed to be thermodynamically attainable compared with that in the absence of goethite at acidic pH (4-5) and low ionic strength (0.1 mM NaCl). Under this condition, the dipeptide-to-monomer molecular ratio in the adsorbed state reached 20%. In contrast, no significant enhancement by goethite was predicted at alkaline pH (>8), where the electrostatic interactions of the goethite surface with Asp and Asp dipeptide are weak. Thus, mineral surfaces should have had a significant impact on the thermodynamics of prebiotic peptide bond formation on the early Earth, although the influences likely depended largely on the environmental conditions. Future experimental studies for various amino acid-mineral interactions using our proposed methodology will provide a quantitative constraint on favorable geochemical settings for the chemical evolution on Earth. This approach can also offer important clues for future exploration of extraterrestrial life.
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Affiliation(s)
- Norio Kitadai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Kumiko Nishiuchi
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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16
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Chemistry of Homocysteine Thiolactone in A Prebiotic Perspective. Life (Basel) 2019; 9:life9020040. [PMID: 31100840 PMCID: PMC6616635 DOI: 10.3390/life9020040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 01/29/2023] Open
Abstract
Homocysteine is a non-proteinogenic sulfur-containing amino acid. Like cysteine, it can form disulfide bridges and complex metallic cations. It is also closely related to methionine, the first amino acid in the synthesis of all contemporary proteins. Furthermore, its cyclized form, a five-membered ring thiolactone, is stable in acidic and neutral water. Here, we demonstrate that this thiolactone may have been formed in the primitive ocean directly from the Strecker precursor of homocysteine, an aminonitrile. Even though it is poorly reactive, this thiolactone may be open by some amines, yielding amides which, in turn, could be the precursors of longer peptides.
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Ooka H, McGlynn SE, Nakamura R. Electrochemistry at Deep‐Sea Hydrothermal Vents: Utilization of the Thermodynamic Driving Force towards the Autotrophic Origin of Life. ChemElectroChem 2019. [DOI: 10.1002/celc.201801432] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
| | - Shawn E. McGlynn
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
- Blue Marble Space Institute of Science Seattle, WA USA
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
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18
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Affiliation(s)
- Antoine Danchin
- Institut de cardiométabolisme et nutrition, Hôpital de la Pitié-Salpêtrière, 47 boulevard de l'Hôpital 75013 Paris
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