Journal of Geography (Chigaku Zasshi)
Online ISSN : 1884-0884
Print ISSN : 0022-135X
ISSN-L : 0022-135X
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Cover
  • 2020 Volume 129 Issue 6 Pages Cover06_01-Cover06_02
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     A large quantity of external energy is required to synthesize various building blocks of life (BBLs) in order for life to emerge. Solar energy is too weak to drive prebiotic chemical evolution and no energy is supplied at night. Therefore, other sources of energy are needed. Among those external energy sources are natural nuclear reactors, which are thought to have existed ubiquitously in the surface environment of the Hadean Earth. The decay heat of uranium and ionizing radiation from natural nuclear reactors played an important role in promoting prebiotic chemical evolution. Such chemical evolutional reactions are difficult to achieve with solar energy or heat from magma alone. In other words, the initial process towards the emergence of life on the Hadean Earth was probably driven by ionizing radiation. After a natural nuclear reactor and a geyser combined to form a material-energy circulation system, abundant energy allowed various processes of trial and error to proceed toward achieving the emergence of early life. In this way, the functions of metabolism and self-replication were created. The geyser eruptions produced micron-sized droplets, which were released into the atmosphere to form the most primitive cells. Repeated material circulations and geyser eruptions created various combinations of BBLs, including more complex membranes. The wide variety of primitive cells released to the ground eventually led to a new evolutionary path on the Earth's surface. The proto cells, away from the powerful and abundant energy supplying natural nuclear reactors, would eventually have acquired new capabilities to utilize solar energy for life to survive. The cover, depicting a natural nuclear reactor in contrast to the Sun, is a scene from the CG movie series “The Whole History of the Earth and Life,” which presents the emergence, coevolution, and future of the Earth and life1).

    (Shigenori MARUYAMA)

    Notes

    1) YouTube; https://www.youtube.com/c/冥王代生命学の創成 (in Japanese) or https://www.youtube.com/c/HadeanBioscience (in English) [Cited 2020/10/27].

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Special Issue: The Hadean World (Part III): Emergence of Life and Early Evolution
Review Articles
  • Shigenori MARUYAMA, Tomohiko SATO, Yusuke SAWAKI, Konomi SUDA
    2020 Volume 129 Issue 6 Pages 757-777
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     Reported are the origins and chemistry of hot spring water unique to the Ohmi–Hakuba region in the northern Japan Alps, central north Honshu, where a variety of rock types, derived from accretionary complex formed in the Ediacaran (presumably ca. 620 Ma), are regionally exposed. One of the largest bodies of serpentinized peridotite in Japan intersects the Quaternary volcanic front. Featuring an unusual geochemistry, the resulting unique hydrothermal hot springs yield a high pH (ca. 10-11) and a continuous supply of H2. Research reveals four types of hot spring in the Hakuba region: (1) serpentinite hosted hot spring water, (2) high-salinity and carbonated water, (3) Archean type low pO2 hot spring water, and (4) acidic and sulfuric hot spring water with a H2S gas input from magma. The high alkali and H2-enriched hot spring water (Type 1) differs remarkably from other hot springs in this region. In terms of geochemistry, there is a dissolved oxygen content due to the production of abundant H2, which is the reason why a Hadean-type microbial community is present. The origins and evolution of life are closely related to atmospheric oxygen level. Generally, anaerobic microbes inhabit subsurface areas where free oxygen is limited, while oxygen adaptive creatures cannot survive in an anaerobic environment. This means anaerobic microbes have not evolved, and remain as “living fossils”. Hakuba OD1 is one of the most important candidates for the oldest form of life directly connected to LUCA, because it has survived in a Hadean-like environment since emerging. The next research target is the ecosystem in a H2-enriched environment without free oxygen.

