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  1. Article ; Online: How did life become cellular?

    Goldman, Aaron D

    Proceedings. Biological sciences

    2023  Volume 290, Issue 1992, Page(s) 20222327

    Language English
    Publishing date 2023-02-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 209242-6
    ISSN 1471-2954 ; 0080-4649 ; 0962-8452 ; 0950-1193
    ISSN (online) 1471-2954
    ISSN 0080-4649 ; 0962-8452 ; 0950-1193
    DOI 10.1098/rspb.2022.2327
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  2. Article ; Online: Very early evolution from the perspective of microbial ecology

    Goldman, Aaron D. / Kaçar, Betül

    Environmental Microbiology. 2023 Jan., v. 25, no. 1 p.5-10

    2023  

    Abstract: The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most ... ...

    Abstract The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.
    Keywords ancestry ; evolution ; genome ; horizontal gene transfer ; microbial ecology ; microbiology
    Language English
    Dates of publication 2023-01
    Size p. 5-10.
    Publishing place John Wiley & Sons, Inc.
    Document type Article ; Online
    Note EDITORIAL
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16144
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  3. Article ; Online: Very early evolution from the perspective of microbial ecology.

    Goldman, Aaron D / Kaçar, Betül

    Environmental microbiology

    2022  Volume 25, Issue 1, Page(s) 5–10

    Abstract: The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most ... ...

    Abstract The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.
    MeSH term(s) Evolution, Molecular ; Genome ; Ecology ; Gene Transfer, Horizontal ; Microbiota ; Phylogeny ; Biological Evolution
    Language English
    Publishing date 2022-08-09
    Publishing country England
    Document type Editorial ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16144
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  4. Article ; Online: The Journal of Molecular Evolution Turns 50.

    Goldman, Aaron D / Liberles, David A

    Journal of molecular evolution

    2021  Volume 89, Issue 3, Page(s) 119–121

    MeSH term(s) Amino Acid Sequence ; Evolution, Molecular ; Protein Structure, Secondary
    Language English
    Publishing date 2021-02-23
    Publishing country Germany
    Document type Editorial
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s00239-021-10000-w
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  5. Article ; Online: Cofactors are Remnants of Life's Origin and Early Evolution.

    Goldman, Aaron D / Kacar, Betul

    Journal of molecular evolution

    2021  Volume 89, Issue 3, Page(s) 127–133

    Abstract: The RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both ...

    Abstract The RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both stored genetic information and performed the molecular functions encoded by that genetic information. Current research into a potential RNA World revolves around the catalytic properties of RNA-based enzymes, or ribozymes. Well before the discovery of ribozymes, Harold White proposed that evidence for a precursor RNA world could be found within modern proteins in the form of coenzymes, the majority of which contain nucleobases or nucleoside moieties, such as Coenzyme A and S-adenosyl methionine, or are themselves nucleotides, such as ATP and NADH (a dinucleotide). These coenzymes, White suggested, had been the catalytic active sites of ancient ribozymes, which transitioned to their current forms after the surrounding ribozyme scaffolds had been replaced by protein apoenzymes during the evolution of translation. Since its proposal four decades ago, this groundbreaking hypothesis has garnered support from several different research disciplines and motivated similar hypotheses about other classes of cofactors, most notably iron-sulfur cluster cofactors as remnants of the geochemical setting of the origin of life. Evidence from prebiotic geochemistry, ribozyme biochemistry, and evolutionary biology, increasingly supports these hypotheses. Certain coenzymes and cofactors may bridge modern biology with the past and can thus provide insights into the elusive and poorly-recorded period of the origin and early evolution of life.
    MeSH term(s) Coenzymes ; Evolution, Molecular ; Nucleotides ; Origin of Life ; Proteins/genetics ; RNA/genetics ; RNA, Catalytic/genetics
    Chemical Substances Coenzymes ; Nucleotides ; Proteins ; RNA, Catalytic ; RNA (63231-63-0)
    Language English
    Publishing date 2021-02-06
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s00239-020-09988-4
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  6. Article ; Online: Informatic Capabilities of Translation and Its Implications for the Origins of Life.

    Cuevas-Zuviría, Bruno / Adam, Zachary R / Goldman, Aaron D / Kaçar, Betül

    Journal of molecular evolution

    2023  Volume 91, Issue 5, Page(s) 567–569

    Abstract: The ability to encode and convert heritable information into molecular function is a defining feature of life as we know it. The conversion of information into molecular function is performed by the translation process, in which triplets of nucleotides ... ...

    Abstract The ability to encode and convert heritable information into molecular function is a defining feature of life as we know it. The conversion of information into molecular function is performed by the translation process, in which triplets of nucleotides in a nucleic acid polymer (mRNA) encode specific amino acids in a protein polymer that folds into a three-dimensional structure. The folded protein then performs one or more molecular activities, often as one part of a complex and coordinated physiological network. Prebiotic systems, lacking the ability to explicitly translate information between genotype and phenotype, would have depended upon either chemosynthetic pathways to generate its components-constraining its complexity and evolvability- or on the ambivalence of RNA as both carrier of information and of catalytic functions-a possibility which is still supported by a very limited set of catalytic RNAs. Thus, the emergence of translation during early evolutionary history may have allowed life to unmoor from the setting of its origin. The origin of translation machinery also represents an entirely novel and distinct threshold of behavior for which there is no abiotic counterpart-it could be the only known example of computing that emerged naturally at the chemical level. Here we describe translation machinery's decoding system as the basis of cellular translation's information-processing capabilities, and the four operation types that find parallels in computer systems engineering that this biological machinery exhibits.
    Language English
    Publishing date 2023-08-01
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s00239-023-10125-0
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  7. Article: A consensus view of the proteome of the last universal common ancestor.

