Aaron Goldman

Aaron Goldman

Oberlin College

H-index: 16

North America-United States

About Aaron Goldman

Aaron Goldman, With an exceptional h-index of 16 and a recent h-index of 15 (since 2020), a distinguished researcher at Oberlin College,

His recent articles reflect a diverse array of research interests and contributions to the field:

How did life become cellular?

Very early evolution from the perspective of microbial ecology

Informatic Capabilities of Translation and Its Implications for the Origins of Life

Origin and Evolution of Translation: A Unifying Perspective Across Time

Electron transport chains as a window into the earliest stages of evolution

Abiotic Redox Reactions of Quinones Driven by Ocean World Relevant Minerals

Scaling laws in enzyme function reveal a new kind of biochemical universality

Testing Abiotic Reduction of NAD+ Directly Mediated by Iron/Sulfur Minerals

Aaron Goldman Information

University

Oberlin College

Position

___

Citations(all)

2053

Citations(since 2020)

1140

Cited By

1342

hIndex(all)

16

hIndex(since 2020)

15

i10Index(all)

23

i10Index(since 2020)

20

Email

University Profile Page

Oberlin College

Top articles of Aaron Goldman

How did life become cellular?

Authors

Aaron D Goldman

Journal

Proceedings of the Royal Society B

Published Date

2023/2/8

All organisms on the Earth are composed of one or more cells, making cellularity a fundamental organizing principle of life. Cellular organization as we see it today is complex, requiring the metabolic maintenance of membranes and their constituents as well as genetic control over the timing and coordination of cell division. Despite this complexity, phylogenetic evidence suggests that metabolic pathways for membrane phospholipid biosynthesis had evolved by the time of the last universal common ancestor of life [1]. Some components of a molecular system that embeds proteins into membranes appear to have emerged even earlier than the last universal common ancestor [2], around the same time that the final amino acids were being added to the canonical genetic code. Given the complexity of cellular organization and its reliance on a similarly complex metabolism and genome, the ancient precursors to …

Very early evolution from the perspective of microbial ecology

Authors

Aaron D Goldman,Betül Kaçar

Published Date

2023/1

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 …

Informatic Capabilities of Translation and Its Implications for the Origins of Life

Authors

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

Journal

Journal of Molecular Evolution

Published Date

2023/10

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 …

Origin and Evolution of Translation: A Unifying Perspective Across Time

Authors

Evrim Fer,Bruno Cuevas-Zuviría,Aaron D Goldman,Zachary R Adam,Betul Kacar

Published Date

2023/8/23

Translation is a foundational biological process that decodes genetic information provided by an mRNA template. Over the past decade major advancements have been made towards understanding the origins and early evolution of translation. There remain two critical gaps: First, we lack a coherent view of how translation factors emerged and co-evolved to regulate the cellular protein synthesis. Second, we know little about the evolutionary and environmental basis of variation and complexity of translation across the tree of life. Here we present a comprehensive survey of translation machinery diversity and similarity across bacteria, eukaryotes, and archaea with particular emphasis on the translation factors and ribosome. Finally, we interrogate translation at the sub-ribosomal, ribosomal and cellular scales and highlight research questions for the origin and early evolution of translation studies. The broad array of perspectives that range from the molecular to ecosystem levels may provide an opportunity to advance our understanding of the origins, complexity, and evolution of this fascinating machinery.

Electron transport chains as a window into the earliest stages of evolution

Authors

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

Journal

Proceedings of the National Academy of Sciences

Published Date

2023/8/22

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 …

Abiotic Redox Reactions of Quinones Driven by Ocean World Relevant Minerals

Authors

KA Dzurilla,JM Weber,DE LaRowe,AD Goldman,BL Henderson,LM Barge

Journal

LPI Contributions

Published Date

2023/3

Abiotic Redox Reactions of Quinones Driven by Ocean World Relevant Minerals - NASA/ADS Now on home page ads icon ads Enable full ADS view NASA/ADS Abiotic Redox Reactions of Quinones Driven by Ocean World Relevant Minerals Dzurilla, KA ; Weber, JM ; LaRowe, DE ; Goldman, AD ; Henderson, BL ; Barge, LM Abstract An investigation of FeS's ability to facilitate the production of biologically important compounds. Publication: LPI Contributions Pub Date: March 2023 Bibcode: 2023LPICo2806.2362D full text sources Publisher | © The SAO/NASA Astrophysics Data System adshelp[at]cfa.harvard.edu The ADS is operated by the Smithsonian Astrophysical Observatory under NASA Cooperative Agreement NNX16AC86A NASA logo Smithsonian logo Resources About ADS ADS Help What's New Careers@ADS Social @adsabs ADS Blog Project Switch to full ADS Is ADS down? (or is it just me...) …