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  • Toshikazu EBISUZKI, Hidenori NISHIHARA, Ken KUROKAWA, Hiroshi MORI, Yo ...
    2020 Volume 129 Issue 6 Pages 779-804
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS
    Supplementary material

     Previously proposed hypotheses on the origin of life are reviewed and it is demonstrated that none of them can provide the energy flux of ionizing radiation (UV/X/γ photons, and high-energy charged particles and neutrons) required to synthesize organic materials as demonstrated by the experiments by Miller and Urey in 1953. In order to overcome this difficulty, Ebisuzaki and Maruyama, in 2017, proposed a new hypothesis called the “Nuclear Geyser Model” of the origin of life, in which high-energy flux from a natural nuclear reactor drives chemical reactions to produce major biological molecules, such as amino acids, nucleotides, sugars, and fatty acids from raw molecules (H2O, N2, and CO2). Natural nuclear reactors were common on the surface of Hadean Earth, because the 235U/238U ratio was as high as 20%, which is much higher than the present value (0.7%), due to the shorter half-life of 235U than 238U. Ebisuzaki and Maruyama further posited that aqueous electrons and glyceraldehyde play key roles in the networks of chemical reactions in a nuclear geyser and suggested that primordial life depended on glyceraldehyde phosphate (GAP) from the nuclear geyser system as energy, carbon, and phosphate sources, pointing to a possible parallelism with the anaerobic glycolysis pathway; in particular, the lower stem path starting from GAP through Acetyl Coenzyme A to produce ATP and reduction power. It is shown that microbes (members of candidate division OD1) inhabiting high alkali hot springs, a modern analogue of the Hadean Earth environment, do not possess genes associated with conventional metabolisms, such as those of the TCA cycle, but only have genes in the lower stem path of the glycolysis. This is named the “Hadean Primordial Pathway”, because it is believed that this striking result points to a plausible origin of metabolic pathways of extant organisms. Also proposed is a step-by-step scenario of the evolution of the metabolism: 1) Chemical degradation of GAP supplied from the nuclear geyser to lactate; 2) Catalytic reactions to produce reductive power and acetyl coenzyme A (or its primitive form) and self-reproductive reactions by ribozymes on the surface of minerals (pyrite and struvite), which precipitate in a nuclear geyser (RNA world); 3) Enzymatic reactions by proteins with pyrites and the struvite in their reaction centers (RNP world); and, 4) Metabolism of extant organisms with the full assembly of enzymes produced by translating molecular machines with information stored in DNA sequences (DNA world). It is further inferred that relics of primordial metabolic evolution in the Hadean nuclear geyser can be seen at the reaction centers of enzymes of both pyrite and struvite types, nucleotide-like molecules as a cofactor of the enzymes, Calvin Cycle of photosynthesis, and chemical abundance of cytoplasm.

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  • Tomoya BABA, Shigeyuki KAKIZAWA, Hiroshi MORI, Yutetsu KURUMA, Ken KUR ...
    2020 Volume 129 Issue 6 Pages 805-824
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     Estimating the “minimal gene set” for a cell to be viable is an important issue in understanding “living” cells, creating “artificial” cells, and revealing “ancient” cells. The minimal gene set is critical information for understanding a cell system and designing an artificial genome, which is an essential element for creating an artificial cell. Artificial cells can provide many clues to understanding primordial life on Earth. To reveal minimal gene sets, “essential genes” in many bacteria, which could not be removed from bacterial genomes, have been identified. Bacteria are the most useful organisms for identifying essential genes from their specific characteristics: small genomes, rapid growth, and species that are easy to manipulate genetically. Therefore, various investigations on minimal gene sets or minimal genome of bacteria are reviewed, and “the minimal gene set for a viable cell” is discussed.

