Faculty & Staff

Start and Promotion Dates

  • Assistant Professor: 2021

Education

PhD: Emory University, Department of Chemistry
Postdoctoral research: NASA Astrobiology Institute and Harvard University

Areas of Study

Origins of life, astrobiology, early life and evolution, systems and synthetic biology, molecular paleobiology

Research Overview

The Kaçar Lab investigates the origins of life, the biology of early Earth and how understanding life’s emergence and early mechanisms may assist finding life beyond Earth. We are home to the NASA Astrobiology Center for Early Life and Evolution. Our integrative approach enables the study of biomolecule-scale macroevolutionary trends that span billions of years of history and is a fundamentally new methodology with which to study the origins and early evolution of life. The overall goal of our work is to assess the possible environmental impacts of ancient enzymes on global-scale signatures that record biological activity. Our work has been recognized by various media outlets, such as the UN Women, UNICEF, Library of Congress, European Union Delegation on Education, NOVA Science, BBC, NPR Science Friday, MIT Technology Review, Vice News, Wired, PBS, CNN and others. 

 

For more please visit the following links:

 

Lab Personnel

Picture of Adam
Zachary Adam
Associate Scientist
zadam2@wisc.edu
Picture of Amritkar
Kaustubh Amritkar
Grad Student
amritkar@wisc.edu
Picture of Carruthers
Brooke Carruthers
Grad Student
bcarruthers@wisc.edu
Picture of Cuevas Zuviria
Bruno Cuevas Zuviria
Postdoc
cuevaszuviri@wisc.edu
Picture of Fer
Evrim Fer
Grad Student
fer@wisc.edu
Picture of Garcia
Amanda Garcia
Assistant Scientist
akgarcia3@wisc.edu
Picture of Katsoulidis
Maria Katsoulidis
Project Coordinator
katsoulidis@wisc.edu
Picture of McGrath
Kaitlyn McGrath
Honorary Associate
kmcgrath5@wisc.edu
Picture of Meikle
Cameron Meikle
Grad Student
cmeikle@wisc.edu
Picture of Peng
Zhen Peng
Postdoc
peng69@wisc.edu
Picture of Rivier
Alex Rivier
Grad Student
rivier@wisc.edu
Picture of Rucker
Holly Rucker
Grad Student
hrucker@wisc.edu
Picture of Russell
Steven Russell
Research Specialist
sjrussell@wisc.edu

Research Papers

  • Schwartz SL, Garcia AK, Kaçar B, Fournier GP (2022) Early Nitrogenase Ancestors Encompassed Novel Active Site Diversity. Molecular biology and evolution 39((11)): PMC9549741 · Pubmed · DOI

    Ancestral sequence reconstruction (ASR) infers predicted ancestral states for sites within sequences and can constrain the functions and properties of ancestors of extant protein families. Here, we compare the likely sequences of inferred nitrogenase ancestors to extant nitrogenase sequence diversity. We show that the most-likely combinations of ancestral states for key substrate channel residues are not represented in extant sequence space, and rarely found within a more broadly defined physiochemical space-supporting that the earliest ancestors of extant nitrogenases likely had alternative substrate channel composition. These differences may indicate differing environmental selection pressures acting on nitrogenase substrate specificity in ancient environments. These results highlight ASR's potential as an in silico tool for developing hypotheses about ancestral enzyme functions, as well as improving hypothesis testing through more targeted in vitro and in vivo experiments.

  • Fer E, McGrath KM, Guy L, Hockenberry AJ, Kaçar B (2022) Early divergence of translation initiation and elongation factors. Protein science : a publication of the Protein Society 31((9)):e4393 PMC1570152 · Pubmed · DOI

    Protein translation is a foundational attribute of all living cells. The translation function carried out by the ribosome critically depends on an assortment of protein interaction partners, collectively referred to as the translation machinery. Various studies suggest that the diversification of the translation machinery occurred prior to the last universal common ancestor, yet it is unclear whether the predecessors of the extant translation machinery factors were functionally distinct from their modern counterparts. Here we reconstructed the shared ancestral trajectory and subsequent evolution of essential translation factor GTPases, elongation factor EF-Tu (aEF-1A/eEF-1A), and initiation factor IF2 (aIF5B/eIF5B). Based upon their similar functions and structural homologies, it has been proposed that EF-Tu and IF2 emerged from an ancient common ancestor. We generated the phylogenetic tree of IF2 and EF-Tu proteins and reconstructed ancestral sequences corresponding to the deepest nodes in their shared evolutionary history, including the last common IF2 and EF-Tu ancestor. By identifying the residue and domain substitutions, as well as structural changes along the phylogenetic history, we developed an evolutionary scenario for the origins, divergence and functional refinement of EF-Tu and IF2 proteins. Our analyses suggest that the common ancestor of IF2 and EF-Tu was an IF2-like GTPase protein. Given the central importance of the translation machinery to all cellular life, its earliest evolutionary constraints and trajectories are key to characterizing the universal constraints and capabilities of cellular evolution.