Scaling laws in enzyme function reveal a new kind of biochemical universality

Authors

and Sara I. Walker. Gagler,Dylan C.,Bradley Karas,Christopher P. Kempes,John Malloy,Veronica Mierzejewski,Aaron D. Goldman,Hyunju Kim

Journal

Proceedings of the National Academy of Sciences

Published Date

2022/3/1

All life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to known biochemistry and does not allow quantitative predictions about examples not yet observed. Here, we introduce a more generalizable concept of biochemical universality that is more akin to the kind of universality found in physics. Using annotated genomic datasets including an ensemble of 11,955 metagenomes, 1,282 archaea, 11,759 bacteria, and 200 eukaryotic taxa, we show how enzyme functions form universality classes with common scaling behavior in their relative abundances across the datasets. We verify that these scaling laws are not explained by the presence of compounds, reactions, and enzyme functions shared across known examples of life. We demonstrate how these scaling laws can …

Testing Abiotic Reduction of NAD+ Directly Mediated by Iron/Sulfur Minerals

Authors

Jessica M Weber,Bryana L Henderson,Douglas E LaRowe,Aaron D Goldman,Scott M Perl,Keith Billings,Laura M Barge

Journal

Astrobiology

Published Date

2022/1/1

Life emerged in a geochemical context, possibly in the midst of mineral substrates. However, it is not known to what extent minerals and dissolved inorganic ions could have facilitated the evolution of biochemical reactions. Herein, we have experimentally shown that iron sulfide minerals can act as electron transfer agents for the reduction of the ubiquitous biological protein cofactor nicotinamide adenine dinucleotide (NAD+) under anaerobic prebiotic conditions, observing the NAD+/NADH redox transition by using ultraviolet-visible spectroscopy and 1H nuclear magnetic resonance. This reaction was mediated with iron sulfide minerals, which were likely abundant on early Earth in seafloor and hydrothermal settings; and the NAD+/NADH redox reaction occurred in the absence of UV light, peptide ligand(s), or dissolved mediators. To better understand this reaction, thermodynamic modeling was also performed. The …

Nucleobases in Meteorites to Nucleobases in RNA and DNA?

Authors

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

Journal

Journal of molecular evolution

Published Date

2022/10

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 …

Investigation of Prebiotic Metabolic Redox Reactions Involving Cofactors NAD+ and Ubiquinone

Authors

Jessica Weber,Bryana L Henderson,Douglas LaRowe,Aaron David Goldman,Scott M Perl,Keith Billings,Laura M Barge

Journal

The Astrobiology Science Conference (AbSciCon) 2022

Published Date

2022/5

The origin of metabolism is not well understood and there are many theories for how it could have occurred. Currently, metabolism uses enzymes and cofactors, which are molecules required for enzyme reactivity. We explored if important metabolic cofactor redox reactions could occur under geologic conditions with minerals instead of enzymes. We tested the reactions of 2 cofactors with iron sulfur minerals.

Replication Fidelity and Random Drift at the Origin of Life

Authors

Aaron David Goldman

Journal

The Astrobiology Science Conference (AbSciCon) 2022

Published Date

2022/5

In the most early stages of evolution, many traits would have begun at a minimum value and increased over time, eg, genome size, gene number, metabolic network size, etc. If a trait begins at a minimum value, it can increase over time in certain lineages due solely to random drift causing a change in the variance across all lineages. This can occur without any natural selection on the trait. Here we show that when random drift occurs on traits that enhance replication fidelity, the entire population evolves toward higher values of the trait, not just a subset of the population at the tail of the distribution. In this way, the random drift of phenotypes that enhance replication fidelity could have propelled early replicators toward greater capabilities even before the onset of natural selection.

The very early evolution of protein translocation across membranes

Authors

AJ Harris,Aaron David Goldman

Journal

PLoS Computational Biology

Published Date

2021/3/8

In this study, we used a computational approach to investigate the early evolutionary history of a system of proteins that, together, embed and translocate other proteins across cell membranes. Cell membranes comprise the basis for cellularity, which is an ancient, fundamental organizing principle shared by all organisms and a key innovation in the evolution of life on Earth. Two related requirements for cellularity are that organisms are able to both embed proteins into membranes and translocate proteins across membranes. One system that accomplishes these tasks is the signal recognition particle (SRP) system, in which the core protein components are the paralogs, FtsY and Ffh. Complementary to the SRP system is the Sec translocation channel, in which the primary channel-forming protein is SecY. We performed phylogenetic analyses that strongly supported prior inferences that FtsY, Ffh, and SecY were all present by the time of the last universal common ancestor of life, the LUCA, and that the ancestor of FtsY and Ffh existed before the LUCA. Further, we combined ancestral sequence reconstruction and protein structure and function prediction to show that the LUCA had an SRP system and Sec translocation channel that were similar to those of extant organisms. We also show that the ancestor of Ffh and FtsY that predated the LUCA was more similar to FtsY than Ffh but could still have comprised a rudimentary protein translocation system on its own. Duplication of the ancestor of FtsY and Ffh facilitated the specialization of FtsY as a membrane bound receptor and Ffh as a cytoplasmic protein that could bind nascent proteins with specific …

Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life

Authors

Aaron Goldman,Greg Fournier,Johann Peter Gogarten,Anton S Petrov,Lynn Rothschild,Daniel Segrè,Eric Smith,Loren Williams

Journal

Bulletin of the American Astronomical Society

Published Date

2021/5

We describe current research areas and future directions related to ancient proteins and proteomes and their implications for ancient organismal ancestors. We conclude that early evolution research must continue to play an indispensable role in origin of life research and a more prominent role in the design of life detection strategies.

The Journal of Molecular Evolution Turns 50

Authors

Aaron D Goldman,David A Liberles

Published Date

2021/4

Molecular evolution as a distinct discipline began to take shape in the 1960s as insights from biochemistry and population genetics combined with the emerging field of molecular biology, which offered new tools for comparing biomolecules and their sequences across evolutionary distance. Two early achievements, the establishment of molecular clocks and the subsequent development of the neutral theory, laid the foundation for molecular evolution (Suárez-Díaz 2016). Following on these accomplishments, the Journal of Molecular Evolution was founded and its first issue was published 50 years ago this month (see Liberles 2019). In this special issue, we celebrate the history of this journal and the field that it chronicled over the last half century. Just as molecular evolution emerged from the techniques and insights of molecular biology, biological chemistry, and population genetics, the field has kept pace through …

Cofactors are remnants of life’s origin and early evolution

Authors

Aaron D Goldman,Betul Kacar

Journal

Journal of Molecular Evolution

Published Date

2021/4

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 …

The coevolution of cellularity and metabolism following the origin of life

Authors

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

Journal

Journal of molecular evolution

Published Date

2020/9

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 …

Reactivity of metabolic intermediates and cofactor stability under model early Earth conditions

Authors

Thora R Maltais,David VanderVelde,Douglas E LaRowe,Aaron D Goldman,Laura M Barge

Journal

Origins of Life and Evolution of Biospheres

Published Date

2020/6

Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth’s early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are …

The Complex Phylogenetic Relationships of a 4mC/6mA DNA Methyltransferase in Prokaryotes

Authors

AJ Harris,Aaron David Goldman

Journal

Molecular Phylogenetics and Evolution

Published Date

2020/4/15

DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the …

Emerging frontiers in the study of molecular evolution

Authors

David A Liberles,Belinda Chang,Kerry Geiler-Samerotte,Aaron Goldman,Jody Hey,Betül Kaçar,Michelle Meyer,William Murphy,David Posada,Andrew Storfer

Journal

Journal of molecular evolution

Published Date

2020/4

A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.

See List of Professors in Aaron Goldman University(Oberlin College)

Aaron Goldman FAQs

What is Aaron Goldman's h-index at Oberlin College?

The h-index of Aaron Goldman has been 15 since 2020 and 16 in total.

What are Aaron Goldman's top articles?

The articles with the titles of

How did life become cellular?

Very early evolution from the perspective of microbial ecology

Informatic Capabilities of Translation and Its Implications for the Origins of Life

Origin and Evolution of Translation: A Unifying Perspective Across Time

Electron transport chains as a window into the earliest stages of evolution

Abiotic Redox Reactions of Quinones Driven by Ocean World Relevant Minerals

Scaling laws in enzyme function reveal a new kind of biochemical universality

Testing Abiotic Reduction of NAD+ Directly Mediated by Iron/Sulfur Minerals

...

are the top articles of Aaron Goldman at Oberlin College.

What is Aaron Goldman's total number of citations?

Aaron Goldman has 2,053 citations in total.

What are the co-authors of Aaron Goldman?

The co-authors of Aaron Goldman are Chris T. Amemiya, Mark Claire, Thomas G Doak, Shawn E. McGlynn, Jeff Bowman, Rika Anderson.

    Co-Authors

    H-index: 67
    Chris T. Amemiya

    Chris T. Amemiya

    University of California, Merced

    H-index: 33
    Mark Claire

    Mark Claire

    University of St Andrews

    H-index: 33
    Thomas G Doak

    Thomas G Doak

    Indiana University Bloomington

    H-index: 31
    Shawn E. McGlynn

    Shawn E. McGlynn

    Tokyo Institute of Technology

    H-index: 25
    Jeff Bowman

    Jeff Bowman

    University of California, San Diego

    H-index: 20
    Rika Anderson

    Rika Anderson

    Carleton College

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