    Crapitto, Andrew J / Campbell, Amy / Harris, A J / Goldman, Aaron D

    Ecology and evolution

    2022  Volume 12, Issue 6, Page(s) e8930

    Abstract: The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of ... ...

    Abstract The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide-derived organic cofactors.
    Language English
    Publishing date 2022-06-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2635675-2
    ISSN 2045-7758
    ISSN 2045-7758
    DOI 10.1002/ece3.8930
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  8. Article ; Online: Electron transport chains as a window into the earliest stages of evolution.

    Goldman, Aaron D / Weber, Jessica M / LaRowe, Douglas E / Barge, Laura M

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 34, Page(s) e2210924120

    Abstract: The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" ... ...

    Abstract The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.
    MeSH term(s) Phylogeny ; Electron Transport ; Biochemical Phenomena ; Proteins/chemistry ; Energy Metabolism ; Origin of Life ; Biological Evolution ; Evolution, Molecular
    Chemical Substances Proteins
    Language English
    Publishing date 2023-08-14
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2210924120
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  9. Article ; Online: Nucleobases in Meteorites to Nucleobases in RNA and DNA?

    Krishnamurthy, Ramanarayanan / Goldman, Aaron D / Liberles, David A / Rogers, Karyn L / Tor, Yitzhak

    Journal of molecular evolution

    2022  Volume 90, Issue 5, Page(s) 328–331

    Abstract: Nucleic acids likely played a foundational role in the origin of life. However, the prebiotic chemistry of nucleoside and nucleotide synthesis has proved challenging on a number of fronts. The recent discovery of both pyrimidine and purine nucleobases in ...

    Abstract Nucleic acids likely played a foundational role in the origin of life. However, the prebiotic chemistry of nucleoside and nucleotide synthesis has proved challenging on a number of fronts. The recent discovery of both pyrimidine and purine nucleobases in carbonaceous chondrite meteorites has garnered much attention from both the popular press and the scientific community. Here, we discuss these findings in the context of nucleoside/nucleotide prebiotic chemistry. We consider that the main challenge of prebiotic nucleoside synthesis, that of nucleosidic bond formation, is not addressed by the identification nucleobases in meteorites. We further discuss issues of selection that arise from the observation that such meteorites contain both canonical and non-canonical nucleobases. In sum, we argue that, despite the major analytical achievement of identifying and characterizing nucleobases in meteorites, this observation does little to advance our understanding of the prebiotic chemistry that could have led to the first genetic molecules that gave rise to us.
    MeSH term(s) DNA ; Meteoroids ; Nucleic Acids ; Nucleosides ; Nucleotides ; Purines ; Pyrimidines ; RNA/chemistry
    Chemical Substances Nucleic Acids ; Nucleosides ; Nucleotides ; Purines ; Pyrimidines ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2022-08-12
    Publishing country Germany
    Document type Letter ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s00239-022-10069-x
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  10. Article ; Online: The Coevolution of Cellularity and Metabolism Following the Origin of Life.

    Takagi, Yuta A / Nguyen, Diep H / Wexler, Tom B / Goldman, Aaron D

    Journal of molecular evolution

    2020  Volume 88, Issue 7, Page(s) 598–617

    Abstract: The emergence of cellular organisms occurred sometime between the origin of life and the evolution of the last universal common ancestor and represents one of the major transitions in evolutionary history. Here we describe a series of artificial life ... ...

    Abstract The emergence of cellular organisms occurred sometime between the origin of life and the evolution of the last universal common ancestor and represents one of the major transitions in evolutionary history. Here we describe a series of artificial life simulations that reveal a close relationship between the evolution of cellularity, the evolution of metabolism, and the richness of the environment. When environments are rich in processing energy, a resource that the digital organisms require to both process their genomes and replicate, populations evolve toward a state of non-cellularity. But when processing energy is not readily available in the environment and organisms must produce their own processing energy from food puzzles, populations always evolve both a proficient metabolism and a high level of cellular impermeability. Even between these two environmental extremes, the population-averaged values of cellular impermeability and metabolic proficiency exhibit a very strong correlation with one another. Further investigations show that non-cellularity is selectively advantageous when environmental processing energy is abundant because it allows organisms to access the available energy, while cellularity is selectively advantageous when environmental processing energy is scarce because it affords organisms the genetic fidelity required to incrementally evolve efficient metabolisms. The selection pressures favoring either non-cellularity or cellularity can be reversed when the environment transitions from one of abundant processing energy to one of scarce processing energy. These results have important implications for when and why cellular organisms evolved following the origin of life.
    MeSH term(s) Biological Evolution ; Cell Biology ; Cells/metabolism ; Computer Simulation ; Evolution, Molecular ; Metabolism/genetics ; Models, Biological ; Origin of Life
    Keywords covid19
    Language English
    Publishing date 2020-08-18
    Publishing country Germany
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s00239-020-09961-1
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