  • Garcia AK, Fer E, Sephus C, Kacar B (2022) An Integrated Method to Reconstruct Ancient Proteins. Methods in molecular biology (Clifton, N.J.) 2569:267-281 · Pubmed · DOI

    Proteins have played a fundamental role throughout life's history on Earth. Despite their biological importance, ancient origin, early function, and evolution of proteins are seldom able to be directly studied because few of these attributes are preserved across geologic timescales. Ancestral sequence reconstruction (ASR) provides a method to infer ancestral amino acid sequences and determine the evolutionary predecessors of modern-day proteins using phylogenetic tools. Laboratory application of ASR allows ancient sequences to be deduced from genetic information available in extant organisms and then experimentally resurrected to elucidate ancestral characteristics. In this article, we provide a generalized, stepwise protocol that considers the major elements of a well-designed ASR study and details potential sources of reconstruction bias that can reduce the relevance of historical inferences. We underscore key stages in our approach so that it may be broadly utilized to reconstruct the evolutionary histories of proteins.

  • Goldman AD, Kaçar B (2022) Very early evolution from the perspective of microbial ecology. Environmental microbiology : · Pubmed · DOI

    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.

  • Sephus CD, Fer E, Garcia AK, Adam ZR, Schwieterman EW, Kacar B (2022) Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins. Molecular biology and evolution 39((5)): PMC9117797 · Pubmed · DOI

    For billions of years, life has continuously adapted to dynamic physical conditions near the Earth's surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth's earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as "paleosensors" for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.

  • Kędzior M, Garcia AK, Li M, Taton A, Adam ZR, Young JN, Kaçar B (2022) Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time. Cell reports 39((4)):110726 · Pubmed · DOI

    The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.

  • Garcia AK, Kolaczkowski B, Kaçar B (2022) Reconstruction of Nitrogenase Predecessors Suggests Origin from Maturase-Like Proteins. Genome biology and evolution 14((3)): PMC8890362 · Pubmed · DOI

    The evolution of biological nitrogen fixation, uniquely catalyzed by nitrogenase enzymes, has been one of the most consequential biogeochemical innovations over life's history. Though understanding the early evolution of nitrogen fixation has been a longstanding goal from molecular, biogeochemical, and planetary perspectives, its origins remain enigmatic. In this study, we reconstructed the evolutionary histories of nitrogenases, as well as homologous maturase proteins that participate in the assembly of the nitrogenase active-site cofactor but are not able to fix nitrogen. We combined phylogenetic and ancestral sequence inference with an analysis of predicted functionally divergent sites between nitrogenases and maturases to infer the nitrogen-fixing capabilities of their shared ancestors. Our results provide phylogenetic constraints to the emergence of nitrogen fixation and are consistent with a model wherein nitrogenases emerged from maturase-like predecessors. Though the precise functional role of such a predecessor protein remains speculative, our results highlight evolutionary contingency as a significant factor shaping the evolution of a biogeochemically essential enzyme.

  • Carruthers BM, Garcia AK, Rivier A, Kacar B (2022) Correction: Automated Laboratory Growth Assessment and Maintenance of Azotobacter vinelandii. Current protocols 2((1)):e363 PMC9113642 · Pubmed · DOI

    No abstract available.

  • Kędzior M, Kacar B (2021) Quantification of RuBisCO Expression and Photosynthetic Oxygen Evolution in Cyanobacteria. Bio-protocol 11((20)):e4199 PMC8554809 · Pubmed · DOI

    Phototrophic microorganisms are frequently engineered to regulate the expression and the activity of targeted enzymes of interest for specific biotechnological and agricultural applications. This protocol describes a method to evaluate the expression of RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) in the model cyanobacterium Synechococcus elongatus PCC 7942, at both the transcript and protein levels by quantitative PCR and Western blot, respectively. We further describe an experimental method to determine photosynthetic activity using an oxygen electrode that measures the rate of molecular oxygen production by cyanobacterial cultures. Our protocol can be utilized to assess the effects of RuBisCO engineering at the metabolic and physiological levels.