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Original Article
  • Takashi NARIHIRO, Masaru K. NOBU, Ling LENG, Hideyuki TAMAKI
    2020 Volume 129 Issue 6 Pages 825-835
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     To date, more than 15,000 bacterial and archaeal species have been isolated and characterized. It has become evident from recent biochemical and genomic studies that these microorganisms employ a variety of energy conservation systems to drive thermodynamically unfavorable reactions or harness marginal energy from exergonic reactions in the metabolic pathways required for energy metabolism. For example, a membrane-bound [NiFe] hydrogenase (Mbh) supports critical steps in glycolysis for a hyper-thermophilic archaeon Pyrococcus furiosus: glyceraldehyde 3-phosphate (GAP):ferredoxin (Fd) oxidoreductase and pyruvate:Fd oxidoreductase. However, the molecular evolution of energy conservation systems is still poorly understood. Targets of this study are: [NiFe] hydrogenase-related energy conservation systems including Mbh, energy conserving hydrogenases (Eha, Ehb, and Ech), hydrogenase 3 (Hyc), hydrogenase 4 (Hyf), hydrogen-evolving NADH/quinone-dependent hydrogenases (Hya and Hyb), and bidirectional soluble hydrogenase (Hox). A phylogenetic analysis shows that subunits having a [NiFe] active site of mbh (mbhL), which catalyzes proton reduction, are closely related to subunits of other energy conserving hydrogenases (i.e., ehaO, ehbN, and echE), and are distantly related to other subunits of [NiFe] hydrogenases (i.e., hya and hox) and NADH:ubiquinone oxidoreductase subunit D (nuoD). Combined phylogenetic analysis of hydrogenase-associated proton pomp modules indicates that ancestral Mbh containing mbhL and mbhH may have served as an energy conservation system for primordial metabolism.

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Review Articles
  • Ruiqin YI, Albert FAHRENBACH, Yayoi HONGO
    2020 Volume 129 Issue 6 Pages 837-851
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     Chemical evolution, starting from simple compounds that eventually transform into complex mixtures, is a theme long recognized to be of fundamental importance to origins of life research. Ionizing radiation on simple and small molecules, such as hydrogen cyanide (HCN) and acetonitorile (CH3CN), is proposed to be one of the geochemically plausible mechanism driving multiple reactions yielding prebiotic precursors essential to emergence of life on early-Earth. Water radiolysis forming radicals, proton, and solvated electron also assists developing a reaction network in a one-pot system. Radiolytic mechanisms on an experimental basis are reviewed. Particularly, proposed synthetic strategies and mechanisms of amino acids and nucleotides are presented.

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  • Kensuke IGARASHI, Shigeyuki KAKIZAWA
    2020 Volume 129 Issue 6 Pages 853-870
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     The origin of life has been explained by a number of hypotheses. Depending on the geochemical settings in each hypothesis, model metabolisms of the first life are classified into two major types, namely, heterotrophy and autotrophy. The “Iron-sulfur world” hypothesis explains the development of autotrophic life with a chemical evolution process mediated by metal sulfides. Metal sulfides have been found to catalyze simple carbon/nitrogen reduction reactions in simulated Hadean Earth conditions. Combinations of these reactions are thought to form organic molecules, such as pyruvate and peptide, then ultimately the first cell. Iron-sulfur proteins are found in all life and play a cardinal role in key redox/oxidation reactions, such as carbon/nitrogen fixation, respiration, and translation. Ancient iron-sulfur proteins are hypothesized to be formed by the conjugation of iron-sulfur clusters and simple peptides. First, an overview is given of the “Iron-sulfur world” hypothesis including the chemical evolution process for the formation of ancient iron-sulfur proteins, and then future perspectives for the origin-of-life research are discussed in the context of this hypothesis.

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  • Norikazu ICHIHASHI
    2020 Volume 129 Issue 6 Pages 871-880
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     All living organisms found so far consist of cells with a micro-water droplet surrounded by a lipid bilayer. Such a compartment structure is necessary for living organisms to repress the amplification of parasitic entities. This role of cellular structures is especially important for the primitive lifeforms that first appeared on ancient Earth. This complex lipid-based cell boundary is considered to have been acquired later in the long evolutionary history of life. Instead, ancient life-forms utilized cell-like structures that could be supplied from the ancient Earth environment. What kinds of structure could be utilized by ancient life-forms? Reviewed here are previous hypotheses regarding ancient cell-like structures, such as compartment structures formed inside a hydrothermal vent or on a rock surface, water droplets in the air that spread from geysers, and vesicles composed of simple amphiphilic molecules. Also introduced are a recent experimental verification of droplets in the air repressing parasite amplification using Spiegelman's RNA replication system. Our understanding of the origins of cellular structures is still limited because of a lack of appropriate experimental examinations based on a deeper understanding of the ancient Earth environment, which can be achieved only by collaborations between geologists and biochemists.