  • De Tarafder A, Parajuli NP, Majumdar S, Kaçar B, Sanyal S (2021) Kinetic Analysis Suggests Evolution of Ribosome Specificity in Modern Elongation Factor-Tus from "Generalist" Ancestors. Molecular biology and evolution 38((8)):3436-3444 PMC8321524 · Pubmed · DOI

    It has been hypothesized that early enzymes are more promiscuous than their extant orthologs. Whether or not this hypothesis applies to the translation machinery, the oldest molecular machine of life, is not known. Efficient protein synthesis relies on a cascade of specific interactions between the ribosome and the translation factors. Here, using elongation factor-Tu (EF-Tu) as a model system, we have explored the evolution of ribosome specificity in translation factors. Employing presteady state fast kinetics using quench flow, we have quantitatively characterized the specificity of two sequence-reconstructed 1.3- to 3.3-Gy-old ancestral EF-Tus toward two unrelated bacterial ribosomes, mesophilic Escherichia coli and thermophilic Thermus thermophilus. Although the modern EF-Tus show clear preference for their respective ribosomes, the ancestral EF-Tus show similar specificity for diverse ribosomes. In addition, despite increase in the catalytic activity with temperature, the ribosome specificity of the thermophilic EF-Tus remains virtually unchanged. Our kinetic analysis thus suggests that EF-Tu proteins likely evolved from the catalytically promiscuous, "generalist" ancestors. Furthermore, compatibility of diverse ribosomes with the modern and ancestral EF-Tus suggests that the ribosomal core probably evolved before the diversification of the EF-Tus. This study thus provides important insights regarding the evolution of modern translation machinery.

  • Garcia AK, Cavanaugh CM, Kacar B (2021) The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution. The ISME journal 15((8)):2183-2194 PMC8319343 · Pubmed · DOI

    The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic C/C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth's atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.

  • Carruthers BM, Garcia AK, Rivier A, Kacar B (2021) Automated Laboratory Growth Assessment and Maintenance of Azotobacter vinelandii. Current protocols 1((3)):e57 · Pubmed · DOI

    Azotobacter vinelandii (A. vinelandii) is a commonly used model organism for the study of aerobic respiration, the bacterial production of several industrially relevant compounds, and, perhaps most significantly, the genetics and biochemistry of biological nitrogen fixation. Laboratory growth assessments of A. vinelandii are useful for evaluating the impact of environmental and genetic modifications on physiological properties, including diazotrophy. However, researchers typically rely on manual growth methods that are oftentimes laborious and inefficient. We present a protocol for the automated growth assessment of A. vinelandii on a microplate reader, particularly well-suited for studies of diazotrophic growth. We discuss common pitfalls and strategies for protocol optimization, and demonstrate the protocol's application toward growth evaluation of strains carrying modifications to nitrogen-fixation genes. © 2021 The Authors. Basic Protocol 1: Preparation of A. vinelandii plate cultures from frozen stock Basic Protocol 2: Preparation of A. vinelandii liquid precultures Basic Protocol 3: Automated growth rate experiment of A. vinelandii on a microplate reader.

  • Goldman AD, Kacar B (2021) Cofactors are Remnants of Life's Origin and Early Evolution. Journal of molecular evolution 89((3)):127-133 PMC7982383 · Pubmed · DOI

    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.

  • Adam ZR, Fahrenbach AC, Jacobson SM, Kacar B, Zubarev DY (2021) Radiolysis generates a complex organosynthetic chemical network. Scientific reports 11((1)):1743 PMC7813863 · Pubmed · DOI

    The architectural features of cellular life and its ecologies at larger scales are built upon foundational networks of reactions between molecules that avoid a collapse to equilibrium. The search for life's origins is, in some respects, a search for biotic network attributes in abiotic chemical systems. Radiation chemistry has long been employed to model prebiotic reaction networks, and here we report network-level analyses carried out on a compiled database of radiolysis reactions, acquired by the scientific community over decades of research. The resulting network shows robust connections between abundant geochemical reservoirs and the production of carboxylic acids, amino acids, and ribonucleotide precursors-the chemistry of which is predominantly dependent on radicals. Moreover, the network exhibits the following measurable attributes associated with biological systems: (1) the species connectivity histogram exhibits a heterogeneous (heavy-tailed) distribution, (2) overlapping families of closed-loop cycles, and (3) a hierarchical arrangement of chemical species with a bottom-heavy energy-size spectrum. The latter attribute is implicated with stability and entropy production in complex systems, notably in ecology where it is known as a trophic pyramid. Radiolysis is implicated as a driver of abiotic chemical organization and could provide insights about the complex and perhaps radical-dependent mechanisms associated with life's origins.

  • Kacar B, Garcia AK, Anbar AD (2020) Evolutionary History of Bioessential Elements Can Guide the Search for Life in the Universe. Chembiochem : a European journal of chemical biology 22((1)):114-119 · Pubmed · DOI

    Our understanding of life in the universe comes from one sample, life on Earth. Current and next-generation space missions will target exoplanets as well as planets and moons in our own solar system with the primary goal of detecting, interpreting and characterizing indications of possible biological activity. Thus, understanding life's fundamental characteristics is increasingly critical for detecting and interpreting potential biological signatures elsewhere in the universe. Astrobiologists have outlined the essential roles of carbon and water for life, but we have yet to decipher the rules governing the evolution of how living organisms use bioessential elements. Does the suite of life's essential chemical elements on Earth constitute only one possible evolutionary outcome? Are some elements so essential for biological functions that evolution will select for them despite low availability? How would this play out on other worlds that have different relative element abundances? When we look for life in the universe, or the conditions that could give rise to life, we must learn how to recognize it in extremely different chemical and environmental conditions from those on Earth. We argue that by exposing self-organizing biotic chemistries to different combinations of abiotic materials, and by mapping the evolutionary history of metalloenzyme biochemistry onto geological availabilities of metals, alternative element choices that are very different from life's present-day molecular structure might result. A greater understanding of the paleomolecular evolutionary history of life on Earth will create a predictive capacity for detecting and assessing life's existence on worlds where alternate evolutionary paths might have been taken.

  • Venkataram S, Monasky R, Sikaroodi SH, Kryazhimskiy S, Kacar B (2020) Evolutionary stalling and a limit on the power of natural selection to improve a cellular module. Proceedings of the National Academy of Sciences of the United States of America 117((31)):18582-18590 PMC7414050 · Pubmed · DOI

    Cells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations of Escherichia coli with genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.

  • Garcia AK, McShea H, Kolaczkowski B, Kaçar B (2020) Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization. Geobiology 18((3)):394-411 PMC7216921 · Pubmed · DOI

    The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active-site sequence features can reliably distinguish extant Mo-nitrogenases from V- and Fe-nitrogenases and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo-nitrogenases. Taxa representing early-branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo-cofactor in studied organisms, suggesting that early Mo-nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein-level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism-level innovations that characterize the Phanerozoic Eon.

  • Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A (2020) Emerging Frontiers in the Study of Molecular Evolution. Journal of molecular evolution 88((3)):211-226 PMC7386396 · Pubmed · DOI

    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.

  • Garcia AK, Kaçar B (2019) How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free radical biology & medicine 140:260-269 · Pubmed · DOI

    Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.

  • Walker SI, Bains W, Cronin L, DasSarma S, Danielache S, Domagal-Goldman S, Kacar B, Kiang NY, Lenardic A, Reinhard CT, Moore W, Schwieterman EW, Shkolnik EL, Smith HB (2018) Exoplanet Biosignatures: Future Directions. Astrobiology 18((6)):779-824 PMC6016573 · Pubmed · DOI

    No abstract available.

  • Kacar B, Guy L, Smith E, Baross J (2017) Resurrecting ancestral genes in bacteria to interpret ancient biosignatures. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 375((2109)): PMC5686408 · Pubmed · DOI

    No abstract available.

  • Kacar B, Garmendia E, Tuncbag N, Andersson DI, Hughes D (2017) Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs. mBio 8((4)): PMC5574714 · Pubmed · DOI

    No abstract available.

  • Kacar B, Hanson-Smith V, Adam ZR, Boekelheide N (2017) Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. Geobiology 15((5)):628-640 PMC5575542 · Pubmed · DOI

    No abstract available.

  • Kacar B, Ge X, Sanyal S, Gaucher EA (2017) Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein. Journal of molecular evolution 84((2-3)):69-84 PMC5371648 · Pubmed · DOI

    No abstract available.

  • Domagal-Goldman SD, Wright KE, Adamala K, Arina de la Rubia L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud ME, Paulino-Lima IG, Singer K, Walther-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, Imari Walker S, Wong T (2016) The Astrobiology Primer v2.0. Astrobiology 16((8)):561-653 PMC5008114 · Pubmed · DOI

    No abstract available.

  • Kaçar B, Gaucher EA (2013) Experimental evolution of protein-protein interaction networks. The Biochemical journal 453((3)):311-9 PMC3727214 · Pubmed · DOI

    The modern synthesis of evolutionary theory and genetics has enabled us to discover underlying molecular mechanisms of organismal evolution. We know that in order to maximize an organism's fitness in a particular environment, individual interactions among components of protein and nucleic acid networks need to be optimized by natural selection, or sometimes through random processes, as the organism responds to changes and/or challenges in the environment. Despite the significant role of molecular networks in determining an organism's adaptation to its environment, we still do not know how such inter- and intra-molecular interactions within networks change over time and contribute to an organism's evolvability while maintaining overall network functions. One way to address this challenge is to identify connections between molecular networks and their host organisms, to manipulate these connections, and then attempt to understand how such perturbations influence molecular dynamics of the network and thus influence evolutionary paths and organismal fitness. In the present review, we discuss how integrating evolutionary history with experimental systems that combine tools drawn from molecular evolution, synthetic biology and biochemistry allow us to identify the underlying mechanisms of organismal evolution, particularly from the perspective of protein interaction networks.

  • (0) :

    No abstract available.