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  • Megumi TSURUMAKI, Motofumi SAITO, Shigenori MARUYAMA, Akio KANAI
    2020 Volume 129 Issue 6 Pages 881-898
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     It is well known that the evolution of life is affected by environmental factors, and this should be a fundamental perspective when investigating the origin of life; however, this perspective has not been fully addressed in biology. The Hadean Earth had a completely different surface environment from that of today, with no free oxygen, but instead a local environment rich in H2 which was generated by serpentinization, while energy–material circulation was driven by nuclear geysers. It is proposed that an anoxic hot-spring environment, with abundant hydrogen produced by serpentinization, was the birthplace of life. It is also proposed that the Hakuba hot spring in Nagano, Japan, is a Hadean-Earth-like environment with an H2-rich environment. A microbe found there, designated Hakuba OD1, is a member of the Candidate Phyla Radiation (CPR) bacteria group. In this review, CPR bacteria are described and their importance for the origin of life is discussed. The CPR is a bacterial supergroup consisting of dozens of phylum-level lineages of very small bacteria. This group was recently discovered with a metagenomics analysis that allowed unculturable environmental samples to be detected. Biochemical approaches to the CPR bacteria have not yet been successful because almost all the bacteria are unculturable or have not been isolated. However, with the development of massive parallel sequencing technology (next-generation sequencing), the phylogenetic characteristics of the CPR bacteria are becoming clear, and genomic analyses of these bacteria have led to unique discoveries. The sizes of the CPR bacterial genomes range from 400 to 1,500 kilobases (kb), and they contain approximately 400-1,500 genes. Thus, their genomes are remarkably small compared to other well-known and ordinary bacteria, represented by Escherichia coli, which have over 4,000 genes, but are similar to those of symbiotic or parasitic bacteria. The CPR bacterial genomes also lack many of the genes involved in essential metabolic pathways, such as the tricarboxylic acid (TCA) cycle and amino acid biosynthesis, so they seem to obtain their essential metabolites from their environments. It is proposed that this knowledge is important when considering the chemical changes that occurred on primitive Earth, which gave rise to the first forms of life through the processes of chemical evolution. Therefore, it is essential to understand the kinds of protein that are encoded in CPR bacterial genomes when studying the origin of life.

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  • Naota TAKEYAMA, Yuka TAKAHASHI, Shohei NAGATA, Yusuke SAWAKI, Tomohiko ...
    2020 Volume 129 Issue 6 Pages 899-912
    Published: December 25, 2020
    Released: January 18, 2021
    JOURNALS FREE ACCESS

     The origin of eukaryotic organisms is one of the most important questions in biology. So far, it has been suggested that eukaryotes are phylogenetically related to Archaea. Indeed, recent progress in archaeal genomic biology seems to have accurately determined the exact position of Archaea in the birth of the Eukaryota. In particular, identifying groups of archaeal species, such as the superphylum TACK and the Asgard archaea, has shown that primitive genes for eukaryotic signature proteins (ESP) already existed in the genomes of these archaeal species. Some ESPs are especially important, including actin and tubulin in the cytoskeleton and the ESCRT complex, which is involved in nuclear membrane formation. There have been many reports that eukaryotic intracellular organelles, such as mitochondria and chloroplasts, evolved from specific symbiotic bacteria. Moreover, eukaryotic genes are disrupted by intronic sequences, which must be removed or “spliced” and the exons connected after the primary transcript is generated, to make a mature functional mRNA. Recently, it has been suggested that the self-splicing factor in both bacterial and archaeal genomes, called “group II intron”, may cause gene disruption. In this review, the frontiers of genome biology are summarized in terms of the importance of prokaryotes (both Archaea and Bacteria) for the origin of Eukarya. From an Earth history perspective, how the increase in atmospheric oxygen concentration at 2.4-2.0 billion years ago may have contributed to the rise of the eukaryotes is discussed.

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